num_rows:\n break\n\n sp_process.update_well(i, j, sample)\n\n sample_plate = sp_process.plate\n return sp_process, sample_plate\n\n\ndef create_gdna_extraction_process(user, plate):\n kingfisher = Equipment(11)\n epmotion = Equipment(6)\n epmotion_tool = Equipment(15)\n extraction_kit = ReagentComposition(1)\n ext_process = GDNAExtractionProcess.create(\n user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,\n 'GDNA test plate %s' % datetime.now())\n gdna_plate = ext_process.plates[0]\n return ext_process, gdna_plate\n\n\ndef create_amplicon_prep(user, plate):\n primer_plate = Plate(11)\n epmotion = Equipment(6)\n master_mix = ReagentComposition(2)\n water_lot = ReagentComposition(3)\n epmotion_tool_tm300 = Equipment(16)\n epmotion_tool_tm50 = Equipment(17)\n amplicon_process = LibraryPrep16SProcess.create(\n user, plate, primer_plate, 'Amplicon test plate %s' % datetime.now(),\n epmotion, epmotion_tool_tm300, epmotion_tool_tm50, master_mix,\n water_lot, 75,)\n amplicon_plate = amplicon_process.plates[0]\n return amplicon_process, amplicon_plate\n\n\ndef create_compression_process(user, gdna_plates):\n comp_process = GDNAPlateCompressionProcess.create(\n user, gdna_plates, 'Compressed test plate %s' % datetime.now(),\n Equipment(6))\n compressed_plate = comp_process.plates[0]\n return comp_process, compressed_plate\n\n\ndef create_quantification_process(user, plate):\n plate_config = plate.plate_configuration\n concentrations = np.around(\n np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)\n quant_process = QuantificationProcess.create(user, plate, concentrations)\n return quant_process\n\n\ndef create_pool_quantification_process(user, pools):\n concentrations = np.around(np.random.rand(len(pools)), 6)\n concentrations = [{'composition': p, 'concentration': c}\n for p, c in zip(pools, concentrations)]\n return QuantificationProcess.create_manual(user, concentrations)\n\n\ndef create_normalization_process(user, quant_process):\n water = ReagentComposition(3)\n norm_process = NormalizationProcess.create(\n user, quant_process, water,\n 'Normalized test plate %s' % datetime.now())\n norm_plate = norm_process.plates[0]\n return norm_process, norm_plate\n\n\ndef create_shotgun_process(user, norm_plate):\n kappa = ReagentComposition(4)\n stub = ReagentComposition(5)\n shotgun_process = LibraryPrepShotgunProcess.create(\n user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,\n stub, 4000, Plate(19), Plate(20))\n shotgun_plate = shotgun_process.plates[0]\n return shotgun_process, shotgun_plate\n\n\ndef create_plate_pool_process(user, quant_process, plate, func_data):\n input_compositions = []\n echo = Equipment(8)\n for well in chain.from_iterable(plate.layout):\n if well is not None:\n input_compositions.append({\n 'composition': well.composition, 'input_volume': 1,\n 'percentage_of_output': 1/9.0})\n pool_process = PoolingProcess.create(\n user, quant_process, 'New test pool name %s' % datetime.now(),\n 4, input_compositions, func_data, robot=echo)\n return pool_process\n\n\ndef create_pools_pool_process(user, quant_process, pools):\n input_compositions = [\n {'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}\n for p in pools]\n pool_process = PoolingProcess.create(\n user, quant_process, 'New pool name %s' % datetime.now(), 5,\n input_compositions, {\"function\": \"amplicon_pool\", \"parameters\": {}})\n return pool_process\n\n\ndef create_sequencing_process(user, pools):\n seq_process = SequencingProcess.create(\n user, pools, 'New sequencing run %s' % datetime.now(),\n 'Run experiment %s' % datetime.now(), Equipment(18), 151, 151,\n User('admin@foo.bar'),\n contacts=[User('test@foo.bar'), User('demo@microbio.me')])\n return seq_process\n\n\ndef amplicon_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # Amplicon library prep\n amplicon_process, amplicon_plate = create_amplicon_prep(user, gdna_plate)\n # Library plate quantification\n amplicon_quant_process = create_quantification_process(\n user, amplicon_plate)\n # Plate pooling process\n plate_pool_process = create_plate_pool_process(\n user, amplicon_quant_process, amplicon_plate,\n {'function': 'amplicon',\n 'parameters': {\"dna_amount\": 240, \"min_val\": 1, \"max_val\": 15,\n \"blank_volume\": 2, \"robot\": 6, \"destination\": 1}})\n # Quantify pools\n pool_quant_process = create_pool_quantification_process(\n user, [plate_pool_process.pool])\n # Create sequencing pool process\n seq_pool_process = create_pools_pool_process(\n user, pool_quant_process, [plate_pool_process.pool])\n # Sequencing process\n seq_process = create_sequencing_process(user, [seq_pool_process.pool])\n return seq_process\n\n\ndef shotgun_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # gDNA compression\n comp_process, compressed_plate = create_compression_process(\n user, [gdna_plate])\n # gDNA compressed quantification\n gdna_comp_quant_process = create_quantification_process(\n user, compressed_plate)\n # Normalization process\n norm_process, norm_plate = create_normalization_process(\n user, gdna_comp_quant_process)\n # Library prep shotgun\n shotgun_process, shotgun_plate = create_shotgun_process(user, norm_plate)\n # Quantify library plate\n shotgun_quant_process = create_quantification_process(user, shotgun_plate)\n # Pooling process\n pool_process = create_plate_pool_process(\n user, shotgun_quant_process, shotgun_plate,\n {'function': 'equal', 'parameters': {'total_vol': 60, 'size': 500}})\n # Sequencing process\n seq_process = create_sequencing_process(user, [pool_process.pool])\n return seq_process\n\n\n@click.command()\ndef integration_tests():\n samples = get_samples()\n user = User('test@foo.bar')\n amplicon_seq_process = amplicon_workflow(user, samples)\n shotgun_seq_process = shotgun_workflow(user, samples)\n\n obs = amplicon_seq_process.generate_sample_sheet()\n res = re.match(EXP_AMPLICON_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Amplicon sample sheet does not match expected regex:\\n%s' % obs)\n\n obs = shotgun_seq_process.generate_sample_sheet()\n res = re.match(EXP_SHOTGUN_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Shotgun sample sheet does not match expected regex:\\n%s' % obs)\n\n\nEXP_AMPLICON_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Amplicon\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,,\nNew_sequencing_run_\\d{4}-\\d{2}-\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{6},,,,,NNNNNNNNNNNN,,,,,\"\"\" # noqa\n\n\nEXP_SHOTGUN_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Metagenomics\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nLane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\n1,1_SKB1_640202,1_SKB1_640202,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A23,iTru7_101_09,TGTACACC,iTru5_08_A,CATCTGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB1.640202\n1,1_SKB2_640194,1_SKB2_640194,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A17,iTru7_101_06,AACAACCG,iTru5_05_A,GGTACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB2.640194\n1,1_SKB3_640195,1_SKB3_640195,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E1,iTru7_102_10,GTTAAGGC,iTru5_09_B,ACGGACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB3.640195\n1,1_SKB4_640189,1_SKB4_640189,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C17,iTru7_102_06,TGTGCGTT,iTru5_05_B,AAGCATCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB4.640189\n1,1_SKB5_640181,1_SKB5_640181,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A13,iTru7_101_04,GATCCATG,iTru5_03_A,AACACCAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB5.640181\n1,1_SKB6_640176,1_SKB6_640176,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E3,iTru7_102_11,AAGCCACA,iTru5_10_B,CATGTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB6.640176\n1,1_SKB7_640196,1_SKB7_640196,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A5,iTru7_115_11,CTTAGGAC,iTru5_123_H,CTCTTGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB7.640196\n1,1_SKB8_640193,1_SKB8_640193,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A1,iTru7_115_09,AGCACTTC,iTru5_121_H,GATGCTAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB8.640193\n1,1_SKB9_640200,1_SKB9_640200,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C9,iTru7_102_02,CTTACCTG,iTru5_01_B,AGTGGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB9.640200\n1,1_SKD1_640179,1_SKD1_640179,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C1,iTru7_101_10,GTATGCTG,iTru5_09_A,CTCTCAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD1.640179\n1,1_SKD2_640178,1_SKD2_640178,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A19,iTru7_101_07,ACTCGTTG,iTru5_06_A,CGATCGAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD2.640178\n1,1_SKD3_640198,1_SKD3_640198,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C3,iTru7_101_11,TGATGTCC,iTru5_10_A,TCGTCTGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD3.640198\n1,1_SKD4_640185,1_SKD4_640185,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C23,iTru7_102_09,ACAGCTCA,iTru5_08_B,ACCTCTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD4.640185\n1,1_SKD5_640186,1_SKD5_640186,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C11,iTru7_102_03,CGTTGCAA,iTru5_02_B,GTGGTATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD5.640186\n1,1_SKD6_640190,1_SKD6_640190,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A15,iTru7_101_05,GCCTATCA,iTru5_04_A,CGTATCTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD6.640190\n1,1_SKD7_640191,1_SKD7_640191,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C19,iTru7_102_07,TAGTTGCG,iTru5_06_B,TACTCCAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD7.640191\n1,1_SKD8_640184,1_SKD8_640184,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A3,iTru7_115_10,GCATACAG,iTru5_122_H,GAACGGTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD8.640184\n1,1_SKD9_640182,1_SKD9_640182,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C15,iTru7_102_05,TCACGTTC,iTru5_04_B,CGTCAAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD9.640182\n1,1_SKM1_640183,1_SKM1_640183,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E5,iTru7_102_12,ACACGGTT,iTru5_11_B,TGCCTCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM1.640183\n1,1_SKM2_640199,1_SKM2_640199,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C7,iTru7_102_01,ATAAGGCG,iTru5_12_A,CATTCGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM2.640199\n1,1_SKM3_640197,1_SKM3_640197,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C13,iTru7_102_04,GATTCAGC,iTru5_03_B,TGAGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM3.640197\n1,1_SKM4_640180,1_SKM4_640180,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A9,iTru7_101_02,CTGTGTTG,iTru5_01_A,ACCGACAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM4.640180\n1,1_SKM5_640177,1_SKM5_640177,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A11,iTru7_101_03,TGAGGTGT,iTru5_02_A,CTTCGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM5.640177\n1,1_SKM6_640187,1_SKM6_640187,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C21,iTru7_102_08,AAGAGCCA,iTru5_07_B,GATACCTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM6.640187\n1,1_SKM7_640188,1_SKM7_640188,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A21,iTru7_101_08,CCTATGGT,iTru5_07_A,AAGACACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM7.640188\n1,1_SKM8_640201,1_SKM8_640201,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C5,iTru7_101_12,GTCCTTCT,iTru5_11_A,CAATAGCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM8.640201\n1,1_SKM9_640192,1_SKM9_640192,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A7,iTru7_211_01,GCTTCTTG,iTru5_124_H,AACGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM9.640192\n1,blank_30_C10,blank_30_C10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E19,iTru7_103_07,TGTGACTG,iTru5_06_C,AGCTACCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C10\n1,blank_30_C11,blank_30_C11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E21,iTru7_103_08,CGAAGAAC,iTru5_07_C,AACCGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C11\n1,blank_30_C12,blank_30_C12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E23,iTru7_103_09,GGTGTCTT,iTru5_08_C,ATCGCAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C12\n1,blank_30_C4,blank_30_C4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E7,iTru7_103_01,CAGCGATT,iTru5_12_B,ATCTGACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C4\n1,blank_30_C5,blank_30_C5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E9,iTru7_103_02,TAGTGACC,iTru5_01_C,CACAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C5\n1,blank_30_C6,blank_30_C6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E11,iTru7_103_03,CGAGACTA,iTru5_02_C,CACTGTAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C6\n1,blank_30_C7,blank_30_C7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E13,iTru7_103_04,GACATGGT,iTru5_03_C,CACAGGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C7\n1,blank_30_C8,blank_30_C8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E15,iTru7_103_05,GCATGTCT,iTru5_04_C,CCATGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C8\n1,blank_30_C9,blank_30_C9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E17,iTru7_103_06,ACTCCATC,iTru5_05_C,GCCAATAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C9\n1,blank_30_D1,blank_30_D1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G1,iTru7_103_10,AAGAAGGC,iTru5_09_C,GTTGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D1\n1,blank_30_D10,blank_30_D10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G19,iTru7_104_07,TTAGGTCG,iTru5_06_D,TCGACAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D10\n1,blank_30_D11,blank_30_D11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G21,iTru7_104_08,GCAAGATC,iTru5_07_D,GCTGAATC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D11\n1,blank_30_D12,blank_30_D12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G23,iTru7_104_09,AGAGCCTT,iTru5_08_D,AGTTGTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D12\n1,blank_30_D2,blank_30_D2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G3,iTru7_103_11,AGGTTCGA,iTru5_10_C,TCTAGTCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D2\n1,blank_30_D3,blank_30_D3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G5,iTru7_103_12,CATGTTCC,iTru5_11_C,GACGAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D3\n1,blank_30_D4,blank_30_D4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G7,iTru7_104_01,GTGCCATA,iTru5_12_C,TTCGTACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D4\n1,blank_30_D5,blank_30_D5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G9,iTru7_104_02,CCTTGTAG,iTru5_01_D,CGACACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D5\n1,blank_30_D6,blank_30_D6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G11,iTru7_104_03,GCTGGATT,iTru5_02_D,AGACGCTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D6\n1,blank_30_D7,blank_30_D7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G13,iTru7_104_04,TAACGAGG,iTru5_03_D,TGACAACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D7\n1,blank_30_D8,blank_30_D8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G15,iTru7_104_05,ATGGTTGC,iTru5_04_D,GGTACTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D8\n1,blank_30_D9,blank_30_D9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G17,iTru7_104_06,CCTATACC,iTru5_05_D,CTGTATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D9\n1,blank_30_E1,blank_30_E1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I1,iTru7_104_10,GCAATGGA,iTru5_09_D,TGTCGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E1\n1,blank_30_E10,blank_30_E10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I19,iTru7_105_07,TGGCATGT,iTru5_06_E,TATGACCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E10\n1,blank_30_E11,blank_30_E11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I21,iTru7_105_08,AGAAGCGT,iTru5_07_E,AGCTAGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E11\n1,blank_30_E12,blank_30_E12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I23,iTru7_105_09,AGCGGAAT,iTru5_08_E,GAACGAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E12\n1,blank_30_E2,blank_30_E2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I3,iTru7_104_11,CTGGAGTA,iTru5_10_D,AAGGCTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E2\n1,blank_30_E3,blank_30_E3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I5,iTru7_104_12,GAACATCG,iTru5_11_D,CCTAACAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E3\n1,blank_30_E4,blank_30_E4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I7,iTru7_105_01,GCACAACT,iTru5_12_D,AAGACGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E4\n1,blank_30_E5,blank_30_E5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I9,iTru7_105_02,TTCTCTCG,iTru5_01_E,GACTTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E5\n1,blank_30_E6,blank_30_E6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I11,iTru7_105_03,AACGGTCA,iTru5_02_E,CAACTCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E6\n1,blank_30_E7,blank_30_E7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I13,iTru7_105_04,ACAGACCT,iTru5_03_E,TGTTCCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E7\n1,blank_30_E8,blank_30_E8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I15,iTru7_105_05,TCTCTTCC,iTru5_04_E,ACCGCTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E8\n1,blank_30_E9,blank_30_E9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I17,iTru7_105_06,AGTGTTGG,iTru5_05_E,CTTAGGAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E9\n1,blank_30_F1,blank_30_F1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K1,iTru7_105_10,TAACCGGT,iTru5_09_E,CGTCTAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F1\n1,blank_30_F10,blank_30_F10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K19,iTru7_106_07,CGTCTTGT,iTru5_06_F,AGCCAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F10\n1,blank_30_F11,blank_30_F11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K21,iTru7_106_08,CGTGATCA,iTru5_07_F,CTAGCTCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F11\n1,blank_30_F12,blank_30_F12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K23,iTru7_106_09,CCAAGTTG,iTru5_08_F,GGAAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F12\n1,blank_30_F2,blank_30_F2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K3,iTru7_105_11,CATGGAAC,iTru5_10_E,AACCAGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F2\n1,blank_30_F3,blank_30_F3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K5,iTru7_105_12,ATGGTCCA,iTru5_11_E,CGCCTTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F3\n1,blank_30_F4,blank_30_F4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K7,iTru7_106_01,CTTCTGAG,iTru5_12_E,CTCGTTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F4\n1,blank_30_F5,blank_30_F5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K9,iTru7_106_02,AACCGAAG,iTru5_01_F,GTGAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F5\n1,blank_30_F6,blank_30_F6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K11,iTru7_106_03,TTCGTACC,iTru5_02_F,AACACGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F6\n1,blank_30_F7,blank_30_F7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K13,iTru7_106_04,CTGTTAGG,iTru5_03_F,CCTAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F7\n1,blank_30_F8,blank_30_F8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K15,iTru7_106_05,CACAAGTC,iTru5_04_F,TTCCAGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F8\n1,blank_30_F9,blank_30_F9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K17,iTru7_106_06,TCTTGACG,iTru5_05_F,TCAGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F9\n1,blank_30_G1,blank_30_G1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M1,iTru7_106_10,GTACCTTG,iTru5_09_F,AACACTGG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G1\n1,blank_30_G10,blank_30_G10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M19,iTru7_107_07,CCGACTAT,iTru5_06_G,GATCTTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G10\n1,blank_30_G11,blank_30_G11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M21,iTru7_107_08,AGCTAACC,iTru5_07_G,GTTAAGCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G11\n1,blank_30_G12,blank_30_G12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M23,iTru7_107_09,GCCTTGTT,iTru5_08_G,GTCATCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G12\n1,blank_30_G2,blank_30_G2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M3,iTru7_106_11,GACTATGC,iTru5_10_F,ACTATCGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G2\n1,blank_30_G3,blank_30_G3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M5,iTru7_106_12,TGGATCAC,iTru5_11_F,ACAACAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G3\n1,blank_30_G4,blank_30_G4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M7,iTru7_107_01,CTCTGGTT,iTru5_12_F,TGTGGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G4\n1,blank_30_G5,blank_30_G5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M9,iTru7_107_02,GTTCATGG,iTru5_01_G,GTTCCATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G5\n1,blank_30_G6,blank_30_G6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M11,iTru7_107_03,GCTGTAAG,iTru5_02_G,TGGATGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G6\n1,blank_30_G7,blank_30_G7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M13,iTru7_107_04,GTCGAAGA,iTru5_03_G,GCATAACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G7\n1,blank_30_G8,blank_30_G8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M15,iTru7_107_05,GAGCTCAA,iTru5_04_G,TCGAACCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G8\n1,blank_30_G9,blank_30_G9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M17,iTru7_107_06,TGAACCTG,iTru5_05_G,ACATGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G9\n1,blank_30_H1,blank_30_H1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O1,iTru7_107_10,AACTTGCC,iTru5_09_G,TCAGACAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H1\n1,blank_30_H10,blank_30_H10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O19,iTru7_108_07,GAAGTACC,iTru5_06_H,CCTCGTTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H10\n1,blank_30_H11,blank_30_H11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O21,iTru7_108_08,CAGGTATC,iTru5_07_H,CGATTGGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H11\n1,blank_30_H12,blank_30_H12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O23,iTru7_108_09,TCTCTAGG,iTru5_08_H,CCAACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H12\n1,blank_30_H2,blank_30_H2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O3,iTru7_107_11,CAATGTGG,iTru5_10_G,GTCCTAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H2\n1,blank_30_H3,blank_30_H3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O5,iTru7_107_12,AAGGCTGA,iTru5_11_G,AGACCTTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H3\n1,blank_30_H4,blank_30_H4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O7,iTru7_108_01,TTACCGAG,iTru5_12_G,AGACATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H4\n1,blank_30_H5,blank_30_H5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O9,iTru7_108_02,GTCCTAAG,iTru5_01_H,TAGCTGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H5\n1,blank_30_H6,blank_30_H6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O11,iTru7_108_03,GAAGGTTC,iTru5_02_H,TTCGAAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H6\n1,blank_30_H7,blank_30_H7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O13,iTru7_108_04,GAAGAGGT,iTru5_03_H,CAGTGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H7\n1,blank_30_H8,blank_30_H8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O15,iTru7_108_05,TCTGAGAG,iTru5_04_H,TAGTGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H8\n1,blank_30_H9,blank_30_H9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O17,iTru7_108_06,ACCGCATA,iTru5_05_H,GATGGAGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H9\"\"\" # noqa\n\n\nif __name__ == '__main__':\n integration_tests()\n```\nPreserve indentation, whitespace, and order.","role":"user"}],"string":"[\n {\n \"content\": \"Replicate the source code:\\n```python\\n#!/usr/bin/env python\\n\\nfrom datetime import datetime\\nfrom itertools import chain\\nimport re\\n\\nimport numpy as np\\nimport click\\n\\nfrom labman.db.process import (\\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,\\n LibraryPrep16SProcess, NormalizationProcess, QuantificationProcess,\\n LibraryPrepShotgunProcess, PoolingProcess, SequencingProcess)\\nfrom labman.db.user import User\\nfrom labman.db.plate import PlateConfiguration, Plate\\nfrom labman.db.equipment import Equipment\\nfrom labman.db.composition import ReagentComposition\\nfrom labman.db.sql_connection import TRN\\n\\n\\ndef get_samples():\\n with TRN:\\n TRN.add(\\\"SELECT sample_id FROM qiita.study_sample\\\")\\n return TRN.execute_fetchflatten()\\n\\n\\ndef create_sample_plate_process(user, samples):\\n plate_config = PlateConfiguration(1)\\n num_rows = plate_config.num_rows\\n num_cols = plate_config.num_columns\\n sp_process = SamplePlatingProcess.create(\\n user, plate_config, 'Test plate %s' % datetime.now())\\n\\n # Plate the samples\\n for idx, sample in enumerate(samples):\\n i = int(idx / num_cols) + 1\\n j = (idx % num_cols) + 1\\n\\n # Make sure that the user didn't pass more samples than wells\\n if i > num_rows:\\n break\\n\\n sp_process.update_well(i, j, sample)\\n\\n sample_plate = sp_process.plate\\n return sp_process, sample_plate\\n\\n\\ndef create_gdna_extraction_process(user, plate):\\n kingfisher = Equipment(11)\\n epmotion = Equipment(6)\\n epmotion_tool = Equipment(15)\\n extraction_kit = ReagentComposition(1)\\n ext_process = GDNAExtractionProcess.create(\\n user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,\\n 'GDNA test plate %s' % datetime.now())\\n gdna_plate = ext_process.plates[0]\\n return ext_process, gdna_plate\\n\\n\\ndef create_amplicon_prep(user, plate):\\n primer_plate = Plate(11)\\n epmotion = Equipment(6)\\n master_mix = ReagentComposition(2)\\n water_lot = ReagentComposition(3)\\n epmotion_tool_tm300 = Equipment(16)\\n epmotion_tool_tm50 = Equipment(17)\\n amplicon_process = LibraryPrep16SProcess.create(\\n user, plate, primer_plate, 'Amplicon test plate %s' % datetime.now(),\\n epmotion, epmotion_tool_tm300, epmotion_tool_tm50, master_mix,\\n water_lot, 75,)\\n amplicon_plate = amplicon_process.plates[0]\\n return amplicon_process, amplicon_plate\\n\\n\\ndef create_compression_process(user, gdna_plates):\\n comp_process = GDNAPlateCompressionProcess.create(\\n user, gdna_plates, 'Compressed test plate %s' % datetime.now(),\\n Equipment(6))\\n compressed_plate = comp_process.plates[0]\\n return comp_process, compressed_plate\\n\\n\\ndef create_quantification_process(user, plate):\\n plate_config = plate.plate_configuration\\n concentrations = np.around(\\n np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)\\n quant_process = QuantificationProcess.create(user, plate, concentrations)\\n return quant_process\\n\\n\\ndef create_pool_quantification_process(user, pools):\\n concentrations = np.around(np.random.rand(len(pools)), 6)\\n concentrations = [{'composition': p, 'concentration': c}\\n for p, c in zip(pools, concentrations)]\\n return QuantificationProcess.create_manual(user, concentrations)\\n\\n\\ndef create_normalization_process(user, quant_process):\\n water = ReagentComposition(3)\\n norm_process = NormalizationProcess.create(\\n user, quant_process, water,\\n 'Normalized test plate %s' % datetime.now())\\n norm_plate = norm_process.plates[0]\\n return norm_process, norm_plate\\n\\n\\ndef create_shotgun_process(user, norm_plate):\\n kappa = ReagentComposition(4)\\n stub = ReagentComposition(5)\\n shotgun_process = LibraryPrepShotgunProcess.create(\\n user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,\\n stub, 4000, Plate(19), Plate(20))\\n shotgun_plate = shotgun_process.plates[0]\\n return shotgun_process, shotgun_plate\\n\\n\\ndef create_plate_pool_process(user, quant_process, plate, func_data):\\n input_compositions = []\\n echo = Equipment(8)\\n for well in chain.from_iterable(plate.layout):\\n if well is not None:\\n input_compositions.append({\\n 'composition': well.composition, 'input_volume': 1,\\n 'percentage_of_output': 1/9.0})\\n pool_process = PoolingProcess.create(\\n user, quant_process, 'New test pool name %s' % datetime.now(),\\n 4, input_compositions, func_data, robot=echo)\\n return pool_process\\n\\n\\ndef create_pools_pool_process(user, quant_process, pools):\\n input_compositions = [\\n {'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}\\n for p in pools]\\n pool_process = PoolingProcess.create(\\n user, quant_process, 'New pool name %s' % datetime.now(), 5,\\n input_compositions, {\\\"function\\\": \\\"amplicon_pool\\\", \\\"parameters\\\": {}})\\n return pool_process\\n\\n\\ndef create_sequencing_process(user, pools):\\n seq_process = SequencingProcess.create(\\n user, pools, 'New sequencing run %s' % datetime.now(),\\n 'Run experiment %s' % datetime.now(), Equipment(18), 151, 151,\\n User('admin@foo.bar'),\\n contacts=[User('test@foo.bar'), User('demo@microbio.me')])\\n return seq_process\\n\\n\\ndef amplicon_workflow(user, samples):\\n # Sample Plating\\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\\n # gDNA extraction\\n ext_process, gdna_plate = create_gdna_extraction_process(\\n user, sample_plate)\\n # Amplicon library prep\\n amplicon_process, amplicon_plate = create_amplicon_prep(user, gdna_plate)\\n # Library plate quantification\\n amplicon_quant_process = create_quantification_process(\\n user, amplicon_plate)\\n # Plate pooling process\\n plate_pool_process = create_plate_pool_process(\\n user, amplicon_quant_process, amplicon_plate,\\n {'function': 'amplicon',\\n 'parameters': {\\\"dna_amount\\\": 240, \\\"min_val\\\": 1, \\\"max_val\\\": 15,\\n \\\"blank_volume\\\": 2, \\\"robot\\\": 6, \\\"destination\\\": 1}})\\n # Quantify pools\\n pool_quant_process = create_pool_quantification_process(\\n user, [plate_pool_process.pool])\\n # Create sequencing pool process\\n seq_pool_process = create_pools_pool_process(\\n user, pool_quant_process, [plate_pool_process.pool])\\n # Sequencing process\\n seq_process = create_sequencing_process(user, [seq_pool_process.pool])\\n return seq_process\\n\\n\\ndef shotgun_workflow(user, samples):\\n # Sample Plating\\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\\n # gDNA extraction\\n ext_process, gdna_plate = create_gdna_extraction_process(\\n user, sample_plate)\\n # gDNA compression\\n comp_process, compressed_plate = create_compression_process(\\n user, [gdna_plate])\\n # gDNA compressed quantification\\n gdna_comp_quant_process = create_quantification_process(\\n user, compressed_plate)\\n # Normalization process\\n norm_process, norm_plate = create_normalization_process(\\n user, gdna_comp_quant_process)\\n # Library prep shotgun\\n shotgun_process, shotgun_plate = create_shotgun_process(user, norm_plate)\\n # Quantify library plate\\n shotgun_quant_process = create_quantification_process(user, shotgun_plate)\\n # Pooling process\\n pool_process = create_plate_pool_process(\\n user, shotgun_quant_process, shotgun_plate,\\n {'function': 'equal', 'parameters': {'total_vol': 60, 'size': 500}})\\n # Sequencing process\\n seq_process = create_sequencing_process(user, [pool_process.pool])\\n return seq_process\\n\\n\\n@click.command()\\ndef integration_tests():\\n samples = get_samples()\\n user = User('test@foo.bar')\\n amplicon_seq_process = amplicon_workflow(user, samples)\\n shotgun_seq_process = shotgun_workflow(user, samples)\\n\\n obs = amplicon_seq_process.generate_sample_sheet()\\n res = re.match(EXP_AMPLICON_SAMPLE_SHEET, obs)\\n if res is None:\\n raise ValueError(\\n 'Amplicon sample sheet does not match expected regex:\\\\n%s' % obs)\\n\\n obs = shotgun_seq_process.generate_sample_sheet()\\n res = re.match(EXP_SHOTGUN_SAMPLE_SHEET, obs)\\n if res is None:\\n raise ValueError(\\n 'Shotgun sample sheet does not match expected regex:\\\\n%s' % obs)\\n\\n\\nEXP_AMPLICON_SAMPLE_SHEET = r\\\"\\\"\\\"# PI,Admin,admin@foo.bar\\n# Contact,Demo,Dude\\n# Contact emails,demo@microbio.me,test@foo.bar\\n\\\\[Header\\\\]\\nIEMFileVersion,4\\nInvestigator Name,Admin\\nExperiment Name,Run experiment \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6}\\nDate,\\\\d{4}-\\\\d{2}-\\\\d{2}\\nWorkflow,GenerateFASTQ\\nApplication,FASTQ Only\\nAssay,Amplicon\\nDescription,\\nChemistry,Default\\n\\n\\\\[Reads\\\\]\\n151\\n151\\n\\n\\\\[Settings\\\\]\\nReverseComplement,0\\n\\n\\\\[Data\\\\]\\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,,\\nNew_sequencing_run_\\\\d{4}-\\\\d{2}-\\\\d{2}_\\\\d{2}_\\\\d{2}_\\\\d{2}_\\\\d{6},,,,,NNNNNNNNNNNN,,,,,\\\"\\\"\\\" # noqa\\n\\n\\nEXP_SHOTGUN_SAMPLE_SHEET = r\\\"\\\"\\\"# PI,Admin,admin@foo.bar\\n# Contact,Demo,Dude\\n# Contact emails,demo@microbio.me,test@foo.bar\\n\\\\[Header\\\\]\\nIEMFileVersion,4\\nInvestigator Name,Admin\\nExperiment Name,Run experiment \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6}\\nDate,\\\\d{4}-\\\\d{2}-\\\\d{2}\\nWorkflow,GenerateFASTQ\\nApplication,FASTQ Only\\nAssay,Metagenomics\\nDescription,\\nChemistry,Default\\n\\n\\\\[Reads\\\\]\\n151\\n151\\n\\n\\\\[Settings\\\\]\\nReverseComplement,0\\n\\n\\\\[Data\\\\]\\nLane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\\n1,1_SKB1_640202,1_SKB1_640202,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A23,iTru7_101_09,TGTACACC,iTru5_08_A,CATCTGCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB1.640202\\n1,1_SKB2_640194,1_SKB2_640194,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A17,iTru7_101_06,AACAACCG,iTru5_05_A,GGTACGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB2.640194\\n1,1_SKB3_640195,1_SKB3_640195,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E1,iTru7_102_10,GTTAAGGC,iTru5_09_B,ACGGACTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB3.640195\\n1,1_SKB4_640189,1_SKB4_640189,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C17,iTru7_102_06,TGTGCGTT,iTru5_05_B,AAGCATCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB4.640189\\n1,1_SKB5_640181,1_SKB5_640181,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A13,iTru7_101_04,GATCCATG,iTru5_03_A,AACACCAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB5.640181\\n1,1_SKB6_640176,1_SKB6_640176,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E3,iTru7_102_11,AAGCCACA,iTru5_10_B,CATGTGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB6.640176\\n1,1_SKB7_640196,1_SKB7_640196,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A5,iTru7_115_11,CTTAGGAC,iTru5_123_H,CTCTTGTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB7.640196\\n1,1_SKB8_640193,1_SKB8_640193,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A1,iTru7_115_09,AGCACTTC,iTru5_121_H,GATGCTAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB8.640193\\n1,1_SKB9_640200,1_SKB9_640200,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C9,iTru7_102_02,CTTACCTG,iTru5_01_B,AGTGGCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB9.640200\\n1,1_SKD1_640179,1_SKD1_640179,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C1,iTru7_101_10,GTATGCTG,iTru5_09_A,CTCTCAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD1.640179\\n1,1_SKD2_640178,1_SKD2_640178,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A19,iTru7_101_07,ACTCGTTG,iTru5_06_A,CGATCGAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD2.640178\\n1,1_SKD3_640198,1_SKD3_640198,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C3,iTru7_101_11,TGATGTCC,iTru5_10_A,TCGTCTGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD3.640198\\n1,1_SKD4_640185,1_SKD4_640185,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C23,iTru7_102_09,ACAGCTCA,iTru5_08_B,ACCTCTTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD4.640185\\n1,1_SKD5_640186,1_SKD5_640186,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C11,iTru7_102_03,CGTTGCAA,iTru5_02_B,GTGGTATG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD5.640186\\n1,1_SKD6_640190,1_SKD6_640190,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A15,iTru7_101_05,GCCTATCA,iTru5_04_A,CGTATCTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD6.640190\\n1,1_SKD7_640191,1_SKD7_640191,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C19,iTru7_102_07,TAGTTGCG,iTru5_06_B,TACTCCAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD7.640191\\n1,1_SKD8_640184,1_SKD8_640184,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A3,iTru7_115_10,GCATACAG,iTru5_122_H,GAACGGTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD8.640184\\n1,1_SKD9_640182,1_SKD9_640182,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C15,iTru7_102_05,TCACGTTC,iTru5_04_B,CGTCAAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD9.640182\\n1,1_SKM1_640183,1_SKM1_640183,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E5,iTru7_102_12,ACACGGTT,iTru5_11_B,TGCCTCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM1.640183\\n1,1_SKM2_640199,1_SKM2_640199,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C7,iTru7_102_01,ATAAGGCG,iTru5_12_A,CATTCGTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM2.640199\\n1,1_SKM3_640197,1_SKM3_640197,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C13,iTru7_102_04,GATTCAGC,iTru5_03_B,TGAGCTGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM3.640197\\n1,1_SKM4_640180,1_SKM4_640180,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A9,iTru7_101_02,CTGTGTTG,iTru5_01_A,ACCGACAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM4.640180\\n1,1_SKM5_640177,1_SKM5_640177,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A11,iTru7_101_03,TGAGGTGT,iTru5_02_A,CTTCGCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM5.640177\\n1,1_SKM6_640187,1_SKM6_640187,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C21,iTru7_102_08,AAGAGCCA,iTru5_07_B,GATACCTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM6.640187\\n1,1_SKM7_640188,1_SKM7_640188,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A21,iTru7_101_08,CCTATGGT,iTru5_07_A,AAGACACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM7.640188\\n1,1_SKM8_640201,1_SKM8_640201,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C5,iTru7_101_12,GTCCTTCT,iTru5_11_A,CAATAGCC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM8.640201\\n1,1_SKM9_640192,1_SKM9_640192,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A7,iTru7_211_01,GCTTCTTG,iTru5_124_H,AACGCCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM9.640192\\n1,blank_30_C10,blank_30_C10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E19,iTru7_103_07,TGTGACTG,iTru5_06_C,AGCTACCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C10\\n1,blank_30_C11,blank_30_C11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E21,iTru7_103_08,CGAAGAAC,iTru5_07_C,AACCGAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C11\\n1,blank_30_C12,blank_30_C12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E23,iTru7_103_09,GGTGTCTT,iTru5_08_C,ATCGCAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C12\\n1,blank_30_C4,blank_30_C4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E7,iTru7_103_01,CAGCGATT,iTru5_12_B,ATCTGACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C4\\n1,blank_30_C5,blank_30_C5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E9,iTru7_103_02,TAGTGACC,iTru5_01_C,CACAGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C5\\n1,blank_30_C6,blank_30_C6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E11,iTru7_103_03,CGAGACTA,iTru5_02_C,CACTGTAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C6\\n1,blank_30_C7,blank_30_C7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E13,iTru7_103_04,GACATGGT,iTru5_03_C,CACAGGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C7\\n1,blank_30_C8,blank_30_C8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E15,iTru7_103_05,GCATGTCT,iTru5_04_C,CCATGAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C8\\n1,blank_30_C9,blank_30_C9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E17,iTru7_103_06,ACTCCATC,iTru5_05_C,GCCAATAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C9\\n1,blank_30_D1,blank_30_D1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G1,iTru7_103_10,AAGAAGGC,iTru5_09_C,GTTGCTGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D1\\n1,blank_30_D10,blank_30_D10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G19,iTru7_104_07,TTAGGTCG,iTru5_06_D,TCGACAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D10\\n1,blank_30_D11,blank_30_D11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G21,iTru7_104_08,GCAAGATC,iTru5_07_D,GCTGAATC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D11\\n1,blank_30_D12,blank_30_D12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G23,iTru7_104_09,AGAGCCTT,iTru5_08_D,AGTTGTGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D12\\n1,blank_30_D2,blank_30_D2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G3,iTru7_103_11,AGGTTCGA,iTru5_10_C,TCTAGTCC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D2\\n1,blank_30_D3,blank_30_D3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G5,iTru7_103_12,CATGTTCC,iTru5_11_C,GACGAACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D3\\n1,blank_30_D4,blank_30_D4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G7,iTru7_104_01,GTGCCATA,iTru5_12_C,TTCGTACG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D4\\n1,blank_30_D5,blank_30_D5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G9,iTru7_104_02,CCTTGTAG,iTru5_01_D,CGACACTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D5\\n1,blank_30_D6,blank_30_D6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G11,iTru7_104_03,GCTGGATT,iTru5_02_D,AGACGCTA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D6\\n1,blank_30_D7,blank_30_D7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G13,iTru7_104_04,TAACGAGG,iTru5_03_D,TGACAACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D7\\n1,blank_30_D8,blank_30_D8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G15,iTru7_104_05,ATGGTTGC,iTru5_04_D,GGTACTTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D8\\n1,blank_30_D9,blank_30_D9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G17,iTru7_104_06,CCTATACC,iTru5_05_D,CTGTATGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D9\\n1,blank_30_E1,blank_30_E1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I1,iTru7_104_10,GCAATGGA,iTru5_09_D,TGTCGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E1\\n1,blank_30_E10,blank_30_E10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I19,iTru7_105_07,TGGCATGT,iTru5_06_E,TATGACCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E10\\n1,blank_30_E11,blank_30_E11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I21,iTru7_105_08,AGAAGCGT,iTru5_07_E,AGCTAGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E11\\n1,blank_30_E12,blank_30_E12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I23,iTru7_105_09,AGCGGAAT,iTru5_08_E,GAACGAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E12\\n1,blank_30_E2,blank_30_E2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I3,iTru7_104_11,CTGGAGTA,iTru5_10_D,AAGGCTCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E2\\n1,blank_30_E3,blank_30_E3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I5,iTru7_104_12,GAACATCG,iTru5_11_D,CCTAACAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E3\\n1,blank_30_E4,blank_30_E4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I7,iTru7_105_01,GCACAACT,iTru5_12_D,AAGACGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E4\\n1,blank_30_E5,blank_30_E5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I9,iTru7_105_02,TTCTCTCG,iTru5_01_E,GACTTGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E5\\n1,blank_30_E6,blank_30_E6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I11,iTru7_105_03,AACGGTCA,iTru5_02_E,CAACTCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E6\\n1,blank_30_E7,blank_30_E7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I13,iTru7_105_04,ACAGACCT,iTru5_03_E,TGTTCCGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E7\\n1,blank_30_E8,blank_30_E8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I15,iTru7_105_05,TCTCTTCC,iTru5_04_E,ACCGCTAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E8\\n1,blank_30_E9,blank_30_E9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I17,iTru7_105_06,AGTGTTGG,iTru5_05_E,CTTAGGAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E9\\n1,blank_30_F1,blank_30_F1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K1,iTru7_105_10,TAACCGGT,iTru5_09_E,CGTCTAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F1\\n1,blank_30_F10,blank_30_F10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K19,iTru7_106_07,CGTCTTGT,iTru5_06_F,AGCCAACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F10\\n1,blank_30_F11,blank_30_F11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K21,iTru7_106_08,CGTGATCA,iTru5_07_F,CTAGCTCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F11\\n1,blank_30_F12,blank_30_F12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K23,iTru7_106_09,CCAAGTTG,iTru5_08_F,GGAAGAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F12\\n1,blank_30_F2,blank_30_F2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K3,iTru7_105_11,CATGGAAC,iTru5_10_E,AACCAGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F2\\n1,blank_30_F3,blank_30_F3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K5,iTru7_105_12,ATGGTCCA,iTru5_11_E,CGCCTTAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F3\\n1,blank_30_F4,blank_30_F4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K7,iTru7_106_01,CTTCTGAG,iTru5_12_E,CTCGTTCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F4\\n1,blank_30_F5,blank_30_F5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K9,iTru7_106_02,AACCGAAG,iTru5_01_F,GTGAGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F5\\n1,blank_30_F6,blank_30_F6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K11,iTru7_106_03,TTCGTACC,iTru5_02_F,AACACGCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F6\\n1,blank_30_F7,blank_30_F7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K13,iTru7_106_04,CTGTTAGG,iTru5_03_F,CCTAGAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F7\\n1,blank_30_F8,blank_30_F8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K15,iTru7_106_05,CACAAGTC,iTru5_04_F,TTCCAGGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F8\\n1,blank_30_F9,blank_30_F9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K17,iTru7_106_06,TCTTGACG,iTru5_05_F,TCAGCCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F9\\n1,blank_30_G1,blank_30_G1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M1,iTru7_106_10,GTACCTTG,iTru5_09_F,AACACTGG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G1\\n1,blank_30_G10,blank_30_G10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M19,iTru7_107_07,CCGACTAT,iTru5_06_G,GATCTTGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G10\\n1,blank_30_G11,blank_30_G11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M21,iTru7_107_08,AGCTAACC,iTru5_07_G,GTTAAGCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G11\\n1,blank_30_G12,blank_30_G12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M23,iTru7_107_09,GCCTTGTT,iTru5_08_G,GTCATCGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G12\\n1,blank_30_G2,blank_30_G2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M3,iTru7_106_11,GACTATGC,iTru5_10_F,ACTATCGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G2\\n1,blank_30_G3,blank_30_G3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M5,iTru7_106_12,TGGATCAC,iTru5_11_F,ACAACAGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G3\\n1,blank_30_G4,blank_30_G4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M7,iTru7_107_01,CTCTGGTT,iTru5_12_F,TGTGGCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G4\\n1,blank_30_G5,blank_30_G5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M9,iTru7_107_02,GTTCATGG,iTru5_01_G,GTTCCATG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G5\\n1,blank_30_G6,blank_30_G6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M11,iTru7_107_03,GCTGTAAG,iTru5_02_G,TGGATGGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G6\\n1,blank_30_G7,blank_30_G7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M13,iTru7_107_04,GTCGAAGA,iTru5_03_G,GCATAACG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G7\\n1,blank_30_G8,blank_30_G8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M15,iTru7_107_05,GAGCTCAA,iTru5_04_G,TCGAACCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G8\\n1,blank_30_G9,blank_30_G9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M17,iTru7_107_06,TGAACCTG,iTru5_05_G,ACATGCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G9\\n1,blank_30_H1,blank_30_H1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O1,iTru7_107_10,AACTTGCC,iTru5_09_G,TCAGACAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H1\\n1,blank_30_H10,blank_30_H10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O19,iTru7_108_07,GAAGTACC,iTru5_06_H,CCTCGTTA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H10\\n1,blank_30_H11,blank_30_H11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O21,iTru7_108_08,CAGGTATC,iTru5_07_H,CGATTGGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H11\\n1,blank_30_H12,blank_30_H12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O23,iTru7_108_09,TCTCTAGG,iTru5_08_H,CCAACGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H12\\n1,blank_30_H2,blank_30_H2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O3,iTru7_107_11,CAATGTGG,iTru5_10_G,GTCCTAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H2\\n1,blank_30_H3,blank_30_H3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O5,iTru7_107_12,AAGGCTGA,iTru5_11_G,AGACCTTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H3\\n1,blank_30_H4,blank_30_H4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O7,iTru7_108_01,TTACCGAG,iTru5_12_G,AGACATGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H4\\n1,blank_30_H5,blank_30_H5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O9,iTru7_108_02,GTCCTAAG,iTru5_01_H,TAGCTGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H5\\n1,blank_30_H6,blank_30_H6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O11,iTru7_108_03,GAAGGTTC,iTru5_02_H,TTCGAAGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H6\\n1,blank_30_H7,blank_30_H7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O13,iTru7_108_04,GAAGAGGT,iTru5_03_H,CAGTGCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H7\\n1,blank_30_H8,blank_30_H8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O15,iTru7_108_05,TCTGAGAG,iTru5_04_H,TAGTGCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H8\\n1,blank_30_H9,blank_30_H9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O17,iTru7_108_06,ACCGCATA,iTru5_05_H,GATGGAGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H9\\\"\\\"\\\" # noqa\\n\\n\\nif __name__ == '__main__':\\n integration_tests()\\n```\\nPreserve indentation, whitespace, and order.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"compression_prompt":{"kind":"list like","value":[{"content":"Replicate the source code:\n<|memory_start|>```python\n#!/usr/bin/env python\n\nfrom datetime import datetime\nfrom itertools import chain\nimport re\n\nimport numpy as np\nimport click\n\nfrom labman.db.process import (\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,\n LibraryPrep16SProcess, NormalizationProcess, QuantificationProcess,\n LibraryPrepShotgunProcess, PoolingProcess, SequencingProcess)\nfrom labman.db.user import User\nfrom labman.db.plate import PlateConfiguration, Plate\nfrom labman.db.equipment import Equipment\nfrom labman.db.composition import ReagentComposition\nfrom labman.db.sql_connection import TRN\n\n\ndef get_samples():\n with TRN:\n TRN.add(\"SELECT sample_id FROM qiita.study_sample\")\n return TRN.execute_fetchflatten()\n\n\ndef create_sample_plate_process(user, samples):\n plate_config = PlateConfiguration(1)\n num_rows = plate_config.num_rows\n num_cols = plate_config.num_columns\n sp_process = SamplePlatingProcess.create(\n user, plate_config, 'Test plate %s' % datetime.now())\n\n # Plate the samples\n for idx, sample in enumerate(samples):\n i = int(idx / num_cols) + 1\n j = (idx % num_cols) + 1\n\n # Make sure that the user didn't pass more samples than wells\n if i > num_rows:\n break\n\n sp_process.update_well(i, j, sample)\n\n sample_plate = sp_process.plate\n return sp_process, sample_plate\n\n\ndef create_gdna_extraction_process(user, plate):\n kingfisher = Equipment(11)\n epmotion = Equipment(6)\n epmotion_tool = Equipment(15)\n extraction_kit = ReagentComposition(1)\n ext_process = GDNAExtractionProcess.create(\n user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,\n 'GDNA test plate %s' % datetime.now())\n gdna_plate = ext_process.plates[0]\n return ext_process, gdna_plate\n\n\ndef create_amplicon_prep(user, plate):\n primer_plate = Plate(11)\n epmotion = Equipment(6)\n master_mix = ReagentComposition(2)\n water_lot = ReagentComposition(3)\n epmotion_tool_tm300 = Equipment(16)\n epmotion_tool_tm50 = Equipment(17)\n amplicon_process = LibraryPrep16SProcess.create(\n user, plate, primer_plate, 'Amplicon test plate %s' % datetime.now(),\n epmotion, epmotion_tool_tm300, epmotion_tool_tm50, master_mix,\n water_lot, 75,)\n amplicon_plate = amplicon_process.plates[0]\n return amplicon_process, amplicon_plate\n\n\ndef create_compression_process(user, gdna_plates):\n comp_process = GDNAPlateCompressionProcess.create(\n user, gdna_plates, 'Compressed test plate %s' % datetime.now(),\n Equipment(6))\n compressed_plate = comp_process.plates[0]\n return comp_process, compressed_plate\n\n\ndef create_quantification_process(user, plate):\n plate_config = plate.plate_configuration\n concentrations = np.around(\n np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)\n quant_process = QuantificationProcess.create(user, plate, concentrations)\n return quant_process\n\n\ndef create_pool_quantification_process(user, pools):\n concentrations = np.around(np.random.rand(len(pools)), 6)\n concentrations = [{'composition': p, 'concentration': c}\n for p, c in zip(pools, concentrations)]\n return QuantificationProcess.create_manual(user, concentrations)\n\n\ndef create_normalization_process(user, quant_process):\n water = ReagentComposition(3)\n norm_process = NormalizationProcess.create(\n user, quant_process, water,\n 'Normalized test plate %s' % datetime.now())\n norm_plate = norm_process.plates[0]\n return norm_process, norm_plate\n\n\ndef create_shotgun_process(user, norm_plate):\n kappa = ReagentComposition(4)\n stub = ReagentComposition(5)\n shotgun_process = LibraryPrepShotgunProcess.create(\n user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,\n stub, 4000, Plate(19), Plate(20))\n shotgun_plate = shotgun_process.plates[0]\n return shotgun_process, shotgun_plate\n\n\ndef create_plate_pool_process(user, quant_process, plate, func_data):\n input_compositions = []\n echo = Equipment(8)\n for well in chain.from_iterable(plate.layout):\n if well is not None:\n input_compositions.append({\n 'composition': well.composition, 'input_volume': 1,\n 'percentage_of_output': 1/9.0})\n pool_process = PoolingProcess.create(\n user, quant_process, 'New test pool name %s' % datetime.now(),\n 4, input_compositions, func_data, robot=echo)\n return pool_process\n\n\ndef create_pools_pool_process(user, quant_process, pools):\n input_compositions = [\n {'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}\n for p in pools]\n pool_process = PoolingProcess.create(\n user, quant_process, 'New pool name %s' % datetime.now(), 5,\n input_compositions, {\"function\": \"amplicon_pool\", \"parameters\": {}})\n return pool_process\n\n\ndef create_sequencing_process(user, pools):\n seq_process = SequencingProcess.create(\n user, pools, 'New sequencing run %s' % datetime.now(),\n 'Run experiment %s' % datetime.now(), Equipment(18), 151, 151,\n User('admin@foo.bar'),\n contacts=[User('test@foo.bar'), User('demo@microbio.me')])\n return seq_process\n\n\ndef amplicon_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # Amplicon library prep\n amplicon_process, amplicon_plate = create_amplicon_prep(user, gdna_plate)\n # Library plate quantification\n amplicon_quant_process = create_quantification_process(\n user, amplicon_plate)\n # Plate pooling process\n plate_pool_process = create_plate_pool_process(\n user, amplicon_quant_process, amplicon_plate,\n {'function': 'amplicon',\n 'parameters': {\"dna_amount\": 240, \"min_val\": 1, \"max_val\": 15,\n \"blank_volume\": 2, \"robot\": 6, \"destination\": 1}})\n # Quantify pools\n pool_quant_process = create_pool_quantification_process(\n user, [plate_pool_process.pool])\n # Create sequencing pool process\n seq_pool_process = create_pools_pool_process(\n user, pool_quant_process, [plate_pool_process.pool])\n # Sequencing process\n seq_process = create_sequencing_process(user, [seq_pool_process.pool])\n return seq_process\n\n\ndef shotgun_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # gDNA compression\n comp_process, compressed_plate = create_compression_process(\n user, [gdna_plate])\n # gDNA compressed quantification\n gdna_comp_quant_process = create_quantification_process(\n user, compressed_plate)\n # Normalization process\n norm_process, norm_plate = create_normalization_process(\n user, gdna_comp_quant_process)\n # Library prep shotgun\n shotgun_process, shotgun_plate = create_shotgun_process(user, norm_plate)\n # Quantify library plate\n shotgun_quant_process = create_quantification_process(user, shotgun_plate)\n # Pooling process\n pool_process = create_plate_pool_process(\n user, shotgun_quant_process, shotgun_plate,\n {'function': 'equal', 'parameters': {'total_vol': 60, 'size': 500}})\n # Sequencing process\n seq_process = create_sequencing_process(user, [pool_process.pool])\n return seq_process\n\n\n@click.command()\ndef integration_tests():\n samples = get_samples()\n user = User('test@foo.bar')\n amplicon_seq_process = amplicon_workflow(user, samples)\n shotgun_seq_process = shotgun_workflow(user, samples)\n\n obs = amplicon_seq_process.generate_sample_sheet()\n res = re.match(EXP_AMPLICON_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Amplicon sample sheet does not match expected regex:\\n%s' % obs)\n\n obs = shotgun_seq_process.generate_sample_sheet()\n res = re.match(EXP_SHOTGUN_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Shotgun sample sheet does not match expected regex:\\n%s' % obs)\n\n\nEXP_AMPLICON_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Amplicon\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,,\nNew_sequencing_run_\\d{4}-\\d{2}-\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{6},,,,,NNNNNNNNNNNN,,,,,\"\"\" # noqa\n\n\nEXP_SHOTGUN_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Metagenomics\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nLane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\n1,1_SKB1_640202,1_SKB1_640202,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A23,iTru7_101_09,TGTACACC,iTru5_08_A,CATCTGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB1.640202\n1,1_SKB2_640194,1_SKB2_640194,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A17,iTru7_101_06,AACAACCG,iTru5_05_A,GGTACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB2.640194\n1,1_SKB3_640195,1_SKB3_640195,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E1,iTru7_102_10,GTTAAGGC,iTru5_09_B,ACGGACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB3.640195\n1,1_SKB4_640189,1_SKB4_640189,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C17,iTru7_102_06,TGTGCGTT,iTru5_05_B,AAGCATCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB4.640189\n1,1_SKB5_640181,1_SKB5_640181,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A13,iTru7_101_04,GATCCATG,iTru5_03_A,AACACCAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB5.640181\n1,1_SKB6_640176,1_SKB6_640176,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E3,iTru7_102_11,AAGCCACA,iTru5_10_B,CATGTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB6.640176\n1,1_SKB7_640196,1_SKB7_640196,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A5,iTru7_115_11,CTTAGGAC,iTru5_123_H,CTCTTGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB7.640196\n1,1_SKB8_640193,1_SKB8_640193,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A1,iTru7_115_09,AGCACTTC,iTru5_121_H,GATGCTAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB8.640193\n1,1_SKB9_640200,1_SKB9_640200,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C9,iTru7_102_02,CTTACCTG,iTru5_01_B,AGTGGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB9.640200\n1,1_SKD1_640179,1_SKD1_640179,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C1,iTru7_101_10,GTATGCTG,iTru5_09_A,CTCTCAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD1.640179\n1,1_SKD2_640178,1_SKD2_640178,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A19,iTru7_101_07,ACTCGTTG,iTru5_06_A,CGATCGAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD2.640178\n1,1_SKD3_640198,1_SKD3_640198,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C3,iTru7_101_11,TGATGTCC,iTru5_10_A,TCGTCTGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD3.640198\n1,1_SKD4_640185,1_SKD4_640185,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C23,iTru7_102_09,ACAGCTCA,iTru5_08_B,ACCTCTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD4.640185\n1,1_SKD5_640186,1_SKD5_640186,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C11,iTru7_102_03,CGTTGCAA,iTru5_02_B,GTGGTATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD5.640186\n1,1_SKD6_640190,1_SKD6_640190,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A15,iTru7_101_05,GCCTATCA,iTru5_04_A,CGTATCTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD6.640190\n1,1_SKD7_640191,1_SKD7_640191,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C19,iTru7_102_07,TAGTTGCG,iTru5_06_B,TACTCCAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD7.640191\n1,1_SKD8_640184,1_SKD8_640184,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A3,iTru7_115_10,GCATACAG,iTru5_122_H,GAACGGTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD8.640184\n1,1_SKD9_640182,1_SKD9_640182,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C15,iTru7_102_05,TCACGTTC,iTru5_04_B,CGTCAAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD9.640182\n1,1_SKM1_640183,1_SKM1_640183,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E5,iTru7_102_12,ACACGGTT,iTru5_11_B,TGCCTCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM1.640183\n1,1_SKM2_640199,1_SKM2_640199,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C7,iTru7_102_01,ATAAGGCG,iTru5_12_A,CATTCGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM2.640199\n1,1_SKM3_640197,1_SKM3_640197,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C13,iTru7_102_04,GATTCAGC,iTru5_03_B,TGAGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM3.640197\n1,1_SKM4_640180,1_SKM4_640180,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A9,iTru7_101_02,CTGTGTTG,iTru5_01_A,ACCGACAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM4.640180\n1,1_SKM5_640177,1_SKM5_640177,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A11,iTru7_101_03,TGAGGTGT,iTru5_02_A,CTTCGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM5.640177\n1,1_SKM6_640187,1_SKM6_640187,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C21,iTru7_102_08,AAGAGCCA,iTru5_07_B,GATACCTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM6.640187\n1,1_SKM7_640188,1_SKM7_640188,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A21,iTru7_101_08,CCTATGGT,iTru5_07_A,AAGACACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM7.640188\n1,1_SKM8_640201,1_SKM8_640201,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C5,iTru7_101_12,GTCCTTCT,iTru5_11_A,CAATAGCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM8.640201\n1,1_SKM9_640192,1_SKM9_640192,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A7,iTru7_211_01,GCTTCTTG,iTru5_124_H,AACGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM9.640192\n1,blank_30_C10,blank_30_C10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E19,iTru7_103_07,TGTGACTG,iTru5_06_C,AGCTACCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C10\n1,blank_30_C11,blank_30_C11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E21,iTru7_103_08,CGAAGAAC,iTru5_07_C,AACCGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C11\n1,blank_30_C12,blank_30_C12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E23,iTru7_103_09,GGTGTCTT,iTru5_08_C,ATCGCAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C12\n1,blank_30_C4,blank_30_C4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E7,iTru7_103_01,CAGCGATT,iTru5_12_B,ATCTGACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C4\n1,blank_30_C5,blank_30_C5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E9,iTru7_103_02,TAGTGACC,iTru5_01_C,CACAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C5\n1,blank_30_C6,blank_30_C6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E11,iTru7_103_03,CGAGACTA,iTru5_02_C,CACTGTAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C6\n1,blank_30_C7,blank_30_C7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E13,iTru7_103_04,GACATGGT,iTru5_03_C,CACAGGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C7\n1,blank_30_C8,blank_30_C8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E15,iTru7_103_05,GCATGTCT,iTru5_04_C,CCATGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C8\n1,blank_30_C9,blank_30_C9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E17,iTru7_103_06,ACTCCATC,iTru5_05_C,GCCAATAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C9\n1,blank_30_D1,blank_30_D1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G1,iTru7_103_10,AAGAAGGC,iTru5_09_C,GTTGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D1\n1,blank_30_D10,blank_30_D10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G19,iTru7_104_07,TTAGGTCG,iTru5_06_D,TCGACAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D10\n1,blank_30_D11,blank_30_D11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G21,iTru7_104_08,GCAAGATC,iTru5_07_D,GCTGAATC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D11\n1,blank_30_D12,blank_30_D12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G23,iTru7_104_09,AGAGCCTT,iTru5_08_D,AGTTGTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D12\n1,blank_30_D2,blank_30_D2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G3,iTru7_103_11,AGGTTCGA,iTru5_10_C,TCTAGTCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D2\n1,blank_30_D3,blank_30_D3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G5,iTru7_103_12,CATGTTCC,iTru5_11_C,GACGAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D3\n1,blank_30_D4,blank_30_D4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G7,iTru7_104_01,GTGCCATA,iTru5_12_C,TTCGTACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D4\n1,blank_30_D5,blank_30_D5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G9,iTru7_104_02,CCTTGTAG,iTru5_01_D,CGACACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D5\n1,blank_30_D6,blank_30_D6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G11,iTru7_104_03,GCTGGATT,iTru5_02_D,AGACGCTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D6\n1,blank_30_D7,blank_30_D7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G13,iTru7_104_04,TAACGAGG,iTru5_03_D,TGACAACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D7\n1,blank_30_D8,blank_30_D8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G15,iTru7_104_05,ATGGTTGC,iTru5_04_D,GGTACTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D8\n1,blank_30_D9,blank_30_D9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G17,iTru7_104_06,CCTATACC,iTru5_05_D,CTGTATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D9\n1,blank_30_E1,blank_30_E1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I1,iTru7_104_10,GCAATGGA,iTru5_09_D,TGTCGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E1\n1,blank_30_E10,blank_30_E10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I19,iTru7_105_07,TGGCATGT,iTru5_06_E,TATGACCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E10\n1,blank_30_E11,blank_30_E11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I21,iTru7_105_08,AGAAGCGT,iTru5_07_E,AGCTAGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E11\n1,blank_30_E12,blank_30_E12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I23,iTru7_105_09,AGCGGAAT,iTru5_08_E,GAACGAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E12\n1,blank_30_E2,blank_30_E2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I3,iTru7_104_11,CTGGAGTA,iTru5_10_D,AAGGCTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E2\n1,blank_30_E3,blank_30_E3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I5,iTru7_104_12,GAACATCG,iTru5_11_D,CCTAACAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E3\n1,blank_30_E4,blank_30_E4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I7,iTru7_105_01,GCACAACT,iTru5_12_D,AAGACGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E4\n1,blank_30_E5,blank_30_E5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I9,iTru7_105_02,TTCTCTCG,iTru5_01_E,GACTTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E5\n1,blank_30_E6,blank_30_E6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I11,iTru7_105_03,AACGGTCA,iTru5_02_E,CAACTCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E6\n1,blank_30_E7,blank_30_E7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I13,iTru7_105_04,ACAGACCT,iTru5_03_E,TGTTCCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E7\n1,blank_30_E8,blank_30_E8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I15,iTru7_105_05,TCTCTTCC,iTru5_04_E,ACCGCTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E8\n1,blank_30_E9,blank_30_E9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I17,iTru7_105_06,AGTGTTGG,iTru5_05_E,CTTAGGAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E9\n1,blank_30_F1,blank_30_F1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K1,iTru7_105_10,TAACCGGT,iTru5_09_E,CGTCTAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F1\n1,blank_30_F10,blank_30_F10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K19,iTru7_106_07,CGTCTTGT,iTru5_06_F,AGCCAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F10\n1,blank_30_F11,blank_30_F11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K21,iTru7_106_08,CGTGATCA,iTru5_07_F,CTAGCTCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F11\n1,blank_30_F12,blank_30_F12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K23,iTru7_106_09,CCAAGTTG,iTru5_08_F,GGAAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F12\n1,blank_30_F2,blank_30_F2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K3,iTru7_105_11,CATGGAAC,iTru5_10_E,AACCAGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F2\n1,blank_30_F3,blank_30_F3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K5,iTru7_105_12,ATGGTCCA,iTru5_11_E,CGCCTTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F3\n1,blank_30_F4,blank_30_F4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K7,iTru7_106_01,CTTCTGAG,iTru5_12_E,CTCGTTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F4\n1,blank_30_F5,blank_30_F5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K9,iTru7_106_02,AACCGAAG,iTru5_01_F,GTGAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F5\n1,blank_30_F6,blank_30_F6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K11,iTru7_106_03,TTCGTACC,iTru5_02_F,AACACGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F6\n1,blank_30_F7,blank_30_F7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K13,iTru7_106_04,CTGTTAGG,iTru5_03_F,CCTAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F7\n1,blank_30_F8,blank_30_F8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K15,iTru7_106_05,CACAAGTC,iTru5_04_F,TTCCAGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F8\n1,blank_30_F9,blank_30_F9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K17,iTru7_106_06,TCTTGACG,iTru5_05_F,TCAGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F9\n1,blank_30_G1,blank_30_G1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M1,iTru7_106_10,GTACCTTG,iTru5_09_F,AACACTGG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G1\n1,blank_30_G10,blank_30_G10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M19,iTru7_107_07,CCGACTAT,iTru5_06_G,GATCTTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G10\n1,blank_30_G11,blank_30_G11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M21,iTru7_107_08,AGCTAACC,iTru5_07_G,GTTAAGCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G11\n1,blank_30_G12,blank_30_G12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M23,iTru7_107_09,GCCTTGTT,iTru5_08_G,GTCATCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G12\n1,blank_30_G2,blank_30_G2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M3,iTru7_106_11,GACTATGC,iTru5_10_F,ACTATCGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G2\n1,blank_30_G3,blank_30_G3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M5,iTru7_106_12,TGGATCAC,iTru5_11_F,ACAACAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G3\n1,blank_30_G4,blank_30_G4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M7,iTru7_107_01,CTCTGGTT,iTru5_12_F,TGTGGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G4\n1,blank_30_G5,blank_30_G5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M9,iTru7_107_02,GTTCATGG,iTru5_01_G,GTTCCATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G5\n1,blank_30_G6,blank_30_G6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M11,iTru7_107_03,GCTGTAAG,iTru5_02_G,TGGATGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G6\n1,blank_30_G7,blank_30_G7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M13,iTru7_107_04,GTCGAAGA,iTru5_03_G,GCATAACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G7\n1,blank_30_G8,blank_30_G8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M15,iTru7_107_05,GAGCTCAA,iTru5_04_G,TCGAACCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G8\n1,blank_30_G9,blank_30_G9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M17,iTru7_107_06,TGAACCTG,iTru5_05_G,ACATGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G9\n1,blank_30_H1,blank_30_H1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O1,iTru7_107_10,AACTTGCC,iTru5_09_G,TCAGACAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H1\n1,blank_30_H10,blank_30_H10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O19,iTru7_108_07,GAAGTACC,iTru5_06_H,CCTCGTTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H10\n1,blank_30_H11,blank_30_H11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O21,iTru7_108_08,CAGGTATC,iTru5_07_H,CGATTGGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H11\n1,blank_30_H12,blank_30_H12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O23,iTru7_108_09,TCTCTAGG,iTru5_08_H,CCAACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H12\n1,blank_30_H2,blank_30_H2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O3,iTru7_107_11,CAATGTGG,iTru5_10_G,GTCCTAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H2\n1,blank_30_H3,blank_30_H3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O5,iTru7_107_12,AAGGCTGA,iTru5_11_G,AGACCTTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H3\n1,blank_30_H4,blank_30_H4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O7,iTru7_108_01,TTACCGAG,iTru5_12_G,AGACATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H4\n1,blank_30_H5,blank_30_H5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O9,iTru7_108_02,GTCCTAAG,iTru5_01_H,TAGCTGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H5\n1,blank_30_H6,blank_30_H6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O11,iTru7_108_03,GAAGGTTC,iTru5_02_H,TTCGAAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H6\n1,blank_30_H7,blank_30_H7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O13,iTru7_108_04,GAAGAGGT,iTru5_03_H,CAGTGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H7\n1,blank_30_H8,blank_30_H8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O15,iTru7_108_05,TCTGAGAG,iTru5_04_H,TAGTGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H8\n1,blank_30_H9,blank_30_H9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O17,iTru7_108_06,ACCGCATA,iTru5_05_H,GATGGAGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H9\"\"\" # noqa\n\n\nif __name__ == '__main__':\n integration_tests()\n```<|memory_end|>\nPreserve indentation, whitespace, and order.","role":"user"}],"string":"[\n {\n \"content\": \"Replicate the source code:\\n<|memory_start|>```python\\n#!/usr/bin/env python\\n\\nfrom datetime import datetime\\nfrom itertools import chain\\nimport re\\n\\nimport numpy as np\\nimport click\\n\\nfrom labman.db.process import (\\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,\\n LibraryPrep16SProcess, NormalizationProcess, QuantificationProcess,\\n LibraryPrepShotgunProcess, PoolingProcess, SequencingProcess)\\nfrom labman.db.user import User\\nfrom labman.db.plate import PlateConfiguration, Plate\\nfrom labman.db.equipment import Equipment\\nfrom labman.db.composition import ReagentComposition\\nfrom labman.db.sql_connection import TRN\\n\\n\\ndef get_samples():\\n with TRN:\\n TRN.add(\\\"SELECT sample_id FROM qiita.study_sample\\\")\\n return TRN.execute_fetchflatten()\\n\\n\\ndef create_sample_plate_process(user, samples):\\n plate_config = PlateConfiguration(1)\\n num_rows = plate_config.num_rows\\n num_cols = plate_config.num_columns\\n sp_process = SamplePlatingProcess.create(\\n user, plate_config, 'Test plate %s' % datetime.now())\\n\\n # Plate the samples\\n for idx, sample in enumerate(samples):\\n i = int(idx / num_cols) + 1\\n j = (idx % num_cols) + 1\\n\\n # Make sure that the user didn't pass more samples than wells\\n if i > num_rows:\\n break\\n\\n sp_process.update_well(i, j, sample)\\n\\n sample_plate = sp_process.plate\\n return sp_process, sample_plate\\n\\n\\ndef create_gdna_extraction_process(user, plate):\\n kingfisher = Equipment(11)\\n epmotion = Equipment(6)\\n epmotion_tool = Equipment(15)\\n extraction_kit = ReagentComposition(1)\\n ext_process = GDNAExtractionProcess.create(\\n user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,\\n 'GDNA test plate %s' % datetime.now())\\n gdna_plate = ext_process.plates[0]\\n return ext_process, gdna_plate\\n\\n\\ndef create_amplicon_prep(user, plate):\\n primer_plate = Plate(11)\\n epmotion = Equipment(6)\\n master_mix = ReagentComposition(2)\\n water_lot = ReagentComposition(3)\\n epmotion_tool_tm300 = Equipment(16)\\n epmotion_tool_tm50 = Equipment(17)\\n amplicon_process = LibraryPrep16SProcess.create(\\n user, plate, primer_plate, 'Amplicon test plate %s' % datetime.now(),\\n epmotion, epmotion_tool_tm300, epmotion_tool_tm50, master_mix,\\n water_lot, 75,)\\n amplicon_plate = amplicon_process.plates[0]\\n return amplicon_process, amplicon_plate\\n\\n\\ndef create_compression_process(user, gdna_plates):\\n comp_process = GDNAPlateCompressionProcess.create(\\n user, gdna_plates, 'Compressed test plate %s' % datetime.now(),\\n Equipment(6))\\n compressed_plate = comp_process.plates[0]\\n return comp_process, compressed_plate\\n\\n\\ndef create_quantification_process(user, plate):\\n plate_config = plate.plate_configuration\\n concentrations = np.around(\\n np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)\\n quant_process = QuantificationProcess.create(user, plate, concentrations)\\n return quant_process\\n\\n\\ndef create_pool_quantification_process(user, pools):\\n concentrations = np.around(np.random.rand(len(pools)), 6)\\n concentrations = [{'composition': p, 'concentration': c}\\n for p, c in zip(pools, concentrations)]\\n return QuantificationProcess.create_manual(user, concentrations)\\n\\n\\ndef create_normalization_process(user, quant_process):\\n water = ReagentComposition(3)\\n norm_process = NormalizationProcess.create(\\n user, quant_process, water,\\n 'Normalized test plate %s' % datetime.now())\\n norm_plate = norm_process.plates[0]\\n return norm_process, norm_plate\\n\\n\\ndef create_shotgun_process(user, norm_plate):\\n kappa = ReagentComposition(4)\\n stub = ReagentComposition(5)\\n shotgun_process = LibraryPrepShotgunProcess.create(\\n user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,\\n stub, 4000, Plate(19), Plate(20))\\n shotgun_plate = shotgun_process.plates[0]\\n return shotgun_process, shotgun_plate\\n\\n\\ndef create_plate_pool_process(user, quant_process, plate, func_data):\\n input_compositions = []\\n echo = Equipment(8)\\n for well in chain.from_iterable(plate.layout):\\n if well is not None:\\n input_compositions.append({\\n 'composition': well.composition, 'input_volume': 1,\\n 'percentage_of_output': 1/9.0})\\n pool_process = PoolingProcess.create(\\n user, quant_process, 'New test pool name %s' % datetime.now(),\\n 4, input_compositions, func_data, robot=echo)\\n return pool_process\\n\\n\\ndef create_pools_pool_process(user, quant_process, pools):\\n input_compositions = [\\n {'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}\\n for p in pools]\\n pool_process = PoolingProcess.create(\\n user, quant_process, 'New pool name %s' % datetime.now(), 5,\\n input_compositions, {\\\"function\\\": \\\"amplicon_pool\\\", \\\"parameters\\\": {}})\\n return pool_process\\n\\n\\ndef create_sequencing_process(user, pools):\\n seq_process = SequencingProcess.create(\\n user, pools, 'New sequencing run %s' % datetime.now(),\\n 'Run experiment %s' % datetime.now(), Equipment(18), 151, 151,\\n User('admin@foo.bar'),\\n contacts=[User('test@foo.bar'), User('demo@microbio.me')])\\n return seq_process\\n\\n\\ndef amplicon_workflow(user, samples):\\n # Sample Plating\\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\\n # gDNA extraction\\n ext_process, gdna_plate = create_gdna_extraction_process(\\n user, sample_plate)\\n # Amplicon library prep\\n amplicon_process, amplicon_plate = create_amplicon_prep(user, gdna_plate)\\n # Library plate quantification\\n amplicon_quant_process = create_quantification_process(\\n user, amplicon_plate)\\n # Plate pooling process\\n plate_pool_process = create_plate_pool_process(\\n user, amplicon_quant_process, amplicon_plate,\\n {'function': 'amplicon',\\n 'parameters': {\\\"dna_amount\\\": 240, \\\"min_val\\\": 1, \\\"max_val\\\": 15,\\n \\\"blank_volume\\\": 2, \\\"robot\\\": 6, \\\"destination\\\": 1}})\\n # Quantify pools\\n pool_quant_process = create_pool_quantification_process(\\n user, [plate_pool_process.pool])\\n # Create sequencing pool process\\n seq_pool_process = create_pools_pool_process(\\n user, pool_quant_process, [plate_pool_process.pool])\\n # Sequencing process\\n seq_process = create_sequencing_process(user, [seq_pool_process.pool])\\n return seq_process\\n\\n\\ndef shotgun_workflow(user, samples):\\n # Sample Plating\\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\\n # gDNA extraction\\n ext_process, gdna_plate = create_gdna_extraction_process(\\n user, sample_plate)\\n # gDNA compression\\n comp_process, compressed_plate = create_compression_process(\\n user, [gdna_plate])\\n # gDNA compressed quantification\\n gdna_comp_quant_process = create_quantification_process(\\n user, compressed_plate)\\n # Normalization process\\n norm_process, norm_plate = create_normalization_process(\\n user, gdna_comp_quant_process)\\n # Library prep shotgun\\n shotgun_process, shotgun_plate = create_shotgun_process(user, norm_plate)\\n # Quantify library plate\\n shotgun_quant_process = create_quantification_process(user, shotgun_plate)\\n # Pooling process\\n pool_process = create_plate_pool_process(\\n user, shotgun_quant_process, shotgun_plate,\\n {'function': 'equal', 'parameters': {'total_vol': 60, 'size': 500}})\\n # Sequencing process\\n seq_process = create_sequencing_process(user, [pool_process.pool])\\n return seq_process\\n\\n\\n@click.command()\\ndef integration_tests():\\n samples = get_samples()\\n user = User('test@foo.bar')\\n amplicon_seq_process = amplicon_workflow(user, samples)\\n shotgun_seq_process = shotgun_workflow(user, samples)\\n\\n obs = amplicon_seq_process.generate_sample_sheet()\\n res = re.match(EXP_AMPLICON_SAMPLE_SHEET, obs)\\n if res is None:\\n raise ValueError(\\n 'Amplicon sample sheet does not match expected regex:\\\\n%s' % obs)\\n\\n obs = shotgun_seq_process.generate_sample_sheet()\\n res = re.match(EXP_SHOTGUN_SAMPLE_SHEET, obs)\\n if res is None:\\n raise ValueError(\\n 'Shotgun sample sheet does not match expected regex:\\\\n%s' % obs)\\n\\n\\nEXP_AMPLICON_SAMPLE_SHEET = r\\\"\\\"\\\"# PI,Admin,admin@foo.bar\\n# Contact,Demo,Dude\\n# Contact emails,demo@microbio.me,test@foo.bar\\n\\\\[Header\\\\]\\nIEMFileVersion,4\\nInvestigator Name,Admin\\nExperiment Name,Run experiment \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6}\\nDate,\\\\d{4}-\\\\d{2}-\\\\d{2}\\nWorkflow,GenerateFASTQ\\nApplication,FASTQ Only\\nAssay,Amplicon\\nDescription,\\nChemistry,Default\\n\\n\\\\[Reads\\\\]\\n151\\n151\\n\\n\\\\[Settings\\\\]\\nReverseComplement,0\\n\\n\\\\[Data\\\\]\\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,,\\nNew_sequencing_run_\\\\d{4}-\\\\d{2}-\\\\d{2}_\\\\d{2}_\\\\d{2}_\\\\d{2}_\\\\d{6},,,,,NNNNNNNNNNNN,,,,,\\\"\\\"\\\" # noqa\\n\\n\\nEXP_SHOTGUN_SAMPLE_SHEET = r\\\"\\\"\\\"# PI,Admin,admin@foo.bar\\n# Contact,Demo,Dude\\n# Contact emails,demo@microbio.me,test@foo.bar\\n\\\\[Header\\\\]\\nIEMFileVersion,4\\nInvestigator Name,Admin\\nExperiment Name,Run experiment \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6}\\nDate,\\\\d{4}-\\\\d{2}-\\\\d{2}\\nWorkflow,GenerateFASTQ\\nApplication,FASTQ Only\\nAssay,Metagenomics\\nDescription,\\nChemistry,Default\\n\\n\\\\[Reads\\\\]\\n151\\n151\\n\\n\\\\[Settings\\\\]\\nReverseComplement,0\\n\\n\\\\[Data\\\\]\\nLane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\\n1,1_SKB1_640202,1_SKB1_640202,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A23,iTru7_101_09,TGTACACC,iTru5_08_A,CATCTGCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB1.640202\\n1,1_SKB2_640194,1_SKB2_640194,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A17,iTru7_101_06,AACAACCG,iTru5_05_A,GGTACGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB2.640194\\n1,1_SKB3_640195,1_SKB3_640195,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E1,iTru7_102_10,GTTAAGGC,iTru5_09_B,ACGGACTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB3.640195\\n1,1_SKB4_640189,1_SKB4_640189,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C17,iTru7_102_06,TGTGCGTT,iTru5_05_B,AAGCATCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB4.640189\\n1,1_SKB5_640181,1_SKB5_640181,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A13,iTru7_101_04,GATCCATG,iTru5_03_A,AACACCAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB5.640181\\n1,1_SKB6_640176,1_SKB6_640176,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E3,iTru7_102_11,AAGCCACA,iTru5_10_B,CATGTGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB6.640176\\n1,1_SKB7_640196,1_SKB7_640196,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A5,iTru7_115_11,CTTAGGAC,iTru5_123_H,CTCTTGTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB7.640196\\n1,1_SKB8_640193,1_SKB8_640193,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A1,iTru7_115_09,AGCACTTC,iTru5_121_H,GATGCTAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB8.640193\\n1,1_SKB9_640200,1_SKB9_640200,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C9,iTru7_102_02,CTTACCTG,iTru5_01_B,AGTGGCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKB9.640200\\n1,1_SKD1_640179,1_SKD1_640179,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C1,iTru7_101_10,GTATGCTG,iTru5_09_A,CTCTCAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD1.640179\\n1,1_SKD2_640178,1_SKD2_640178,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A19,iTru7_101_07,ACTCGTTG,iTru5_06_A,CGATCGAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD2.640178\\n1,1_SKD3_640198,1_SKD3_640198,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C3,iTru7_101_11,TGATGTCC,iTru5_10_A,TCGTCTGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD3.640198\\n1,1_SKD4_640185,1_SKD4_640185,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C23,iTru7_102_09,ACAGCTCA,iTru5_08_B,ACCTCTTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD4.640185\\n1,1_SKD5_640186,1_SKD5_640186,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C11,iTru7_102_03,CGTTGCAA,iTru5_02_B,GTGGTATG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD5.640186\\n1,1_SKD6_640190,1_SKD6_640190,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A15,iTru7_101_05,GCCTATCA,iTru5_04_A,CGTATCTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD6.640190\\n1,1_SKD7_640191,1_SKD7_640191,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C19,iTru7_102_07,TAGTTGCG,iTru5_06_B,TACTCCAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD7.640191\\n1,1_SKD8_640184,1_SKD8_640184,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A3,iTru7_115_10,GCATACAG,iTru5_122_H,GAACGGTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD8.640184\\n1,1_SKD9_640182,1_SKD9_640182,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C15,iTru7_102_05,TCACGTTC,iTru5_04_B,CGTCAAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKD9.640182\\n1,1_SKM1_640183,1_SKM1_640183,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E5,iTru7_102_12,ACACGGTT,iTru5_11_B,TGCCTCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM1.640183\\n1,1_SKM2_640199,1_SKM2_640199,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C7,iTru7_102_01,ATAAGGCG,iTru5_12_A,CATTCGTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM2.640199\\n1,1_SKM3_640197,1_SKM3_640197,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C13,iTru7_102_04,GATTCAGC,iTru5_03_B,TGAGCTGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM3.640197\\n1,1_SKM4_640180,1_SKM4_640180,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A9,iTru7_101_02,CTGTGTTG,iTru5_01_A,ACCGACAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM4.640180\\n1,1_SKM5_640177,1_SKM5_640177,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A11,iTru7_101_03,TGAGGTGT,iTru5_02_A,CTTCGCAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM5.640177\\n1,1_SKM6_640187,1_SKM6_640187,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C21,iTru7_102_08,AAGAGCCA,iTru5_07_B,GATACCTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM6.640187\\n1,1_SKM7_640188,1_SKM7_640188,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A21,iTru7_101_08,CCTATGGT,iTru5_07_A,AAGACACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM7.640188\\n1,1_SKM8_640201,1_SKM8_640201,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},C5,iTru7_101_12,GTCCTTCT,iTru5_11_A,CAATAGCC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM8.640201\\n1,1_SKM9_640192,1_SKM9_640192,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},A7,iTru7_211_01,GCTTCTTG,iTru5_124_H,AACGCCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},1.SKM9.640192\\n1,blank_30_C10,blank_30_C10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E19,iTru7_103_07,TGTGACTG,iTru5_06_C,AGCTACCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C10\\n1,blank_30_C11,blank_30_C11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E21,iTru7_103_08,CGAAGAAC,iTru5_07_C,AACCGAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C11\\n1,blank_30_C12,blank_30_C12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E23,iTru7_103_09,GGTGTCTT,iTru5_08_C,ATCGCAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C12\\n1,blank_30_C4,blank_30_C4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E7,iTru7_103_01,CAGCGATT,iTru5_12_B,ATCTGACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C4\\n1,blank_30_C5,blank_30_C5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E9,iTru7_103_02,TAGTGACC,iTru5_01_C,CACAGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C5\\n1,blank_30_C6,blank_30_C6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E11,iTru7_103_03,CGAGACTA,iTru5_02_C,CACTGTAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C6\\n1,blank_30_C7,blank_30_C7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E13,iTru7_103_04,GACATGGT,iTru5_03_C,CACAGGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C7\\n1,blank_30_C8,blank_30_C8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E15,iTru7_103_05,GCATGTCT,iTru5_04_C,CCATGAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C8\\n1,blank_30_C9,blank_30_C9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},E17,iTru7_103_06,ACTCCATC,iTru5_05_C,GCCAATAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.C9\\n1,blank_30_D1,blank_30_D1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G1,iTru7_103_10,AAGAAGGC,iTru5_09_C,GTTGCTGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D1\\n1,blank_30_D10,blank_30_D10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G19,iTru7_104_07,TTAGGTCG,iTru5_06_D,TCGACAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D10\\n1,blank_30_D11,blank_30_D11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G21,iTru7_104_08,GCAAGATC,iTru5_07_D,GCTGAATC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D11\\n1,blank_30_D12,blank_30_D12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G23,iTru7_104_09,AGAGCCTT,iTru5_08_D,AGTTGTGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D12\\n1,blank_30_D2,blank_30_D2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G3,iTru7_103_11,AGGTTCGA,iTru5_10_C,TCTAGTCC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D2\\n1,blank_30_D3,blank_30_D3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G5,iTru7_103_12,CATGTTCC,iTru5_11_C,GACGAACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D3\\n1,blank_30_D4,blank_30_D4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G7,iTru7_104_01,GTGCCATA,iTru5_12_C,TTCGTACG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D4\\n1,blank_30_D5,blank_30_D5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G9,iTru7_104_02,CCTTGTAG,iTru5_01_D,CGACACTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D5\\n1,blank_30_D6,blank_30_D6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G11,iTru7_104_03,GCTGGATT,iTru5_02_D,AGACGCTA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D6\\n1,blank_30_D7,blank_30_D7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G13,iTru7_104_04,TAACGAGG,iTru5_03_D,TGACAACC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D7\\n1,blank_30_D8,blank_30_D8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G15,iTru7_104_05,ATGGTTGC,iTru5_04_D,GGTACTTC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D8\\n1,blank_30_D9,blank_30_D9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},G17,iTru7_104_06,CCTATACC,iTru5_05_D,CTGTATGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.D9\\n1,blank_30_E1,blank_30_E1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I1,iTru7_104_10,GCAATGGA,iTru5_09_D,TGTCGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E1\\n1,blank_30_E10,blank_30_E10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I19,iTru7_105_07,TGGCATGT,iTru5_06_E,TATGACCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E10\\n1,blank_30_E11,blank_30_E11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I21,iTru7_105_08,AGAAGCGT,iTru5_07_E,AGCTAGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E11\\n1,blank_30_E12,blank_30_E12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I23,iTru7_105_09,AGCGGAAT,iTru5_08_E,GAACGAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E12\\n1,blank_30_E2,blank_30_E2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I3,iTru7_104_11,CTGGAGTA,iTru5_10_D,AAGGCTCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E2\\n1,blank_30_E3,blank_30_E3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I5,iTru7_104_12,GAACATCG,iTru5_11_D,CCTAACAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E3\\n1,blank_30_E4,blank_30_E4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I7,iTru7_105_01,GCACAACT,iTru5_12_D,AAGACGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E4\\n1,blank_30_E5,blank_30_E5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I9,iTru7_105_02,TTCTCTCG,iTru5_01_E,GACTTGTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E5\\n1,blank_30_E6,blank_30_E6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I11,iTru7_105_03,AACGGTCA,iTru5_02_E,CAACTCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E6\\n1,blank_30_E7,blank_30_E7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I13,iTru7_105_04,ACAGACCT,iTru5_03_E,TGTTCCGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E7\\n1,blank_30_E8,blank_30_E8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I15,iTru7_105_05,TCTCTTCC,iTru5_04_E,ACCGCTAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E8\\n1,blank_30_E9,blank_30_E9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},I17,iTru7_105_06,AGTGTTGG,iTru5_05_E,CTTAGGAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.E9\\n1,blank_30_F1,blank_30_F1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K1,iTru7_105_10,TAACCGGT,iTru5_09_E,CGTCTAAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F1\\n1,blank_30_F10,blank_30_F10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K19,iTru7_106_07,CGTCTTGT,iTru5_06_F,AGCCAACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F10\\n1,blank_30_F11,blank_30_F11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K21,iTru7_106_08,CGTGATCA,iTru5_07_F,CTAGCTCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F11\\n1,blank_30_F12,blank_30_F12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K23,iTru7_106_09,CCAAGTTG,iTru5_08_F,GGAAGAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F12\\n1,blank_30_F2,blank_30_F2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K3,iTru7_105_11,CATGGAAC,iTru5_10_E,AACCAGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F2\\n1,blank_30_F3,blank_30_F3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K5,iTru7_105_12,ATGGTCCA,iTru5_11_E,CGCCTTAT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F3\\n1,blank_30_F4,blank_30_F4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K7,iTru7_106_01,CTTCTGAG,iTru5_12_E,CTCGTTCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F4\\n1,blank_30_F5,blank_30_F5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K9,iTru7_106_02,AACCGAAG,iTru5_01_F,GTGAGACT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F5\\n1,blank_30_F6,blank_30_F6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K11,iTru7_106_03,TTCGTACC,iTru5_02_F,AACACGCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F6\\n1,blank_30_F7,blank_30_F7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K13,iTru7_106_04,CTGTTAGG,iTru5_03_F,CCTAGAGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F7\\n1,blank_30_F8,blank_30_F8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K15,iTru7_106_05,CACAAGTC,iTru5_04_F,TTCCAGGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F8\\n1,blank_30_F9,blank_30_F9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},K17,iTru7_106_06,TCTTGACG,iTru5_05_F,TCAGCCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.F9\\n1,blank_30_G1,blank_30_G1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M1,iTru7_106_10,GTACCTTG,iTru5_09_F,AACACTGG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G1\\n1,blank_30_G10,blank_30_G10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M19,iTru7_107_07,CCGACTAT,iTru5_06_G,GATCTTGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G10\\n1,blank_30_G11,blank_30_G11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M21,iTru7_107_08,AGCTAACC,iTru5_07_G,GTTAAGCG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G11\\n1,blank_30_G12,blank_30_G12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M23,iTru7_107_09,GCCTTGTT,iTru5_08_G,GTCATCGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G12\\n1,blank_30_G2,blank_30_G2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M3,iTru7_106_11,GACTATGC,iTru5_10_F,ACTATCGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G2\\n1,blank_30_G3,blank_30_G3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M5,iTru7_106_12,TGGATCAC,iTru5_11_F,ACAACAGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G3\\n1,blank_30_G4,blank_30_G4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M7,iTru7_107_01,CTCTGGTT,iTru5_12_F,TGTGGCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G4\\n1,blank_30_G5,blank_30_G5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M9,iTru7_107_02,GTTCATGG,iTru5_01_G,GTTCCATG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G5\\n1,blank_30_G6,blank_30_G6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M11,iTru7_107_03,GCTGTAAG,iTru5_02_G,TGGATGGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G6\\n1,blank_30_G7,blank_30_G7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M13,iTru7_107_04,GTCGAAGA,iTru5_03_G,GCATAACG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G7\\n1,blank_30_G8,blank_30_G8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M15,iTru7_107_05,GAGCTCAA,iTru5_04_G,TCGAACCT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G8\\n1,blank_30_G9,blank_30_G9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},M17,iTru7_107_06,TGAACCTG,iTru5_05_G,ACATGCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.G9\\n1,blank_30_H1,blank_30_H1,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O1,iTru7_107_10,AACTTGCC,iTru5_09_G,TCAGACAC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H1\\n1,blank_30_H10,blank_30_H10,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O19,iTru7_108_07,GAAGTACC,iTru5_06_H,CCTCGTTA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H10\\n1,blank_30_H11,blank_30_H11,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O21,iTru7_108_08,CAGGTATC,iTru5_07_H,CGATTGGA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H11\\n1,blank_30_H12,blank_30_H12,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O23,iTru7_108_09,TCTCTAGG,iTru5_08_H,CCAACGAA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H12\\n1,blank_30_H2,blank_30_H2,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O3,iTru7_107_11,CAATGTGG,iTru5_10_G,GTCCTAAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H2\\n1,blank_30_H3,blank_30_H3,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O5,iTru7_107_12,AAGGCTGA,iTru5_11_G,AGACCTTG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H3\\n1,blank_30_H4,blank_30_H4,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O7,iTru7_108_01,TTACCGAG,iTru5_12_G,AGACATGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H4\\n1,blank_30_H5,blank_30_H5,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O9,iTru7_108_02,GTCCTAAG,iTru5_01_H,TAGCTGAG,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H5\\n1,blank_30_H6,blank_30_H6,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O11,iTru7_108_03,GAAGGTTC,iTru5_02_H,TTCGAAGC,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H6\\n1,blank_30_H7,blank_30_H7,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O13,iTru7_108_04,GAAGAGGT,iTru5_03_H,CAGTGCTT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H7\\n1,blank_30_H8,blank_30_H8,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O15,iTru7_108_05,TCTGAGAG,iTru5_04_H,TAGTGCCA,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H8\\n1,blank_30_H9,blank_30_H9,Test Shotgun Library \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},O17,iTru7_108_06,ACCGCATA,iTru5_05_H,GATGGAGT,New sequencing run \\\\d{4}-\\\\d{2}-\\\\d{2} \\\\d{2}:\\\\d{2}:\\\\d{2}.\\\\d{6},blank.30.H9\\\"\\\"\\\" # noqa\\n\\n\\nif __name__ == '__main__':\\n integration_tests()\\n```<|memory_end|>\\nPreserve indentation, whitespace, and order.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"target":{"kind":"string","value":"```python\n#!/usr/bin/env python\n\nfrom datetime import datetime\nfrom itertools import chain\nimport re\n\nimport numpy as np\nimport click\n\nfrom labman.db.process import (\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,\n LibraryPrep16SProcess, NormalizationProcess, QuantificationProcess,\n LibraryPrepShotgunProcess, PoolingProcess, SequencingProcess)\nfrom labman.db.user import User\nfrom labman.db.plate import PlateConfiguration, Plate\nfrom labman.db.equipment import Equipment\nfrom labman.db.composition import ReagentComposition\nfrom labman.db.sql_connection import TRN\n\n\ndef get_samples():\n with TRN:\n TRN.add(\"SELECT sample_id FROM qiita.study_sample\")\n return TRN.execute_fetchflatten()\n\n\ndef create_sample_plate_process(user, samples):\n plate_config = PlateConfiguration(1)\n num_rows = plate_config.num_rows\n num_cols = plate_config.num_columns\n sp_process = SamplePlatingProcess.create(\n user, plate_config, 'Test plate %s' % datetime.now())\n\n # Plate the samples\n for idx, sample in enumerate(samples):\n i = int(idx / num_cols) + 1\n j = (idx % num_cols) + 1\n\n # Make sure that the user didn't pass more samples than wells\n if i > num_rows:\n break\n\n sp_process.update_well(i, j, sample)\n\n sample_plate = sp_process.plate\n return sp_process, sample_plate\n\n\ndef create_gdna_extraction_process(user, plate):\n kingfisher = Equipment(11)\n epmotion = Equipment(6)\n epmotion_tool = Equipment(15)\n extraction_kit = ReagentComposition(1)\n ext_process = GDNAExtractionProcess.create(\n user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,\n 'GDNA test plate %s' % datetime.now())\n gdna_plate = ext_process.plates[0]\n return ext_process, gdna_plate\n\n\ndef create_amplicon_prep(user, plate):\n primer_plate = Plate(11)\n epmotion = Equipment(6)\n master_mix = ReagentComposition(2)\n water_lot = ReagentComposition(3)\n epmotion_tool_tm300 = Equipment(16)\n epmotion_tool_tm50 = Equipment(17)\n amplicon_process = LibraryPrep16SProcess.create(\n user, plate, primer_plate, 'Amplicon test plate %s' % datetime.now(),\n epmotion, epmotion_tool_tm300, epmotion_tool_tm50, master_mix,\n water_lot, 75,)\n amplicon_plate = amplicon_process.plates[0]\n return amplicon_process, amplicon_plate\n\n\ndef create_compression_process(user, gdna_plates):\n comp_process = GDNAPlateCompressionProcess.create(\n user, gdna_plates, 'Compressed test plate %s' % datetime.now(),\n Equipment(6))\n compressed_plate = comp_process.plates[0]\n return comp_process, compressed_plate\n\n\ndef create_quantification_process(user, plate):\n plate_config = plate.plate_configuration\n concentrations = np.around(\n np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)\n quant_process = QuantificationProcess.create(user, plate, concentrations)\n return quant_process\n\n\ndef create_pool_quantification_process(user, pools):\n concentrations = np.around(np.random.rand(len(pools)), 6)\n concentrations = [{'composition': p, 'concentration': c}\n for p, c in zip(pools, concentrations)]\n return QuantificationProcess.create_manual(user, concentrations)\n\n\ndef create_normalization_process(user, quant_process):\n water = ReagentComposition(3)\n norm_process = NormalizationProcess.create(\n user, quant_process, water,\n 'Normalized test plate %s' % datetime.now())\n norm_plate = norm_process.plates[0]\n return norm_process, norm_plate\n\n\ndef create_shotgun_process(user, norm_plate):\n kappa = ReagentComposition(4)\n stub = ReagentComposition(5)\n shotgun_process = LibraryPrepShotgunProcess.create(\n user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,\n stub, 4000, Plate(19), Plate(20))\n shotgun_plate = shotgun_process.plates[0]\n return shotgun_process, shotgun_plate\n\n\ndef create_plate_pool_process(user, quant_process, plate, func_data):\n input_compositions = []\n echo = Equipment(8)\n for well in chain.from_iterable(plate.layout):\n if well is not None:\n input_compositions.append({\n 'composition': well.composition, 'input_volume': 1,\n 'percentage_of_output': 1/9.0})\n pool_process = PoolingProcess.create(\n user, quant_process, 'New test pool name %s' % datetime.now(),\n 4, input_compositions, func_data, robot=echo)\n return pool_process\n\n\ndef create_pools_pool_process(user, quant_process, pools):\n input_compositions = [\n {'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}\n for p in pools]\n pool_process = PoolingProcess.create(\n user, quant_process, 'New pool name %s' % datetime.now(), 5,\n input_compositions, {\"function\": \"amplicon_pool\", \"parameters\": {}})\n return pool_process\n\n\ndef create_sequencing_process(user, pools):\n seq_process = SequencingProcess.create(\n user, pools, 'New sequencing run %s' % datetime.now(),\n 'Run experiment %s' % datetime.now(), Equipment(18), 151, 151,\n User('admin@foo.bar'),\n contacts=[User('test@foo.bar'), User('demo@microbio.me')])\n return seq_process\n\n\ndef amplicon_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # Amplicon library prep\n amplicon_process, amplicon_plate = create_amplicon_prep(user, gdna_plate)\n # Library plate quantification\n amplicon_quant_process = create_quantification_process(\n user, amplicon_plate)\n # Plate pooling process\n plate_pool_process = create_plate_pool_process(\n user, amplicon_quant_process, amplicon_plate,\n {'function': 'amplicon',\n 'parameters': {\"dna_amount\": 240, \"min_val\": 1, \"max_val\": 15,\n \"blank_volume\": 2, \"robot\": 6, \"destination\": 1}})\n # Quantify pools\n pool_quant_process = create_pool_quantification_process(\n user, [plate_pool_process.pool])\n # Create sequencing pool process\n seq_pool_process = create_pools_pool_process(\n user, pool_quant_process, [plate_pool_process.pool])\n # Sequencing process\n seq_process = create_sequencing_process(user, [seq_pool_process.pool])\n return seq_process\n\n\ndef shotgun_workflow(user, samples):\n # Sample Plating\n sp_process, sample_plate = create_sample_plate_process(user, samples[:96])\n # gDNA extraction\n ext_process, gdna_plate = create_gdna_extraction_process(\n user, sample_plate)\n # gDNA compression\n comp_process, compressed_plate = create_compression_process(\n user, [gdna_plate])\n # gDNA compressed quantification\n gdna_comp_quant_process = create_quantification_process(\n user, compressed_plate)\n # Normalization process\n norm_process, norm_plate = create_normalization_process(\n user, gdna_comp_quant_process)\n # Library prep shotgun\n shotgun_process, shotgun_plate = create_shotgun_process(user, norm_plate)\n # Quantify library plate\n shotgun_quant_process = create_quantification_process(user, shotgun_plate)\n # Pooling process\n pool_process = create_plate_pool_process(\n user, shotgun_quant_process, shotgun_plate,\n {'function': 'equal', 'parameters': {'total_vol': 60, 'size': 500}})\n # Sequencing process\n seq_process = create_sequencing_process(user, [pool_process.pool])\n return seq_process\n\n\n@click.command()\ndef integration_tests():\n samples = get_samples()\n user = User('test@foo.bar')\n amplicon_seq_process = amplicon_workflow(user, samples)\n shotgun_seq_process = shotgun_workflow(user, samples)\n\n obs = amplicon_seq_process.generate_sample_sheet()\n res = re.match(EXP_AMPLICON_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Amplicon sample sheet does not match expected regex:\\n%s' % obs)\n\n obs = shotgun_seq_process.generate_sample_sheet()\n res = re.match(EXP_SHOTGUN_SAMPLE_SHEET, obs)\n if res is None:\n raise ValueError(\n 'Shotgun sample sheet does not match expected regex:\\n%s' % obs)\n\n\nEXP_AMPLICON_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Amplicon\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,,\nNew_sequencing_run_\\d{4}-\\d{2}-\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{6},,,,,NNNNNNNNNNNN,,,,,\"\"\" # noqa\n\n\nEXP_SHOTGUN_SAMPLE_SHEET = r\"\"\"# PI,Admin,admin@foo.bar\n# Contact,Demo,Dude\n# Contact emails,demo@microbio.me,test@foo.bar\n\\[Header\\]\nIEMFileVersion,4\nInvestigator Name,Admin\nExperiment Name,Run experiment \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6}\nDate,\\d{4}-\\d{2}-\\d{2}\nWorkflow,GenerateFASTQ\nApplication,FASTQ Only\nAssay,Metagenomics\nDescription,\nChemistry,Default\n\n\\[Reads\\]\n151\n151\n\n\\[Settings\\]\nReverseComplement,0\n\n\\[Data\\]\nLane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\n1,1_SKB1_640202,1_SKB1_640202,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A23,iTru7_101_09,TGTACACC,iTru5_08_A,CATCTGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB1.640202\n1,1_SKB2_640194,1_SKB2_640194,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A17,iTru7_101_06,AACAACCG,iTru5_05_A,GGTACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB2.640194\n1,1_SKB3_640195,1_SKB3_640195,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E1,iTru7_102_10,GTTAAGGC,iTru5_09_B,ACGGACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB3.640195\n1,1_SKB4_640189,1_SKB4_640189,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C17,iTru7_102_06,TGTGCGTT,iTru5_05_B,AAGCATCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB4.640189\n1,1_SKB5_640181,1_SKB5_640181,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A13,iTru7_101_04,GATCCATG,iTru5_03_A,AACACCAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB5.640181\n1,1_SKB6_640176,1_SKB6_640176,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E3,iTru7_102_11,AAGCCACA,iTru5_10_B,CATGTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB6.640176\n1,1_SKB7_640196,1_SKB7_640196,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A5,iTru7_115_11,CTTAGGAC,iTru5_123_H,CTCTTGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB7.640196\n1,1_SKB8_640193,1_SKB8_640193,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A1,iTru7_115_09,AGCACTTC,iTru5_121_H,GATGCTAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB8.640193\n1,1_SKB9_640200,1_SKB9_640200,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C9,iTru7_102_02,CTTACCTG,iTru5_01_B,AGTGGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKB9.640200\n1,1_SKD1_640179,1_SKD1_640179,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C1,iTru7_101_10,GTATGCTG,iTru5_09_A,CTCTCAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD1.640179\n1,1_SKD2_640178,1_SKD2_640178,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A19,iTru7_101_07,ACTCGTTG,iTru5_06_A,CGATCGAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD2.640178\n1,1_SKD3_640198,1_SKD3_640198,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C3,iTru7_101_11,TGATGTCC,iTru5_10_A,TCGTCTGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD3.640198\n1,1_SKD4_640185,1_SKD4_640185,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C23,iTru7_102_09,ACAGCTCA,iTru5_08_B,ACCTCTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD4.640185\n1,1_SKD5_640186,1_SKD5_640186,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C11,iTru7_102_03,CGTTGCAA,iTru5_02_B,GTGGTATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD5.640186\n1,1_SKD6_640190,1_SKD6_640190,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A15,iTru7_101_05,GCCTATCA,iTru5_04_A,CGTATCTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD6.640190\n1,1_SKD7_640191,1_SKD7_640191,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C19,iTru7_102_07,TAGTTGCG,iTru5_06_B,TACTCCAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD7.640191\n1,1_SKD8_640184,1_SKD8_640184,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A3,iTru7_115_10,GCATACAG,iTru5_122_H,GAACGGTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD8.640184\n1,1_SKD9_640182,1_SKD9_640182,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C15,iTru7_102_05,TCACGTTC,iTru5_04_B,CGTCAAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKD9.640182\n1,1_SKM1_640183,1_SKM1_640183,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E5,iTru7_102_12,ACACGGTT,iTru5_11_B,TGCCTCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM1.640183\n1,1_SKM2_640199,1_SKM2_640199,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C7,iTru7_102_01,ATAAGGCG,iTru5_12_A,CATTCGTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM2.640199\n1,1_SKM3_640197,1_SKM3_640197,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C13,iTru7_102_04,GATTCAGC,iTru5_03_B,TGAGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM3.640197\n1,1_SKM4_640180,1_SKM4_640180,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A9,iTru7_101_02,CTGTGTTG,iTru5_01_A,ACCGACAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM4.640180\n1,1_SKM5_640177,1_SKM5_640177,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A11,iTru7_101_03,TGAGGTGT,iTru5_02_A,CTTCGCAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM5.640177\n1,1_SKM6_640187,1_SKM6_640187,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C21,iTru7_102_08,AAGAGCCA,iTru5_07_B,GATACCTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM6.640187\n1,1_SKM7_640188,1_SKM7_640188,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A21,iTru7_101_08,CCTATGGT,iTru5_07_A,AAGACACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM7.640188\n1,1_SKM8_640201,1_SKM8_640201,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},C5,iTru7_101_12,GTCCTTCT,iTru5_11_A,CAATAGCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM8.640201\n1,1_SKM9_640192,1_SKM9_640192,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},A7,iTru7_211_01,GCTTCTTG,iTru5_124_H,AACGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},1.SKM9.640192\n1,blank_30_C10,blank_30_C10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E19,iTru7_103_07,TGTGACTG,iTru5_06_C,AGCTACCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C10\n1,blank_30_C11,blank_30_C11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E21,iTru7_103_08,CGAAGAAC,iTru5_07_C,AACCGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C11\n1,blank_30_C12,blank_30_C12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E23,iTru7_103_09,GGTGTCTT,iTru5_08_C,ATCGCAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C12\n1,blank_30_C4,blank_30_C4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E7,iTru7_103_01,CAGCGATT,iTru5_12_B,ATCTGACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C4\n1,blank_30_C5,blank_30_C5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E9,iTru7_103_02,TAGTGACC,iTru5_01_C,CACAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C5\n1,blank_30_C6,blank_30_C6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E11,iTru7_103_03,CGAGACTA,iTru5_02_C,CACTGTAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C6\n1,blank_30_C7,blank_30_C7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E13,iTru7_103_04,GACATGGT,iTru5_03_C,CACAGGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C7\n1,blank_30_C8,blank_30_C8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E15,iTru7_103_05,GCATGTCT,iTru5_04_C,CCATGAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C8\n1,blank_30_C9,blank_30_C9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},E17,iTru7_103_06,ACTCCATC,iTru5_05_C,GCCAATAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.C9\n1,blank_30_D1,blank_30_D1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G1,iTru7_103_10,AAGAAGGC,iTru5_09_C,GTTGCTGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D1\n1,blank_30_D10,blank_30_D10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G19,iTru7_104_07,TTAGGTCG,iTru5_06_D,TCGACAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D10\n1,blank_30_D11,blank_30_D11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G21,iTru7_104_08,GCAAGATC,iTru5_07_D,GCTGAATC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D11\n1,blank_30_D12,blank_30_D12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G23,iTru7_104_09,AGAGCCTT,iTru5_08_D,AGTTGTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D12\n1,blank_30_D2,blank_30_D2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G3,iTru7_103_11,AGGTTCGA,iTru5_10_C,TCTAGTCC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D2\n1,blank_30_D3,blank_30_D3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G5,iTru7_103_12,CATGTTCC,iTru5_11_C,GACGAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D3\n1,blank_30_D4,blank_30_D4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G7,iTru7_104_01,GTGCCATA,iTru5_12_C,TTCGTACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D4\n1,blank_30_D5,blank_30_D5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G9,iTru7_104_02,CCTTGTAG,iTru5_01_D,CGACACTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D5\n1,blank_30_D6,blank_30_D6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G11,iTru7_104_03,GCTGGATT,iTru5_02_D,AGACGCTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D6\n1,blank_30_D7,blank_30_D7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G13,iTru7_104_04,TAACGAGG,iTru5_03_D,TGACAACC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D7\n1,blank_30_D8,blank_30_D8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G15,iTru7_104_05,ATGGTTGC,iTru5_04_D,GGTACTTC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D8\n1,blank_30_D9,blank_30_D9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},G17,iTru7_104_06,CCTATACC,iTru5_05_D,CTGTATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.D9\n1,blank_30_E1,blank_30_E1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I1,iTru7_104_10,GCAATGGA,iTru5_09_D,TGTCGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E1\n1,blank_30_E10,blank_30_E10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I19,iTru7_105_07,TGGCATGT,iTru5_06_E,TATGACCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E10\n1,blank_30_E11,blank_30_E11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I21,iTru7_105_08,AGAAGCGT,iTru5_07_E,AGCTAGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E11\n1,blank_30_E12,blank_30_E12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I23,iTru7_105_09,AGCGGAAT,iTru5_08_E,GAACGAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E12\n1,blank_30_E2,blank_30_E2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I3,iTru7_104_11,CTGGAGTA,iTru5_10_D,AAGGCTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E2\n1,blank_30_E3,blank_30_E3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I5,iTru7_104_12,GAACATCG,iTru5_11_D,CCTAACAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E3\n1,blank_30_E4,blank_30_E4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I7,iTru7_105_01,GCACAACT,iTru5_12_D,AAGACGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E4\n1,blank_30_E5,blank_30_E5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I9,iTru7_105_02,TTCTCTCG,iTru5_01_E,GACTTGTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E5\n1,blank_30_E6,blank_30_E6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I11,iTru7_105_03,AACGGTCA,iTru5_02_E,CAACTCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E6\n1,blank_30_E7,blank_30_E7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I13,iTru7_105_04,ACAGACCT,iTru5_03_E,TGTTCCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E7\n1,blank_30_E8,blank_30_E8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I15,iTru7_105_05,TCTCTTCC,iTru5_04_E,ACCGCTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E8\n1,blank_30_E9,blank_30_E9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},I17,iTru7_105_06,AGTGTTGG,iTru5_05_E,CTTAGGAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.E9\n1,blank_30_F1,blank_30_F1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K1,iTru7_105_10,TAACCGGT,iTru5_09_E,CGTCTAAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F1\n1,blank_30_F10,blank_30_F10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K19,iTru7_106_07,CGTCTTGT,iTru5_06_F,AGCCAACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F10\n1,blank_30_F11,blank_30_F11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K21,iTru7_106_08,CGTGATCA,iTru5_07_F,CTAGCTCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F11\n1,blank_30_F12,blank_30_F12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K23,iTru7_106_09,CCAAGTTG,iTru5_08_F,GGAAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F12\n1,blank_30_F2,blank_30_F2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K3,iTru7_105_11,CATGGAAC,iTru5_10_E,AACCAGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F2\n1,blank_30_F3,blank_30_F3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K5,iTru7_105_12,ATGGTCCA,iTru5_11_E,CGCCTTAT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F3\n1,blank_30_F4,blank_30_F4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K7,iTru7_106_01,CTTCTGAG,iTru5_12_E,CTCGTTCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F4\n1,blank_30_F5,blank_30_F5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K9,iTru7_106_02,AACCGAAG,iTru5_01_F,GTGAGACT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F5\n1,blank_30_F6,blank_30_F6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K11,iTru7_106_03,TTCGTACC,iTru5_02_F,AACACGCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F6\n1,blank_30_F7,blank_30_F7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K13,iTru7_106_04,CTGTTAGG,iTru5_03_F,CCTAGAGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F7\n1,blank_30_F8,blank_30_F8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K15,iTru7_106_05,CACAAGTC,iTru5_04_F,TTCCAGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F8\n1,blank_30_F9,blank_30_F9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},K17,iTru7_106_06,TCTTGACG,iTru5_05_F,TCAGCCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.F9\n1,blank_30_G1,blank_30_G1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M1,iTru7_106_10,GTACCTTG,iTru5_09_F,AACACTGG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G1\n1,blank_30_G10,blank_30_G10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M19,iTru7_107_07,CCGACTAT,iTru5_06_G,GATCTTGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G10\n1,blank_30_G11,blank_30_G11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M21,iTru7_107_08,AGCTAACC,iTru5_07_G,GTTAAGCG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G11\n1,blank_30_G12,blank_30_G12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M23,iTru7_107_09,GCCTTGTT,iTru5_08_G,GTCATCGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G12\n1,blank_30_G2,blank_30_G2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M3,iTru7_106_11,GACTATGC,iTru5_10_F,ACTATCGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G2\n1,blank_30_G3,blank_30_G3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M5,iTru7_106_12,TGGATCAC,iTru5_11_F,ACAACAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G3\n1,blank_30_G4,blank_30_G4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M7,iTru7_107_01,CTCTGGTT,iTru5_12_F,TGTGGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G4\n1,blank_30_G5,blank_30_G5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M9,iTru7_107_02,GTTCATGG,iTru5_01_G,GTTCCATG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G5\n1,blank_30_G6,blank_30_G6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M11,iTru7_107_03,GCTGTAAG,iTru5_02_G,TGGATGGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G6\n1,blank_30_G7,blank_30_G7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M13,iTru7_107_04,GTCGAAGA,iTru5_03_G,GCATAACG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G7\n1,blank_30_G8,blank_30_G8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M15,iTru7_107_05,GAGCTCAA,iTru5_04_G,TCGAACCT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G8\n1,blank_30_G9,blank_30_G9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},M17,iTru7_107_06,TGAACCTG,iTru5_05_G,ACATGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.G9\n1,blank_30_H1,blank_30_H1,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O1,iTru7_107_10,AACTTGCC,iTru5_09_G,TCAGACAC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H1\n1,blank_30_H10,blank_30_H10,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O19,iTru7_108_07,GAAGTACC,iTru5_06_H,CCTCGTTA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H10\n1,blank_30_H11,blank_30_H11,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O21,iTru7_108_08,CAGGTATC,iTru5_07_H,CGATTGGA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H11\n1,blank_30_H12,blank_30_H12,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O23,iTru7_108_09,TCTCTAGG,iTru5_08_H,CCAACGAA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H12\n1,blank_30_H2,blank_30_H2,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O3,iTru7_107_11,CAATGTGG,iTru5_10_G,GTCCTAAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H2\n1,blank_30_H3,blank_30_H3,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O5,iTru7_107_12,AAGGCTGA,iTru5_11_G,AGACCTTG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H3\n1,blank_30_H4,blank_30_H4,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O7,iTru7_108_01,TTACCGAG,iTru5_12_G,AGACATGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H4\n1,blank_30_H5,blank_30_H5,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O9,iTru7_108_02,GTCCTAAG,iTru5_01_H,TAGCTGAG,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H5\n1,blank_30_H6,blank_30_H6,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O11,iTru7_108_03,GAAGGTTC,iTru5_02_H,TTCGAAGC,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H6\n1,blank_30_H7,blank_30_H7,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O13,iTru7_108_04,GAAGAGGT,iTru5_03_H,CAGTGCTT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H7\n1,blank_30_H8,blank_30_H8,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O15,iTru7_108_05,TCTGAGAG,iTru5_04_H,TAGTGCCA,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H8\n1,blank_30_H9,blank_30_H9,Test Shotgun Library \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},O17,iTru7_108_06,ACCGCATA,iTru5_05_H,GATGGAGT,New sequencing run \\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}.\\d{6},blank.30.H9\"\"\" # noqa\n\n\nif __name__ == '__main__':\n integration_tests()\n```"}}},{"rowIdx":698,"cells":{"prompt":{"kind":"list like","value":[{"content":"Here is the code content:\n```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n\n# Import smtplib for the actual sending function\nimport sys, os\nimport smtplib\nimport email\n# Import the email modules we'll need\nfrom email.mime.text import MIMEText\nfrom email.mime.multipart import MIMEMultipart\nfrom email.mime.text import MIMEText\nfrom email.header import Header\n\ndef sendEmail(fromEmail=\"\", password=None, toEmails=[], smtp=\"smtp.gmail.com\",\\\n port=25, msg=\"\"):\n\n server = smtplib.SMTP(smtp, port)\n server.ehlo()\n if password!=None:\n server.starttls()\n server.login(fromEmail, password)\n\n server.sendmail(fromEmail, toEmails, msg.as_string())\n server.close()\n\nif __name__=='__main__':\n pass\n\n \"\"\"fromEmail = \"noreply@malmo.se\" #\"johanlahti@gmail.com\"\n password = None\n smtp = \"mail2.malmo.se\"\n port = 25\n toEmails = [\"johan.lahti@malmo.se\"]\n subject = \"Testar ÅÄÖ åäö\"\n content = \"ÅÄÖ åäö Nu testar jag skicka en länk...\\n\\n/Johan\"\n\n msg = MIMEText(content, \"plain\", \"utf-8\")\n msg['Subject'] = subject\n msg['From'] = fromEmail\n msg['To'] = \";\".join(toEmails)\n\n sendEmail(fromEmail, password, \\\n toEmails=toEmails, msg=msg, \\\n smtp=smtp, port=port)\"\"\"\n```\nRepeat the code exactly.","role":"user"}],"string":"[\n {\n \"content\": \"Here is the code content:\\n```python\\n#!/usr/bin/env python\\n# -*- coding: utf-8 -*-\\n\\n# Import smtplib for the actual sending function\\nimport sys, os\\nimport smtplib\\nimport email\\n# Import the email modules we'll need\\nfrom email.mime.text import MIMEText\\nfrom email.mime.multipart import MIMEMultipart\\nfrom email.mime.text import MIMEText\\nfrom email.header import Header\\n\\ndef sendEmail(fromEmail=\\\"\\\", password=None, toEmails=[], smtp=\\\"smtp.gmail.com\\\",\\\\\\n port=25, msg=\\\"\\\"):\\n\\n server = smtplib.SMTP(smtp, port)\\n server.ehlo()\\n if password!=None:\\n server.starttls()\\n server.login(fromEmail, password)\\n\\n server.sendmail(fromEmail, toEmails, msg.as_string())\\n server.close()\\n\\nif __name__=='__main__':\\n pass\\n\\n \\\"\\\"\\\"fromEmail = \\\"noreply@malmo.se\\\" #\\\"johanlahti@gmail.com\\\"\\n password = None\\n smtp = \\\"mail2.malmo.se\\\"\\n port = 25\\n toEmails = [\\\"johan.lahti@malmo.se\\\"]\\n subject = \\\"Testar ÅÄÖ åäö\\\"\\n content = \\\"ÅÄÖ åäö Nu testar jag skicka en länk...\\\\n\\\\n/Johan\\\"\\n\\n msg = MIMEText(content, \\\"plain\\\", \\\"utf-8\\\")\\n msg['Subject'] = subject\\n msg['From'] = fromEmail\\n msg['To'] = \\\";\\\".join(toEmails)\\n\\n sendEmail(fromEmail, password, \\\\\\n toEmails=toEmails, msg=msg, \\\\\\n smtp=smtp, port=port)\\\"\\\"\\\"\\n```\\nRepeat the code exactly.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"compression_prompt":{"kind":"list like","value":[{"content":"Here is the code content:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n\n# Import smtplib for the actual sending function\nimport sys, os\nimport smtplib\nimport email\n# Import the email modules we'll need\nfrom email.mime.text import MIMEText\nfrom email.mime.multipart import MIMEMultipart\nfrom email.mime.text import MIMEText\nfrom email.header import Header\n\ndef sendEmail(fromEmail=\"\", password=None, toEmails=[], smtp=\"smtp.gmail.com\",\\\n port=25, msg=\"\"):\n\n server = smtplib.SMTP(smtp, port)\n server.ehlo()\n if password!=None:\n server.starttls()\n server.login(fromEmail, password)\n\n server.sendmail(fromEmail, toEmails, msg.as_string())\n server.close()\n\nif __name__=='__main__':\n pass\n\n \"\"\"fromEmail = \"noreply@malmo.se\" #\"johanlahti@gmail.com\"\n password = None\n smtp = \"mail2.malmo.se\"\n port = 25\n toEmails = [\"johan.lahti@malmo.se\"]\n subject = \"Testar ÅÄÖ åäö\"\n content = \"ÅÄÖ åäö Nu testar jag skicka en länk...\\n\\n/Johan\"\n\n msg = MIMEText(content, \"plain\", \"utf-8\")\n msg['Subject'] = subject\n msg['From'] = fromEmail\n msg['To'] = \";\".join(toEmails)\n\n sendEmail(fromEmail, password, \\\n toEmails=toEmails, msg=msg, \\\n smtp=smtp, port=port)\"\"\"\n```<|memory_end|>\nRepeat the code exactly.","role":"user"}],"string":"[\n {\n \"content\": \"Here is the code content:\\n<|memory_start|>```python\\n#!/usr/bin/env python\\n# -*- coding: utf-8 -*-\\n\\n# Import smtplib for the actual sending function\\nimport sys, os\\nimport smtplib\\nimport email\\n# Import the email modules we'll need\\nfrom email.mime.text import MIMEText\\nfrom email.mime.multipart import MIMEMultipart\\nfrom email.mime.text import MIMEText\\nfrom email.header import Header\\n\\ndef sendEmail(fromEmail=\\\"\\\", password=None, toEmails=[], smtp=\\\"smtp.gmail.com\\\",\\\\\\n port=25, msg=\\\"\\\"):\\n\\n server = smtplib.SMTP(smtp, port)\\n server.ehlo()\\n if password!=None:\\n server.starttls()\\n server.login(fromEmail, password)\\n\\n server.sendmail(fromEmail, toEmails, msg.as_string())\\n server.close()\\n\\nif __name__=='__main__':\\n pass\\n\\n \\\"\\\"\\\"fromEmail = \\\"noreply@malmo.se\\\" #\\\"johanlahti@gmail.com\\\"\\n password = None\\n smtp = \\\"mail2.malmo.se\\\"\\n port = 25\\n toEmails = [\\\"johan.lahti@malmo.se\\\"]\\n subject = \\\"Testar ÅÄÖ åäö\\\"\\n content = \\\"ÅÄÖ åäö Nu testar jag skicka en länk...\\\\n\\\\n/Johan\\\"\\n\\n msg = MIMEText(content, \\\"plain\\\", \\\"utf-8\\\")\\n msg['Subject'] = subject\\n msg['From'] = fromEmail\\n msg['To'] = \\\";\\\".join(toEmails)\\n\\n sendEmail(fromEmail, password, \\\\\\n toEmails=toEmails, msg=msg, \\\\\\n smtp=smtp, port=port)\\\"\\\"\\\"\\n```<|memory_end|>\\nRepeat the code exactly.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"target":{"kind":"string","value":"```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n\n# Import smtplib for the actual sending function\nimport sys, os\nimport smtplib\nimport email\n# Import the email modules we'll need\nfrom email.mime.text import MIMEText\nfrom email.mime.multipart import MIMEMultipart\nfrom email.mime.text import MIMEText\nfrom email.header import Header\n\ndef sendEmail(fromEmail=\"\", password=None, toEmails=[], smtp=\"smtp.gmail.com\",\\\n port=25, msg=\"\"):\n\n server = smtplib.SMTP(smtp, port)\n server.ehlo()\n if password!=None:\n server.starttls()\n server.login(fromEmail, password)\n\n server.sendmail(fromEmail, toEmails, msg.as_string())\n server.close()\n\nif __name__=='__main__':\n pass\n\n \"\"\"fromEmail = \"noreply@malmo.se\" #\"johanlahti@gmail.com\"\n password = None\n smtp = \"mail2.malmo.se\"\n port = 25\n toEmails = [\"johan.lahti@malmo.se\"]\n subject = \"Testar ÅÄÖ åäö\"\n content = \"ÅÄÖ åäö Nu testar jag skicka en länk...\\n\\n/Johan\"\n\n msg = MIMEText(content, \"plain\", \"utf-8\")\n msg['Subject'] = subject\n msg['From'] = fromEmail\n msg['To'] = \";\".join(toEmails)\n\n sendEmail(fromEmail, password, \\\n toEmails=toEmails, msg=msg, \\\n smtp=smtp, port=port)\"\"\"\n```"}}},{"rowIdx":699,"cells":{"prompt":{"kind":"list like","value":[{"content":"Here is the snippet:\n```python\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\nimport package_file\nimport copy\n\n\ndef extract_checker_info(name_string):\n package_file.list_of_detection_info_sa0[name_string] = []\n package_file.list_of_detection_info_sa1[name_string] = []\n\n package_file.list_of_true_misses_sa0[name_string] = []\n package_file.list_of_true_misses_sa1[name_string] = []\n area_report_file = open(\"coverage_results/fstat\" + str(name_string), 'r')\n line = area_report_file.readline()\n while line != \"\":\n line = area_report_file.readline()\n if \".CHECKERS DETECTION INFO - amount of detections\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_detection_info_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_detection_info_sa1[name_string].append(item.split(\"|\")[1])\n if \"amount of True Misses\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_true_misses_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_true_misses_sa1[name_string].append(item.split(\"|\")[1])\n # print package_file.list_of_detection_info_sa0\n # print package_file.list_of_detection_info_sa1\n return None\n\n\ndef find_essential_checker():\n print \"------------------------------------------------------------------------------------------------\"\n print \" Extracting essential checkers\"\n print \"------------------------------------------------------------------------------------------------\"\n temp_copy_sa0 = copy.deepcopy(package_file.list_of_true_misses_sa0)\n temp_copy_sa1 = copy.deepcopy(package_file.list_of_true_misses_sa1)\n\n random_item = temp_copy_sa0.keys()[0]\n\n selected_checkers_sa0 = []\n selected_checkers_sa1 = []\n checkers_for_optimization = []\n\n for node in range(0, len(temp_copy_sa0[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa0:\n true_miss_rate = int(temp_copy_sa0[checker][node])\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa0:\n if int(package_file.list_of_true_misses_sa0[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n temp_copy_sa0[checker][node] = 1\n count += 1\n else:\n temp_copy_sa0[checker][node] = 0\n else:\n temp_copy_sa0[checker][node] = 0\n if count == 1:\n if best_checker not in selected_checkers_sa0:\n selected_checkers_sa0.append(best_checker)\n # else:\n # for checker in temp_copy_sa0:\n # temp_copy_sa0[checker][node] = 0\n\n print \"single dominant checkers for sta0:\", selected_checkers_sa0\n\n for node in range(0, len(temp_copy_sa1[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa1:\n true_miss_rate = int(temp_copy_sa1[checker][node])\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n # print checker, int(package_file.list_of_detection_info_sa1[str(checker)][node])\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa1:\n if int(package_file.list_of_true_misses_sa1[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n temp_copy_sa1[checker][node] = 1\n count += 1\n else:\n temp_copy_sa1[checker][node] = 0\n else:\n temp_copy_sa1[checker][node] = 0\n # print \"best checker\", best_checker\n if count == 1:\n if best_checker not in selected_checkers_sa1:\n selected_checkers_sa1.append(best_checker)\n # else:\n # for checker in temp_copy_sa1:\n # temp_copy_sa1[checker][node] = 0\n\n print \"single dominant checkers for sta1:\", selected_checkers_sa1\n for checker in selected_checkers_sa0:\n for node in range(0, len(temp_copy_sa0[checker])):\n if temp_copy_sa0[checker][node] == 1:\n for checker2 in temp_copy_sa0.keys():\n if checker2 not in selected_checkers_sa0:\n if temp_copy_sa0[checker2][node] == 1:\n temp_copy_sa0[checker2][node] = 0\n\n for checker in selected_checkers_sa1:\n for node in range(0, len(temp_copy_sa1[checker])):\n if temp_copy_sa1[checker][node] == 1:\n for checker2 in temp_copy_sa1.keys():\n if checker2 not in selected_checkers_sa1:\n if temp_copy_sa1[checker2][node] == 1:\n temp_copy_sa1[checker2][node] = 0\n\n if package_file.debug:\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 0:\"\n for checker in sorted(temp_copy_sa0.keys()):\n print checker,\n for item in temp_copy_sa0[checker]:\n print item,\n print \"\"\n\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 1:\"\n for checker in sorted(temp_copy_sa1.keys()):\n print checker,\n for item in temp_copy_sa1[checker]:\n print item,\n print \"\"\n print \"-----------------\"\n\n final_selected_list = []\n for item in selected_checkers_sa0:\n final_selected_list.append(str(item))\n for item in selected_checkers_sa1:\n if item not in selected_checkers_sa0:\n final_selected_list.append(str(item))\n\n for item in temp_copy_sa0.keys():\n if str(item) not in final_selected_list:\n if str(item) not in checkers_for_optimization:\n checkers_for_optimization.append(str(item))\n\n print \"selected single dominant checkers:\", final_selected_list\n print \"selected checkers for optimization:\", checkers_for_optimization\n return final_selected_list, checkers_for_optimization\n```\nOutput a verbatim copy.","role":"user"}],"string":"[\n {\n \"content\": \"Here is the snippet:\\n```python\\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\\nimport package_file\\nimport copy\\n\\n\\ndef extract_checker_info(name_string):\\n package_file.list_of_detection_info_sa0[name_string] = []\\n package_file.list_of_detection_info_sa1[name_string] = []\\n\\n package_file.list_of_true_misses_sa0[name_string] = []\\n package_file.list_of_true_misses_sa1[name_string] = []\\n area_report_file = open(\\\"coverage_results/fstat\\\" + str(name_string), 'r')\\n line = area_report_file.readline()\\n while line != \\\"\\\":\\n line = area_report_file.readline()\\n if \\\".CHECKERS DETECTION INFO - amount of detections\\\" in line:\\n line = area_report_file.readline()\\n for item in line.split(\\\" \\\"):\\n if \\\"|\\\" in item:\\n package_file.list_of_detection_info_sa0[name_string].append(item.split(\\\"|\\\")[0])\\n package_file.list_of_detection_info_sa1[name_string].append(item.split(\\\"|\\\")[1])\\n if \\\"amount of True Misses\\\" in line:\\n line = area_report_file.readline()\\n for item in line.split(\\\" \\\"):\\n if \\\"|\\\" in item:\\n package_file.list_of_true_misses_sa0[name_string].append(item.split(\\\"|\\\")[0])\\n package_file.list_of_true_misses_sa1[name_string].append(item.split(\\\"|\\\")[1])\\n # print package_file.list_of_detection_info_sa0\\n # print package_file.list_of_detection_info_sa1\\n return None\\n\\n\\ndef find_essential_checker():\\n print \\\"------------------------------------------------------------------------------------------------\\\"\\n print \\\" Extracting essential checkers\\\"\\n print \\\"------------------------------------------------------------------------------------------------\\\"\\n temp_copy_sa0 = copy.deepcopy(package_file.list_of_true_misses_sa0)\\n temp_copy_sa1 = copy.deepcopy(package_file.list_of_true_misses_sa1)\\n\\n random_item = temp_copy_sa0.keys()[0]\\n\\n selected_checkers_sa0 = []\\n selected_checkers_sa1 = []\\n checkers_for_optimization = []\\n\\n for node in range(0, len(temp_copy_sa0[random_item])):\\n best_checker = None\\n best_true_miss_rate = float('inf')\\n for checker in temp_copy_sa0:\\n true_miss_rate = int(temp_copy_sa0[checker][node])\\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\\n if true_miss_rate >= 0:\\n if true_miss_rate < best_true_miss_rate:\\n best_true_miss_rate = true_miss_rate\\n best_checker = checker\\n\\n # if best_true_miss_rate == 0:\\n count = 0\\n for checker in temp_copy_sa0:\\n if int(package_file.list_of_true_misses_sa0[checker][node]) == best_true_miss_rate:\\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\\n temp_copy_sa0[checker][node] = 1\\n count += 1\\n else:\\n temp_copy_sa0[checker][node] = 0\\n else:\\n temp_copy_sa0[checker][node] = 0\\n if count == 1:\\n if best_checker not in selected_checkers_sa0:\\n selected_checkers_sa0.append(best_checker)\\n # else:\\n # for checker in temp_copy_sa0:\\n # temp_copy_sa0[checker][node] = 0\\n\\n print \\\"single dominant checkers for sta0:\\\", selected_checkers_sa0\\n\\n for node in range(0, len(temp_copy_sa1[random_item])):\\n best_checker = None\\n best_true_miss_rate = float('inf')\\n for checker in temp_copy_sa1:\\n true_miss_rate = int(temp_copy_sa1[checker][node])\\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\\n # print checker, int(package_file.list_of_detection_info_sa1[str(checker)][node])\\n if true_miss_rate >= 0:\\n if true_miss_rate < best_true_miss_rate:\\n best_true_miss_rate = true_miss_rate\\n best_checker = checker\\n # if best_true_miss_rate == 0:\\n count = 0\\n for checker in temp_copy_sa1:\\n if int(package_file.list_of_true_misses_sa1[checker][node]) == best_true_miss_rate:\\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\\n temp_copy_sa1[checker][node] = 1\\n count += 1\\n else:\\n temp_copy_sa1[checker][node] = 0\\n else:\\n temp_copy_sa1[checker][node] = 0\\n # print \\\"best checker\\\", best_checker\\n if count == 1:\\n if best_checker not in selected_checkers_sa1:\\n selected_checkers_sa1.append(best_checker)\\n # else:\\n # for checker in temp_copy_sa1:\\n # temp_copy_sa1[checker][node] = 0\\n\\n print \\\"single dominant checkers for sta1:\\\", selected_checkers_sa1\\n for checker in selected_checkers_sa0:\\n for node in range(0, len(temp_copy_sa0[checker])):\\n if temp_copy_sa0[checker][node] == 1:\\n for checker2 in temp_copy_sa0.keys():\\n if checker2 not in selected_checkers_sa0:\\n if temp_copy_sa0[checker2][node] == 1:\\n temp_copy_sa0[checker2][node] = 0\\n\\n for checker in selected_checkers_sa1:\\n for node in range(0, len(temp_copy_sa1[checker])):\\n if temp_copy_sa1[checker][node] == 1:\\n for checker2 in temp_copy_sa1.keys():\\n if checker2 not in selected_checkers_sa1:\\n if temp_copy_sa1[checker2][node] == 1:\\n temp_copy_sa1[checker2][node] = 0\\n\\n if package_file.debug:\\n print \\\"-----------------\\\"\\n print \\\"printing the checkers true misses table (0-1)\\\"\\n print \\\"stuck at 0:\\\"\\n for checker in sorted(temp_copy_sa0.keys()):\\n print checker,\\n for item in temp_copy_sa0[checker]:\\n print item,\\n print \\\"\\\"\\n\\n print \\\"-----------------\\\"\\n print \\\"printing the checkers true misses table (0-1)\\\"\\n print \\\"stuck at 1:\\\"\\n for checker in sorted(temp_copy_sa1.keys()):\\n print checker,\\n for item in temp_copy_sa1[checker]:\\n print item,\\n print \\\"\\\"\\n print \\\"-----------------\\\"\\n\\n final_selected_list = []\\n for item in selected_checkers_sa0:\\n final_selected_list.append(str(item))\\n for item in selected_checkers_sa1:\\n if item not in selected_checkers_sa0:\\n final_selected_list.append(str(item))\\n\\n for item in temp_copy_sa0.keys():\\n if str(item) not in final_selected_list:\\n if str(item) not in checkers_for_optimization:\\n checkers_for_optimization.append(str(item))\\n\\n print \\\"selected single dominant checkers:\\\", final_selected_list\\n print \\\"selected checkers for optimization:\\\", checkers_for_optimization\\n return final_selected_list, checkers_for_optimization\\n```\\nOutput a verbatim copy.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"compression_prompt":{"kind":"list like","value":[{"content":"Here is the snippet:\n<|memory_start|>```python\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\nimport package_file\nimport copy\n\n\ndef extract_checker_info(name_string):\n package_file.list_of_detection_info_sa0[name_string] = []\n package_file.list_of_detection_info_sa1[name_string] = []\n\n package_file.list_of_true_misses_sa0[name_string] = []\n package_file.list_of_true_misses_sa1[name_string] = []\n area_report_file = open(\"coverage_results/fstat\" + str(name_string), 'r')\n line = area_report_file.readline()\n while line != \"\":\n line = area_report_file.readline()\n if \".CHECKERS DETECTION INFO - amount of detections\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_detection_info_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_detection_info_sa1[name_string].append(item.split(\"|\")[1])\n if \"amount of True Misses\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_true_misses_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_true_misses_sa1[name_string].append(item.split(\"|\")[1])\n # print package_file.list_of_detection_info_sa0\n # print package_file.list_of_detection_info_sa1\n return None\n\n\ndef find_essential_checker():\n print \"------------------------------------------------------------------------------------------------\"\n print \" Extracting essential checkers\"\n print \"------------------------------------------------------------------------------------------------\"\n temp_copy_sa0 = copy.deepcopy(package_file.list_of_true_misses_sa0)\n temp_copy_sa1 = copy.deepcopy(package_file.list_of_true_misses_sa1)\n\n random_item = temp_copy_sa0.keys()[0]\n\n selected_checkers_sa0 = []\n selected_checkers_sa1 = []\n checkers_for_optimization = []\n\n for node in range(0, len(temp_copy_sa0[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa0:\n true_miss_rate = int(temp_copy_sa0[checker][node])\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa0:\n if int(package_file.list_of_true_misses_sa0[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n temp_copy_sa0[checker][node] = 1\n count += 1\n else:\n temp_copy_sa0[checker][node] = 0\n else:\n temp_copy_sa0[checker][node] = 0\n if count == 1:\n if best_checker not in selected_checkers_sa0:\n selected_checkers_sa0.append(best_checker)\n # else:\n # for checker in temp_copy_sa0:\n # temp_copy_sa0[checker][node] = 0\n\n print \"single dominant checkers for sta0:\", selected_checkers_sa0\n\n for node in range(0, len(temp_copy_sa1[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa1:\n true_miss_rate = int(temp_copy_sa1[checker][node])\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n # print checker, int(package_file.list_of_detection_info_sa1[str(checker)][node])\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa1:\n if int(package_file.list_of_true_misses_sa1[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n temp_copy_sa1[checker][node] = 1\n count += 1\n else:\n temp_copy_sa1[checker][node] = 0\n else:\n temp_copy_sa1[checker][node] = 0\n # print \"best checker\", best_checker\n if count == 1:\n if best_checker not in selected_checkers_sa1:\n selected_checkers_sa1.append(best_checker)\n # else:\n # for checker in temp_copy_sa1:\n # temp_copy_sa1[checker][node] = 0\n\n print \"single dominant checkers for sta1:\", selected_checkers_sa1\n for checker in selected_checkers_sa0:\n for node in range(0, len(temp_copy_sa0[checker])):\n if temp_copy_sa0[checker][node] == 1:\n for checker2 in temp_copy_sa0.keys():\n if checker2 not in selected_checkers_sa0:\n if temp_copy_sa0[checker2][node] == 1:\n temp_copy_sa0[checker2][node] = 0\n\n for checker in selected_checkers_sa1:\n for node in range(0, len(temp_copy_sa1[checker])):\n if temp_copy_sa1[checker][node] == 1:\n for checker2 in temp_copy_sa1.keys():\n if checker2 not in selected_checkers_sa1:\n if temp_copy_sa1[checker2][node] == 1:\n temp_copy_sa1[checker2][node] = 0\n\n if package_file.debug:\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 0:\"\n for checker in sorted(temp_copy_sa0.keys()):\n print checker,\n for item in temp_copy_sa0[checker]:\n print item,\n print \"\"\n\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 1:\"\n for checker in sorted(temp_copy_sa1.keys()):\n print checker,\n for item in temp_copy_sa1[checker]:\n print item,\n print \"\"\n print \"-----------------\"\n\n final_selected_list = []\n for item in selected_checkers_sa0:\n final_selected_list.append(str(item))\n for item in selected_checkers_sa1:\n if item not in selected_checkers_sa0:\n final_selected_list.append(str(item))\n\n for item in temp_copy_sa0.keys():\n if str(item) not in final_selected_list:\n if str(item) not in checkers_for_optimization:\n checkers_for_optimization.append(str(item))\n\n print \"selected single dominant checkers:\", final_selected_list\n print \"selected checkers for optimization:\", checkers_for_optimization\n return final_selected_list, checkers_for_optimization\n```<|memory_end|>\nOutput a verbatim copy.","role":"user"}],"string":"[\n {\n \"content\": \"Here is the snippet:\\n<|memory_start|>```python\\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\\nimport package_file\\nimport copy\\n\\n\\ndef extract_checker_info(name_string):\\n package_file.list_of_detection_info_sa0[name_string] = []\\n package_file.list_of_detection_info_sa1[name_string] = []\\n\\n package_file.list_of_true_misses_sa0[name_string] = []\\n package_file.list_of_true_misses_sa1[name_string] = []\\n area_report_file = open(\\\"coverage_results/fstat\\\" + str(name_string), 'r')\\n line = area_report_file.readline()\\n while line != \\\"\\\":\\n line = area_report_file.readline()\\n if \\\".CHECKERS DETECTION INFO - amount of detections\\\" in line:\\n line = area_report_file.readline()\\n for item in line.split(\\\" \\\"):\\n if \\\"|\\\" in item:\\n package_file.list_of_detection_info_sa0[name_string].append(item.split(\\\"|\\\")[0])\\n package_file.list_of_detection_info_sa1[name_string].append(item.split(\\\"|\\\")[1])\\n if \\\"amount of True Misses\\\" in line:\\n line = area_report_file.readline()\\n for item in line.split(\\\" \\\"):\\n if \\\"|\\\" in item:\\n package_file.list_of_true_misses_sa0[name_string].append(item.split(\\\"|\\\")[0])\\n package_file.list_of_true_misses_sa1[name_string].append(item.split(\\\"|\\\")[1])\\n # print package_file.list_of_detection_info_sa0\\n # print package_file.list_of_detection_info_sa1\\n return None\\n\\n\\ndef find_essential_checker():\\n print \\\"------------------------------------------------------------------------------------------------\\\"\\n print \\\" Extracting essential checkers\\\"\\n print \\\"------------------------------------------------------------------------------------------------\\\"\\n temp_copy_sa0 = copy.deepcopy(package_file.list_of_true_misses_sa0)\\n temp_copy_sa1 = copy.deepcopy(package_file.list_of_true_misses_sa1)\\n\\n random_item = temp_copy_sa0.keys()[0]\\n\\n selected_checkers_sa0 = []\\n selected_checkers_sa1 = []\\n checkers_for_optimization = []\\n\\n for node in range(0, len(temp_copy_sa0[random_item])):\\n best_checker = None\\n best_true_miss_rate = float('inf')\\n for checker in temp_copy_sa0:\\n true_miss_rate = int(temp_copy_sa0[checker][node])\\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\\n if true_miss_rate >= 0:\\n if true_miss_rate < best_true_miss_rate:\\n best_true_miss_rate = true_miss_rate\\n best_checker = checker\\n\\n # if best_true_miss_rate == 0:\\n count = 0\\n for checker in temp_copy_sa0:\\n if int(package_file.list_of_true_misses_sa0[checker][node]) == best_true_miss_rate:\\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\\n temp_copy_sa0[checker][node] = 1\\n count += 1\\n else:\\n temp_copy_sa0[checker][node] = 0\\n else:\\n temp_copy_sa0[checker][node] = 0\\n if count == 1:\\n if best_checker not in selected_checkers_sa0:\\n selected_checkers_sa0.append(best_checker)\\n # else:\\n # for checker in temp_copy_sa0:\\n # temp_copy_sa0[checker][node] = 0\\n\\n print \\\"single dominant checkers for sta0:\\\", selected_checkers_sa0\\n\\n for node in range(0, len(temp_copy_sa1[random_item])):\\n best_checker = None\\n best_true_miss_rate = float('inf')\\n for checker in temp_copy_sa1:\\n true_miss_rate = int(temp_copy_sa1[checker][node])\\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\\n # print checker, int(package_file.list_of_detection_info_sa1[str(checker)][node])\\n if true_miss_rate >= 0:\\n if true_miss_rate < best_true_miss_rate:\\n best_true_miss_rate = true_miss_rate\\n best_checker = checker\\n # if best_true_miss_rate == 0:\\n count = 0\\n for checker in temp_copy_sa1:\\n if int(package_file.list_of_true_misses_sa1[checker][node]) == best_true_miss_rate:\\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\\n temp_copy_sa1[checker][node] = 1\\n count += 1\\n else:\\n temp_copy_sa1[checker][node] = 0\\n else:\\n temp_copy_sa1[checker][node] = 0\\n # print \\\"best checker\\\", best_checker\\n if count == 1:\\n if best_checker not in selected_checkers_sa1:\\n selected_checkers_sa1.append(best_checker)\\n # else:\\n # for checker in temp_copy_sa1:\\n # temp_copy_sa1[checker][node] = 0\\n\\n print \\\"single dominant checkers for sta1:\\\", selected_checkers_sa1\\n for checker in selected_checkers_sa0:\\n for node in range(0, len(temp_copy_sa0[checker])):\\n if temp_copy_sa0[checker][node] == 1:\\n for checker2 in temp_copy_sa0.keys():\\n if checker2 not in selected_checkers_sa0:\\n if temp_copy_sa0[checker2][node] == 1:\\n temp_copy_sa0[checker2][node] = 0\\n\\n for checker in selected_checkers_sa1:\\n for node in range(0, len(temp_copy_sa1[checker])):\\n if temp_copy_sa1[checker][node] == 1:\\n for checker2 in temp_copy_sa1.keys():\\n if checker2 not in selected_checkers_sa1:\\n if temp_copy_sa1[checker2][node] == 1:\\n temp_copy_sa1[checker2][node] = 0\\n\\n if package_file.debug:\\n print \\\"-----------------\\\"\\n print \\\"printing the checkers true misses table (0-1)\\\"\\n print \\\"stuck at 0:\\\"\\n for checker in sorted(temp_copy_sa0.keys()):\\n print checker,\\n for item in temp_copy_sa0[checker]:\\n print item,\\n print \\\"\\\"\\n\\n print \\\"-----------------\\\"\\n print \\\"printing the checkers true misses table (0-1)\\\"\\n print \\\"stuck at 1:\\\"\\n for checker in sorted(temp_copy_sa1.keys()):\\n print checker,\\n for item in temp_copy_sa1[checker]:\\n print item,\\n print \\\"\\\"\\n print \\\"-----------------\\\"\\n\\n final_selected_list = []\\n for item in selected_checkers_sa0:\\n final_selected_list.append(str(item))\\n for item in selected_checkers_sa1:\\n if item not in selected_checkers_sa0:\\n final_selected_list.append(str(item))\\n\\n for item in temp_copy_sa0.keys():\\n if str(item) not in final_selected_list:\\n if str(item) not in checkers_for_optimization:\\n checkers_for_optimization.append(str(item))\\n\\n print \\\"selected single dominant checkers:\\\", final_selected_list\\n print \\\"selected checkers for optimization:\\\", checkers_for_optimization\\n return final_selected_list, checkers_for_optimization\\n```<|memory_end|>\\nOutput a verbatim copy.\",\n \"role\": \"user\"\n }\n]","isConversational":true},"target":{"kind":"string","value":"```python\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\nimport package_file\nimport copy\n\n\ndef extract_checker_info(name_string):\n package_file.list_of_detection_info_sa0[name_string] = []\n package_file.list_of_detection_info_sa1[name_string] = []\n\n package_file.list_of_true_misses_sa0[name_string] = []\n package_file.list_of_true_misses_sa1[name_string] = []\n area_report_file = open(\"coverage_results/fstat\" + str(name_string), 'r')\n line = area_report_file.readline()\n while line != \"\":\n line = area_report_file.readline()\n if \".CHECKERS DETECTION INFO - amount of detections\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_detection_info_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_detection_info_sa1[name_string].append(item.split(\"|\")[1])\n if \"amount of True Misses\" in line:\n line = area_report_file.readline()\n for item in line.split(\" \"):\n if \"|\" in item:\n package_file.list_of_true_misses_sa0[name_string].append(item.split(\"|\")[0])\n package_file.list_of_true_misses_sa1[name_string].append(item.split(\"|\")[1])\n # print package_file.list_of_detection_info_sa0\n # print package_file.list_of_detection_info_sa1\n return None\n\n\ndef find_essential_checker():\n print \"------------------------------------------------------------------------------------------------\"\n print \" Extracting essential checkers\"\n print \"------------------------------------------------------------------------------------------------\"\n temp_copy_sa0 = copy.deepcopy(package_file.list_of_true_misses_sa0)\n temp_copy_sa1 = copy.deepcopy(package_file.list_of_true_misses_sa1)\n\n random_item = temp_copy_sa0.keys()[0]\n\n selected_checkers_sa0 = []\n selected_checkers_sa1 = []\n checkers_for_optimization = []\n\n for node in range(0, len(temp_copy_sa0[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa0:\n true_miss_rate = int(temp_copy_sa0[checker][node])\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa0:\n if int(package_file.list_of_true_misses_sa0[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa0[str(checker)][node]) > 0:\n temp_copy_sa0[checker][node] = 1\n count += 1\n else:\n temp_copy_sa0[checker][node] = 0\n else:\n temp_copy_sa0[checker][node] = 0\n if count == 1:\n if best_checker not in selected_checkers_sa0:\n selected_checkers_sa0.append(best_checker)\n # else:\n # for checker in temp_copy_sa0:\n # temp_copy_sa0[checker][node] = 0\n\n print \"single dominant checkers for sta0:\", selected_checkers_sa0\n\n for node in range(0, len(temp_copy_sa1[random_item])):\n best_checker = None\n best_true_miss_rate = float('inf')\n for checker in temp_copy_sa1:\n true_miss_rate = int(temp_copy_sa1[checker][node])\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n # print checker, int(package_file.list_of_detection_info_sa1[str(checker)][node])\n if true_miss_rate >= 0:\n if true_miss_rate < best_true_miss_rate:\n best_true_miss_rate = true_miss_rate\n best_checker = checker\n # if best_true_miss_rate == 0:\n count = 0\n for checker in temp_copy_sa1:\n if int(package_file.list_of_true_misses_sa1[checker][node]) == best_true_miss_rate:\n if int(package_file.list_of_detection_info_sa1[str(checker)][node]) > 0:\n temp_copy_sa1[checker][node] = 1\n count += 1\n else:\n temp_copy_sa1[checker][node] = 0\n else:\n temp_copy_sa1[checker][node] = 0\n # print \"best checker\", best_checker\n if count == 1:\n if best_checker not in selected_checkers_sa1:\n selected_checkers_sa1.append(best_checker)\n # else:\n # for checker in temp_copy_sa1:\n # temp_copy_sa1[checker][node] = 0\n\n print \"single dominant checkers for sta1:\", selected_checkers_sa1\n for checker in selected_checkers_sa0:\n for node in range(0, len(temp_copy_sa0[checker])):\n if temp_copy_sa0[checker][node] == 1:\n for checker2 in temp_copy_sa0.keys():\n if checker2 not in selected_checkers_sa0:\n if temp_copy_sa0[checker2][node] == 1:\n temp_copy_sa0[checker2][node] = 0\n\n for checker in selected_checkers_sa1:\n for node in range(0, len(temp_copy_sa1[checker])):\n if temp_copy_sa1[checker][node] == 1:\n for checker2 in temp_copy_sa1.keys():\n if checker2 not in selected_checkers_sa1:\n if temp_copy_sa1[checker2][node] == 1:\n temp_copy_sa1[checker2][node] = 0\n\n if package_file.debug:\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 0:\"\n for checker in sorted(temp_copy_sa0.keys()):\n print checker,\n for item in temp_copy_sa0[checker]:\n print item,\n print \"\"\n\n print \"-----------------\"\n print \"printing the checkers true misses table (0-1)\"\n print \"stuck at 1:\"\n for checker in sorted(temp_copy_sa1.keys()):\n print checker,\n for item in temp_copy_sa1[checker]:\n print item,\n print \"\"\n print \"-----------------\"\n\n final_selected_list = []\n for item in selected_checkers_sa0:\n final_selected_list.append(str(item))\n for item in selected_checkers_sa1:\n if item not in selected_checkers_sa0:\n final_selected_list.append(str(item))\n\n for item in temp_copy_sa0.keys():\n if str(item) not in final_selected_list:\n if str(item) not in checkers_for_optimization:\n checkers_for_optimization.append(str(item))\n\n print \"selected single dominant checkers:\", final_selected_list\n print \"selected checkers for optimization:\", checkers_for_optimization\n return final_selected_list, checkers_for_optimization\n```"}}}],"truncated":false,"partial":false},"paginationData":{"pageIndex":6,"numItemsPerPage":100,"numTotalItems":2048,"offset":600,"length":100}},"jwt":"eyJhbGciOiJFZERTQSJ9.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc3OTE4OTQyNywic3ViIjoiL2RhdGFzZXRzL2xlb25saTY2L2NvbXByZXNzaW9uLWV2YWwtb2xkIiwiZXhwIjoxNzc5MTkzMDI3LCJpc3MiOiJodHRwczovL2h1Z2dpbmdmYWNlLmNvIn0.pb9vTsEhMpdhhJhymFt6_02-CZlojbP29iAq2nqEfWB0uIdlDR7EifDt3iDCOklx9-wL4XvXatYusYZB8YvJCA","displayUrls":true,"splitSizeSummaries":[{"config":"default","split":"validation","numRows":2048,"numBytesParquet":21891591},{"config":"default","split":"test","numRows":4096,"numBytesParquet":10498455}]},"discussionsStats":{"closed":0,"open":0,"total":0},"fullWidth":true,"hasGatedAccess":true,"hasFullAccess":true,"isEmbedded":false,"savedQueries":{"community":[],"user":[]}}">
prompt listlengths 1 1 | compression_prompt listlengths 1 1 | target stringlengths 1.03k 828k |
|---|---|---|
[
{
"content": "Produce an exact reconstruction of the code:\n```python\n#!/usr/bin/env python\n\n# pylint: disable=broad-except\n\nimport re\nimport json\nimport time\n\nfrom reporting.utilities import getLogger, get_hostname\nfrom reporting.exceptions import InputDataError\n\nlog = getLogger(__name__)\n\nclass ... | [
{
"content": "Produce an exact reconstruction of the code:\n<|memory_start|>```python\n#!/usr/bin/env python\n\n# pylint: disable=broad-except\n\nimport re\nimport json\nimport time\n\nfrom reporting.utilities import getLogger, get_hostname\nfrom reporting.exceptions import InputDataError\n\nlog = getLogger(__n... | ```python
#!/usr/bin/env python
# pylint: disable=broad-except
import re
import json
import time
from reporting.utilities import getLogger, get_hostname
from reporting.exceptions import InputDataError
log = getLogger(__name__)
class IParser(object):
def parse(self):
assert 0, "This method must be defin... |
[
{
"content": "Here is the script:\n```python\n#!/usr/bin/env python\n###############################################################################\n# $Id: elas.py 32163 2015-12-13 17:44:50Z goatbar $\n#\n# Project: GDAL/OGR Test Suite\n# Purpose: Test ELAS driver\n# Author: Even Rouault, <even dot rouault... | [
{
"content": "Here is the script:\n<|memory_start|>```python\n#!/usr/bin/env python\n###############################################################################\n# $Id: elas.py 32163 2015-12-13 17:44:50Z goatbar $\n#\n# Project: GDAL/OGR Test Suite\n# Purpose: Test ELAS driver\n# Author: Even Rouault, <... | ```python
#!/usr/bin/env python
###############################################################################
# $Id: elas.py 32163 2015-12-13 17:44:50Z goatbar $
#
# Project: GDAL/OGR Test Suite
# Purpose: Test ELAS driver
# Author: Even Rouault, <even dot rouault at mines dash paris dot org>
#
##################... |
[
{
"content": "```python\nimport email\r\nimport imaplib\r\nimport json\r\n\r\nfrom input.imap.connection import open_connection\r\n\r\nfrom input.imap.header import get_mail_header\r\nfrom util.read_utils import lines_per_n\r\n\r\n\r\ndef get_unavailable_uid():\r\n \"\"\"\r\n This function returns a list ... | [
{
"content": "<|memory_start|>```python\nimport email\r\nimport imaplib\r\nimport json\r\n\r\nfrom input.imap.connection import open_connection\r\n\r\nfrom input.imap.header import get_mail_header\r\nfrom util.read_utils import lines_per_n\r\n\r\n\r\ndef get_unavailable_uid():\r\n \"\"\"\r\n This function... | ```python
import email
import imaplib
import json
from input.imap.connection import open_connection
from input.imap.header import get_mail_header
from util.read_utils import lines_per_n
def get_unavailable_uid():
"""
This function returns a list of UIDs that are not available in the IMAP server
... |
[
{
"content": "```python\nfrom gobjcreator3.codegen.code_generator import CodeGenerator\nfrom gobjcreator3.codegen.output import StdOut\nfrom gobjcreator3.codegen.name_creator import NameCreator\nfrom gobjcreator3.codegen.c_marshaller_generator import CMarshallerGenerator, CMarshallerNameCreator\nfrom gobjcreato... | [
{
"content": "<|memory_start|>```python\nfrom gobjcreator3.codegen.code_generator import CodeGenerator\nfrom gobjcreator3.codegen.output import StdOut\nfrom gobjcreator3.codegen.name_creator import NameCreator\nfrom gobjcreator3.codegen.c_marshaller_generator import CMarshallerGenerator, CMarshallerNameCreator\... | ```python
from gobjcreator3.codegen.code_generator import CodeGenerator
from gobjcreator3.codegen.output import StdOut
from gobjcreator3.codegen.name_creator import NameCreator
from gobjcreator3.codegen.c_marshaller_generator import CMarshallerGenerator, CMarshallerNameCreator
from gobjcreator3.model.type import Type
f... |
[
{
"content": "```python\n# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:\n\n# Copyright 2014-2016 Florian Bruhin (The Compiler) <mail@qutebrowser.org>\n#\n# This file is part of qutebrowser.\n#\n# qutebrowser is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Pub... | [
{
"content": "<|memory_start|>```python\n# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:\n\n# Copyright 2014-2016 Florian Bruhin (The Compiler) <mail@qutebrowser.org>\n#\n# This file is part of qutebrowser.\n#\n# qutebrowser is free software: you can redistribute it and/or modify\n# it under the terms of the... | ```python
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2016 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# ... |
[
{
"content": "Here is the code block:\n```python\nfrom __future__ import print_function\nfrom icalendar import *\nfrom datetime import date, datetime, timedelta\nimport mysql.connector\nfrom mysql.connector import errorcode\nimport pickle\nimport csv\nimport pandas\nfrom pandas.io import sql\nimport matplotlib.... | [
{
"content": "Here is the code block:\n<|memory_start|>```python\nfrom __future__ import print_function\nfrom icalendar import *\nfrom datetime import date, datetime, timedelta\nimport mysql.connector\nfrom mysql.connector import errorcode\nimport pickle\nimport csv\nimport pandas\nfrom pandas.io import sql\nim... | ```python
from __future__ import print_function
from icalendar import *
from datetime import date, datetime, timedelta
import mysql.connector
from mysql.connector import errorcode
import pickle
import csv
import pandas
from pandas.io import sql
import matplotlib.pyplot as plt
import xlsxwriter
import numpy as np
import... |
[
{
"content": "```python\n# Copyright 2016 AT&T Corp\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of the License at\n#\n# http://www.apache.org/licenses... | [
{
"content": "<|memory_start|>```python\n# Copyright 2016 AT&T Corp\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of the License at\n#\n# http://www.apa... | ```python
# Copyright 2016 AT&T Corp
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... |
[
{
"content": "Output the full code verbatim (no extra comments):\n```python\n# -*- coding: utf-8 -*-\n\"\"\"\nRegression tests for the Test Client, especially the customized assertions.\n\"\"\"\nimport os\nfrom django.conf import settings\n\nfrom django.test import Client, TestCase\nfrom django.test.utils impor... | [
{
"content": "Output the full code verbatim (no extra comments):\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\"\"\"\nRegression tests for the Test Client, especially the customized assertions.\n\"\"\"\nimport os\nfrom django.conf import settings\n\nfrom django.test import Client, TestCase\nfrom django.... | ```python
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
import os
from django.conf import settings
from django.test import Client, TestCase
from django.test.utils import ContextList
from django.core.urlresolvers import reverse
from django.core.exceptions im... |
[
{
"content": "```python\n# This file is part of Py6S.\n#\n# Copyright 2012 Robin Wilson and contributors listed in the CONTRIBUTORS file.\n#\n# Py6S is free software: you can redistribute it and/or modify\n# it under the terms of the GNU Lesser General Public License as published by\n# the Free Software Foundat... | [
{
"content": "<|memory_start|>```python\n# This file is part of Py6S.\n#\n# Copyright 2012 Robin Wilson and contributors listed in the CONTRIBUTORS file.\n#\n# Py6S is free software: you can redistribute it and/or modify\n# it under the terms of the GNU Lesser General Public License as published by\n# the Free ... | ```python
# This file is part of Py6S.
#
# Copyright 2012 Robin Wilson and contributors listed in the CONTRIBUTORS file.
#
# Py6S is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the ... |
[
{
"content": "Produce an exact reconstruction of the code:\n```python\n#\n# Copyright 2010-2011 Red Hat, Inc.\n#\n# This program is free software; you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation; either version 2 of th... | [
{
"content": "Produce an exact reconstruction of the code:\n<|memory_start|>```python\n#\n# Copyright 2010-2011 Red Hat, Inc.\n#\n# This program is free software; you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation; either... | ```python
#
# Copyright 2010-2011 Red Hat, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is di... |
[
{
"content": "Repeat the code precisely:\n```python\n__author__ = 'dev'\n\nimport re\nfrom http.server import SimpleHTTPRequestHandler\n\nHEADERS_HOST_PARAMETER_KEY_NAME = \"Host\"\nREQUEST_LINE_ENCODING = \"iso-8859-1\"\nHOST_PATTERN_KEY_NAME = \"host_pattern\"\nRESPONSE_CONTENT_PATH_KEY_NAME = \"response_cont... | [
{
"content": "Repeat the code precisely:\n<|memory_start|>```python\n__author__ = 'dev'\n\nimport re\nfrom http.server import SimpleHTTPRequestHandler\n\nHEADERS_HOST_PARAMETER_KEY_NAME = \"Host\"\nREQUEST_LINE_ENCODING = \"iso-8859-1\"\nHOST_PATTERN_KEY_NAME = \"host_pattern\"\nRESPONSE_CONTENT_PATH_KEY_NAME =... | ```python
__author__ = 'dev'
import re
from http.server import SimpleHTTPRequestHandler
HEADERS_HOST_PARAMETER_KEY_NAME = "Host"
REQUEST_LINE_ENCODING = "iso-8859-1"
HOST_PATTERN_KEY_NAME = "host_pattern"
RESPONSE_CONTENT_PATH_KEY_NAME = "response_content_path"
class FakeHTTPRequestHandler(SimpleHTTPRequestHandler)... |
[
{
"content": "Here is a code file:\n```python\n# Author: Sari Sabban\n# Email: sari.sabban@gmail.com\n# URL: https://github.com/sarisabban\n#\n# Created By: \tSari Sabban\n# Created Date: \t20 March 2017\n\nimport urllib\n\ndef ProtVR(x):\n\tlis=list() \n\tfilename='HELLO C '\n\tfilename=urllib.urlopen('h... | [
{
"content": "Here is a code file:\n<|memory_start|>```python\n# Author: Sari Sabban\n# Email: sari.sabban@gmail.com\n# URL: https://github.com/sarisabban\n#\n# Created By: \tSari Sabban\n# Created Date: \t20 March 2017\n\nimport urllib\n\ndef ProtVR(x):\n\tlis=list() \n\tfilename='HELLO C '\n\tfilename=u... | ```python
# Author: Sari Sabban
# Email: sari.sabban@gmail.com
# URL: https://github.com/sarisabban
#
# Created By: Sari Sabban
# Created Date: 20 March 2017
import urllib
def ProtVR(x):
lis=list()
filename='HELLO C '
filename=urllib.urlopen('http://files.rcsb.org/view/'+x+'.pdb')
lis.append('<script src... |
[
{
"content": "Reconstruct the code file line-for-line, unmodified:\n```python\n# Copyright 2016 Raytheon BBN Technologies\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# ... | [
{
"content": "Reconstruct the code file line-for-line, unmodified:\n<|memory_start|>```python\n# Copyright 2016 Raytheon BBN Technologies\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the Li... | ```python
# Copyright 2016 Raytheon BBN Technologies
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
__all__ = ['DPO72004C','DPO2024','DPO20... |
[
{
"content": "Produce an exact reconstruction of the code:\n```python\nimport time,random,functools\nimport numpy as np\n\n\nfrom PyQt4 import QtCore, QtGui\nimport pyqtgraph as pg\nimport pyqtgraph.opengl as gl\n\n\nclass utilitiesClass():\n\t\"\"\"\n\tThis class contains methods that simplify setting up and r... | [
{
"content": "Produce an exact reconstruction of the code:\n<|memory_start|>```python\nimport time,random,functools\nimport numpy as np\n\n\nfrom PyQt4 import QtCore, QtGui\nimport pyqtgraph as pg\nimport pyqtgraph.opengl as gl\n\n\nclass utilitiesClass():\n\t\"\"\"\n\tThis class contains methods that simplify ... | ```python
import time,random,functools
import numpy as np
from PyQt4 import QtCore, QtGui
import pyqtgraph as pg
import pyqtgraph.opengl as gl
class utilitiesClass():
"""
This class contains methods that simplify setting up and running
an experiment.
"""
timers=[]
viewBoxes=[]
plots3D=[]
plots2D=[]
axisI... |
[
{
"content": "Here is the source code:\n```python\nimport requests\nimport pytest\nimport re\nfrom _pytest.runner import runtestprotocol\nfrom http.client import RemoteDisconnected\nfrom support.device_stats_db import DeviceStatsDB\nfrom support.test_rerun import should_rerun_test\nfrom tests import test_suite_... | [
{
"content": "Here is the source code:\n<|memory_start|>```python\nimport requests\nimport pytest\nimport re\nfrom _pytest.runner import runtestprotocol\nfrom http.client import RemoteDisconnected\nfrom support.device_stats_db import DeviceStatsDB\nfrom support.test_rerun import should_rerun_test\nfrom tests im... | ```python
import requests
import pytest
import re
from _pytest.runner import runtestprotocol
from http.client import RemoteDisconnected
from support.device_stats_db import DeviceStatsDB
from support.test_rerun import should_rerun_test
from tests import test_suite_data, appium_container
from datetime import datetime
fro... |
[
{
"content": "Here is the snippet:\n```python\n# Copyright (c) 2013 Johan Ceuppens.\n# All rights reserved.\n\n# Redistribution and use in source and binary forms are permitted\n# provided that the above copyright notice and this paragraph are\n# duplicated in all such forms and that any documentation,\n# adver... | [
{
"content": "Here is the snippet:\n<|memory_start|>```python\n# Copyright (c) 2013 Johan Ceuppens.\n# All rights reserved.\n\n# Redistribution and use in source and binary forms are permitted\n# provided that the above copyright notice and this paragraph are\n# duplicated in all such forms and that any documen... | ```python
# Copyright (c) 2013 Johan Ceuppens.
# All rights reserved.
# Redistribution and use in source and binary forms are permitted
# provided that the above copyright notice and this paragraph are
# duplicated in all such forms and that any documentation,
# advertising materials, and other materials related to su... |
[
{
"content": "Provide an exact copy of the source code:\n```python\nimport os\nimport time\nimport json\nimport string\nfrom collections import defaultdict, Counter\nfrom random import random\n\nimport tweepy\n\nclass TwitterAPI:\n \"\"\"\n Class for accessing the Twitter API.\n\n Requires API credenti... | [
{
"content": "Provide an exact copy of the source code:\n<|memory_start|>```python\nimport os\nimport time\nimport json\nimport string\nfrom collections import defaultdict, Counter\nfrom random import random\n\nimport tweepy\n\nclass TwitterAPI:\n \"\"\"\n Class for accessing the Twitter API.\n\n Requi... | ```python
import os
import time
import json
import string
from collections import defaultdict, Counter
from random import random
import tweepy
class TwitterAPI:
"""
Class for accessing the Twitter API.
Requires API credentials to be available in environment
variables. These will be set appropriately ... |
[
{
"content": "Here is the script:\n```python\n# -*- coding: utf-8 -*-\n\"\"\"The gzip file path specification resolver helper implementation.\"\"\"\n\n# This is necessary to prevent a circular import.\nimport dfvfs.file_io.gzip_file_io\nimport dfvfs.vfs.gzip_file_system\n\nfrom dfvfs.lib import definitions\nfro... | [
{
"content": "Here is the script:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\"\"\"The gzip file path specification resolver helper implementation.\"\"\"\n\n# This is necessary to prevent a circular import.\nimport dfvfs.file_io.gzip_file_io\nimport dfvfs.vfs.gzip_file_system\n\nfrom dfvfs.lib import ... | ```python
# -*- coding: utf-8 -*-
"""The gzip file path specification resolver helper implementation."""
# This is necessary to prevent a circular import.
import dfvfs.file_io.gzip_file_io
import dfvfs.vfs.gzip_file_system
from dfvfs.lib import definitions
from dfvfs.resolver import resolver
from dfvfs.resolver impor... |
[
{
"content": "```python\nfrom typing import List\n\nimport typepy\nfrom mbstrdecoder import MultiByteStrDecoder\n\nfrom ....error import EmptyTableNameError\nfrom ._numpy import NumpyTableWriter\n\n\nclass PandasDataFrameWriter(NumpyTableWriter):\n \"\"\"\n A writer class for Pandas DataFrame format.\n\n ... | [
{
"content": "<|memory_start|>```python\nfrom typing import List\n\nimport typepy\nfrom mbstrdecoder import MultiByteStrDecoder\n\nfrom ....error import EmptyTableNameError\nfrom ._numpy import NumpyTableWriter\n\n\nclass PandasDataFrameWriter(NumpyTableWriter):\n \"\"\"\n A writer class for Pandas DataFr... | ```python
from typing import List
import typepy
from mbstrdecoder import MultiByteStrDecoder
from ....error import EmptyTableNameError
from ._numpy import NumpyTableWriter
class PandasDataFrameWriter(NumpyTableWriter):
"""
A writer class for Pandas DataFrame format.
:Example:
:ref:`exam... |
[
{
"content": "Recreate the original code text:\n```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\nimport subprocess\nfrom os.path import exists\n\nfrom setuptools import setup\nfrom setuptools.extension import Extension\nfrom setuptools.command.build_py import build_py as _build_py\n\nfrom Cython.Distu... | [
{
"content": "Recreate the original code text:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\nimport subprocess\nfrom os.path import exists\n\nfrom setuptools import setup\nfrom setuptools.extension import Extension\nfrom setuptools.command.build_py import build_py as _build_py\n\nf... | ```python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import subprocess
from os.path import exists
from setuptools import setup
from setuptools.extension import Extension
from setuptools.command.build_py import build_py as _build_py
from Cython.Distutils import build_ext
class build_py(_build_py):
if exists('... |
[
{
"content": "Write the code verbatim:\n```python\n#%% Libraries\nimport numpy as np\nimport root_funcs as rf\n#%% predict_linear class (Module for Process_Node - Predict)\nclass predict_linear(object):\n \n __lookup_dict = {\n 'beta_init': {\n 'zeros': ('Cluster_Control.Cluster_IO.Predi... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\n#%% Libraries\nimport numpy as np\nimport root_funcs as rf\n#%% predict_linear class (Module for Process_Node - Predict)\nclass predict_linear(object):\n \n __lookup_dict = {\n 'beta_init': {\n 'zeros': ('Cluster_Control.... | ```python
#%% Libraries
import numpy as np
import root_funcs as rf
#%% predict_linear class (Module for Process_Node - Predict)
class predict_linear(object):
__lookup_dict = {
'beta_init': {
'zeros': ('Cluster_Control.Cluster_IO.Predict_Cluster.beta_init', 'beta_zeros')
},
'... |
[
{
"content": "```python\n#!/usr/bin/env python\nimport fileinput\nimport sys\n\n///<summary>\n///Provides a bunch of operations to format and manage hard disks.\n///\n///One cool thing that this class does is allow you to generate a fstab file\n///based on disk formatting operations conducted earlier using this... | [
{
"content": "<|memory_start|>```python\n#!/usr/bin/env python\nimport fileinput\nimport sys\n\n///<summary>\n///Provides a bunch of operations to format and manage hard disks.\n///\n///One cool thing that this class does is allow you to generate a fstab file\n///based on disk formatting operations conducted ea... | ```python
#!/usr/bin/env python
import fileinput
import sys
///<summary>
///Provides a bunch of operations to format and manage hard disks.
///
///One cool thing that this class does is allow you to generate a fstab file
///based on disk formatting operations conducted earlier using this class. This
///is helpful when... |
[
{
"content": "Recreate the original code text:\n```python\nfrom PyQt5.QtWidgets import QWidget, QSplitter, QVBoxLayout, QFrame, QFileDialog, QScrollArea, QMenuBar, QAction, QToolBar\r\nfrom PyQt5.QtCore import Qt\r\nfrom PyQt5.QtGui import QIcon\r\nfrom JamSpace.Views.LaneSpaceView import LaneSpaceView\r\nfrom ... | [
{
"content": "Recreate the original code text:\n<|memory_start|>```python\nfrom PyQt5.QtWidgets import QWidget, QSplitter, QVBoxLayout, QFrame, QFileDialog, QScrollArea, QMenuBar, QAction, QToolBar\r\nfrom PyQt5.QtCore import Qt\r\nfrom PyQt5.QtGui import QIcon\r\nfrom JamSpace.Views.LaneSpaceView import LaneSp... | ```python
from PyQt5.QtWidgets import QWidget, QSplitter, QVBoxLayout, QFrame, QFileDialog, QScrollArea, QMenuBar, QAction, QToolBar
from PyQt5.QtCore import Qt
from PyQt5.QtGui import QIcon
from JamSpace.Views.LaneSpaceView import LaneSpaceView
from JamSpace.Views.ControlBar import ControlBar
class MainView(QWi... |
[
{
"content": "Return the code exactly, with no changes:\n```python\n# -*- coding: utf-8 -*-\n\n\"\"\"\nDon't edit this file manually.\nUpdate it from QGIS console:\n\nfrom processing.tools.translation import updateTranslations\nupdateTranslations()\n\"\"\"\n\nfrom PyQt4.QtCore import QCoreApplication\n\ndef tra... | [
{
"content": "Return the code exactly, with no changes:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n\"\"\"\nDon't edit this file manually.\nUpdate it from QGIS console:\n\nfrom processing.tools.translation import updateTranslations\nupdateTranslations()\n\"\"\"\n\nfrom PyQt4.QtCore import QCoreApplic... | ```python
# -*- coding: utf-8 -*-
"""
Don't edit this file manually.
Update it from QGIS console:
from processing.tools.translation import updateTranslations
updateTranslations()
"""
from PyQt4.QtCore import QCoreApplication
def translationShadow():
"""QGISAlgorithmProvider"""
QCoreApplication.translate("S... |
[
{
"content": "Here is a code file:\n```python\n# -*- coding: utf8 -*-\r\n\r\nimport sys, os\r\nsys.path.append(os.path.abspath('.'))\r\n\r\nimport re\r\n\r\nfrom operator import attrgetter\r\nimport difflib\r\n\r\n# Pylons model init sequence\r\nimport pylons.test\r\nimport logging\r\n\r\nfrom quanthistling.con... | [
{
"content": "Here is a code file:\n<|memory_start|>```python\n# -*- coding: utf8 -*-\r\n\r\nimport sys, os\r\nsys.path.append(os.path.abspath('.'))\r\n\r\nimport re\r\n\r\nfrom operator import attrgetter\r\nimport difflib\r\n\r\n# Pylons model init sequence\r\nimport pylons.test\r\nimport logging\r\n\r\nfrom q... | ```python
# -*- coding: utf8 -*-
import sys, os
sys.path.append(os.path.abspath('.'))
import re
from operator import attrgetter
import difflib
# Pylons model init sequence
import pylons.test
import logging
from quanthistling.config.environment import load_environment
from quanthistling.model.meta im... |
[
{
"content": "Repeat the full code snippet:\n```python\nimport os, serial, time, numpy\n\nwatchTime = 3600\nmeasureInterval = 5\ncalcTime = 1.5\n\ndef receiving(ser):\n global last_received\n buffer_string = ''\n while True:\n buffer_string = buffer_string + ser.read(ser.inWaiting())\n if... | [
{
"content": "Repeat the full code snippet:\n<|memory_start|>```python\nimport os, serial, time, numpy\n\nwatchTime = 3600\nmeasureInterval = 5\ncalcTime = 1.5\n\ndef receiving(ser):\n global last_received\n buffer_string = ''\n while True:\n buffer_string = buffer_string + ser.read(ser.inWaitin... | ```python
import os, serial, time, numpy
watchTime = 3600
measureInterval = 5
calcTime = 1.5
def receiving(ser):
global last_received
buffer_string = ''
while True:
buffer_string = buffer_string + ser.read(ser.inWaiting())
if '\n' in buffer_string:
lines = buffer_string.split('... |
[
{
"content": "Repeat the following code:\n```python\n# Author: Trevor Perrin\n# See the LICENSE file for legal information regarding use of this file.\n\n\"\"\"TLS Lite + poplib.\"\"\"\n\nimport socket\nfrom poplib import POP3, POP3_SSL_PORT\nfrom tlslite.tlsconnection import TLSConnection\nfrom tlslite.integra... | [
{
"content": "Repeat the following code:\n<|memory_start|>```python\n# Author: Trevor Perrin\n# See the LICENSE file for legal information regarding use of this file.\n\n\"\"\"TLS Lite + poplib.\"\"\"\n\nimport socket\nfrom poplib import POP3, POP3_SSL_PORT\nfrom tlslite.tlsconnection import TLSConnection\nfrom... | ```python
# Author: Trevor Perrin
# See the LICENSE file for legal information regarding use of this file.
"""TLS Lite + poplib."""
import socket
from poplib import POP3, POP3_SSL_PORT
from tlslite.tlsconnection import TLSConnection
from tlslite.integration.clienthelper import ClientHelper
class POP3_TLS(POP3, Clien... |
[
{
"content": "Write the code verbatim:\n```python\n#Copyright 2015 B. Johan G. Svensson\r\n#Licensed under the terms of the MIT license (see LICENSE).\r\n\r\nfrom __future__ import division\r\nimport string, struct, collections\r\nimport fsslib, floppytrack\r\n\r\n\r\n\r\n#import floppyinforead\r\n#dsk = floppy... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\n#Copyright 2015 B. Johan G. Svensson\r\n#Licensed under the terms of the MIT license (see LICENSE).\r\n\r\nfrom __future__ import division\r\nimport string, struct, collections\r\nimport fsslib, floppytrack\r\n\r\n\r\n\r\n#import floppyinforead\... | ```python
#Copyright 2015 B. Johan G. Svensson
#Licensed under the terms of the MIT license (see LICENSE).
from __future__ import division
import string, struct, collections
import fsslib, floppytrack
#import floppyinforead
#dsk = floppyinforead.analyzedisc('j:\\Transfer\\CloudKingdom.fss')
##-Take a cof... |
[
{
"content": "Provide a verbatim copy of the code:\n```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\nfrom __future__ import print_function\n\nimport numpy\nfrom util import sigmoid\n\nfrom abc import ABCMeta, abstractmethod\nfrom graph import Bipartite\nfrom collections import deque\n\nclass MCMethod(... | [
{
"content": "Provide a verbatim copy of the code:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\nfrom __future__ import print_function\n\nimport numpy\nfrom util import sigmoid\n\nfrom abc import ABCMeta, abstractmethod\nfrom graph import Bipartite\nfrom collections import deque\n\... | ```python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import numpy
from util import sigmoid
from abc import ABCMeta, abstractmethod
from graph import Bipartite
from collections import deque
class MCMethod(object):
"""Interface for Monte Carlo-like methods."""
__metacla... |
[
{
"content": "```python\n# -*- coding: utf-8 -*-\n\n# Scrapy settings for curation_spider project\n#\n# For simplicity, this file contains only settings considered important or\n# commonly used. You can find more settings consulting the documentation:\n#\n# http://doc.scrapy.org/en/latest/topics/settings.ht... | [
{
"content": "<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n# Scrapy settings for curation_spider project\n#\n# For simplicity, this file contains only settings considered important or\n# commonly used. You can find more settings consulting the documentation:\n#\n# http://doc.scrapy.org/en/latest/to... | ```python
# -*- coding: utf-8 -*-
# Scrapy settings for curation_spider project
#
# For simplicity, this file contains only settings considered important or
# commonly used. You can find more settings consulting the documentation:
#
# http://doc.scrapy.org/en/latest/topics/settings.html
# http://scrapy.readthe... |
[
{
"content": "Here is a code snippet:\n```python\n__author__ = 'olav'\n\nimport sys, os\nimport theano.tensor as T\nimport theano\nimport numpy as np\n\nsys.path.append(os.path.abspath(\"./\"))\nfrom wrapper import create_output_func\nfrom model import ConvModel\n\n\ndef create_threshold_image(image, threshold)... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n__author__ = 'olav'\n\nimport sys, os\nimport theano.tensor as T\nimport theano\nimport numpy as np\n\nsys.path.append(os.path.abspath(\"./\"))\nfrom wrapper import create_output_func\nfrom model import ConvModel\n\n\ndef create_threshold_image(i... | ```python
__author__ = 'olav'
import sys, os
import theano.tensor as T
import theano
import numpy as np
sys.path.append(os.path.abspath("./"))
from wrapper import create_output_func
from model import ConvModel
def create_threshold_image(image, threshold):
binary_arr = np.ones(image.shape)
low_values_indices... |
[
{
"content": "Here is the source code:\n```python\n#!/usr/bin/python3\n\nimport sys\nimport random\nimport math\nimport os\nimport getopt\nimport pygame\nimport shelve\nimport time\nfrom pygame.locals import *\n\nif not pygame.font:\n print('Warning, fonts disabled')\nif not pygame.mixer:\n print('Warning... | [
{
"content": "Here is the source code:\n<|memory_start|>```python\n#!/usr/bin/python3\n\nimport sys\nimport random\nimport math\nimport os\nimport getopt\nimport pygame\nimport shelve\nimport time\nfrom pygame.locals import *\n\nif not pygame.font:\n print('Warning, fonts disabled')\nif not pygame.mixer:\n ... | ```python
#!/usr/bin/python3
import sys
import random
import math
import os
import getopt
import pygame
import shelve
import time
from pygame.locals import *
if not pygame.font:
print('Warning, fonts disabled')
if not pygame.mixer:
print('Warning, sound disabled')
# setting up constants
WINDOW_WIDTH = 640
WI... |
[
{
"content": "Here is a code snippet:\n```python\n# -*- coding: UTF-8 -*-\nimport os,pickle,glob,time,sys\nfrom tools import *\nfrom entity import *\nfrom Word import Word\nfrom Syllable import Syllable\n\nfrom ipa import ipa\nimport codecs\n\nclass Dictionary:\t# cf Word, in that Text.py will really instantiat... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n# -*- coding: UTF-8 -*-\nimport os,pickle,glob,time,sys\nfrom tools import *\nfrom entity import *\nfrom Word import Word\nfrom Syllable import Syllable\n\nfrom ipa import ipa\nimport codecs\n\nclass Dictionary:\t# cf Word, in that Text.py will r... | ```python
# -*- coding: UTF-8 -*-
import os,pickle,glob,time,sys
from tools import *
from entity import *
from Word import Word
from Syllable import Syllable
from ipa import ipa
import codecs
class Dictionary: # cf Word, in that Text.py will really instantiate Dictionary_en,Dictionary_fi,usw.
classnames=['Phoneme','... |
[
{
"content": "Recreate the entire code block with identical formatting:\n```python\n# Copyright (c) 2015, Robert Escriva\n# All rights reserved.\n# \n# Redistribution and use in source and binary forms, with or without\n# modification, are permitted provided that the following conditions are met:\n# \n# * R... | [
{
"content": "Recreate the entire code block with identical formatting:\n<|memory_start|>```python\n# Copyright (c) 2015, Robert Escriva\n# All rights reserved.\n# \n# Redistribution and use in source and binary forms, with or without\n# modification, are permitted provided that the following conditions are met... | ```python
# Copyright (c) 2015, Robert Escriva
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list ... |
[
{
"content": "```python\nimport numpy as np\n\nfrom fos.actor.primitives import AABBPrimitive\nfrom pyglet.gl import GLfloat\nfrom pyglet.gl import *\n\nclass Actor(object):\n \"\"\" Define a visualization object in Fos \"\"\"\n \n def __init__(self,\n affine = None,\n a... | [
{
"content": "<|memory_start|>```python\nimport numpy as np\n\nfrom fos.actor.primitives import AABBPrimitive\nfrom pyglet.gl import GLfloat\nfrom pyglet.gl import *\n\nclass Actor(object):\n \"\"\" Define a visualization object in Fos \"\"\"\n \n def __init__(self,\n affine = None,\n ... | ```python
import numpy as np
from fos.actor.primitives import AABBPrimitive
from pyglet.gl import GLfloat
from pyglet.gl import *
class Actor(object):
""" Define a visualization object in Fos """
def __init__(self,
affine = None,
aabb = None,
force_cente... |
[
{
"content": "Write the code verbatim:\n```python\n#\n# Jinja2 (http://jinja.pocoo.org) based template renderer.\n#\n# Author: Satoru SATOH <ssato redhat.com>\n# License: MIT\n#\n# pylint: disable=unused-argument\n\"\"\"Template rendering module for jinja2-based template config files.\n\"\"\"\nfrom __future__ i... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\n#\n# Jinja2 (http://jinja.pocoo.org) based template renderer.\n#\n# Author: Satoru SATOH <ssato redhat.com>\n# License: MIT\n#\n# pylint: disable=unused-argument\n\"\"\"Template rendering module for jinja2-based template config files.\n\"\"\"\nf... | ```python
#
# Jinja2 (http://jinja.pocoo.org) based template renderer.
#
# Author: Satoru SATOH <ssato redhat.com>
# License: MIT
#
# pylint: disable=unused-argument
"""Template rendering module for jinja2-based template config files.
"""
from __future__ import absolute_import
import logging
import os
import anyconfi... |
[
{
"content": "Recreate the original code text:\n```python\n# -*- coding: utf-8 -*-\n\nimport numpy as np\nimport re\nimport sys\nimport theano\nimport theano.tensor as T\n\nfrom nltk import corpus\nfrom sklearn.metrics import accuracy_score, classification_report\nfrom sklearn.cross_validation import train_test... | [
{
"content": "Recreate the original code text:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\nimport numpy as np\nimport re\nimport sys\nimport theano\nimport theano.tensor as T\n\nfrom nltk import corpus\nfrom sklearn.metrics import accuracy_score, classification_report\nfrom sklearn.cross_validation i... | ```python
# -*- coding: utf-8 -*-
import numpy as np
import re
import sys
import theano
import theano.tensor as T
from nltk import corpus
from sklearn.metrics import accuracy_score, classification_report
from sklearn.cross_validation import train_test_split
from sklearn.datasets import fetch_20newsgroups
from sklearn... |
[
{
"content": "Here is a code snippet:\n```python\n# Copyright (c) 2008,2015,2018 MetPy Developers.\n# Distributed under the terms of the BSD 3-Clause License.\n# SPDX-License-Identifier: BSD-3-Clause\n\"\"\"Collection of generally useful utility code from the cookbook.\"\"\"\n\nimport os\n\nimport numpy as np\n... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n# Copyright (c) 2008,2015,2018 MetPy Developers.\n# Distributed under the terms of the BSD 3-Clause License.\n# SPDX-License-Identifier: BSD-3-Clause\n\"\"\"Collection of generally useful utility code from the cookbook.\"\"\"\n\nimport os\n\nimpo... | ```python
# Copyright (c) 2008,2015,2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Collection of generally useful utility code from the cookbook."""
import os
import numpy as np
import pooch
from . import __version__
try:
string_type ... |
[
{
"content": "```python\n__author__ = 'tjhunter'\n\nimport build\nimport json\nimport pylab as pl\nfrom matplotlib.collections import LineCollection\n# Draws the network as a pdf and SVG file.\n\ndef draw_network(ax, fd, link_style):\n def decode_line(l):\n #print l\n dct = json.loads(l)\n lats = dct[... | [
{
"content": "<|memory_start|>```python\n__author__ = 'tjhunter'\n\nimport build\nimport json\nimport pylab as pl\nfrom matplotlib.collections import LineCollection\n# Draws the network as a pdf and SVG file.\n\ndef draw_network(ax, fd, link_style):\n def decode_line(l):\n #print l\n dct = json.loads(l)\... | ```python
__author__ = 'tjhunter'
import build
import json
import pylab as pl
from matplotlib.collections import LineCollection
# Draws the network as a pdf and SVG file.
def draw_network(ax, fd, link_style):
def decode_line(l):
#print l
dct = json.loads(l)
lats = dct['lats']
lons = dct['lons']
... |
[
{
"content": "Here is a code snippet:\n```python\n# -*- coding: utf-8 -*-\n\n########################## Copyrights and license ############################\n# #\n# Copyright 2011-2015 Christian Lupien <christian.lupien@usherbrooke.ca> ... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n########################## Copyrights and license ############################\n# #\n# Copyright 2011-2015 Christian Lupien <christian.lupien@u... | ```python
# -*- coding: utf-8 -*-
########################## Copyrights and license ############################
# #
# Copyright 2011-2015 Christian Lupien <christian.lupien@usherbrooke.ca> #
# ... |
[
{
"content": "```python\nfrom ..with_request import WithRequest\n\n\nclass Account(WithRequest):\n\n def __init__(self, url, session_id):\n self.base_url = url\n self.session_id=session_id\n\n def account_get_by_id(self, i_account):\n \"\"\"Get account by id\"\"\"\n endpoint = ... | [
{
"content": "<|memory_start|>```python\nfrom ..with_request import WithRequest\n\n\nclass Account(WithRequest):\n\n def __init__(self, url, session_id):\n self.base_url = url\n self.session_id=session_id\n\n def account_get_by_id(self, i_account):\n \"\"\"Get account by id\"\"\"\n ... | ```python
from ..with_request import WithRequest
class Account(WithRequest):
def __init__(self, url, session_id):
self.base_url = url
self.session_id=session_id
def account_get_by_id(self, i_account):
"""Get account by id"""
endpoint = "{0}".format('/rest/Account/get_account_... |
[
{
"content": "Here is a code file:\n```python\nfrom sfsimodels import models\nimport sfsimodels as sm\nimport json\nimport numpy as np\n\n\ndef test_link_building_and_soil():\n number_of_storeys = 6\n interstorey_height = 3.4 # m\n n_bays = 3\n\n fb = models.FrameBuilding(number_of_storeys, n_bays)... | [
{
"content": "Here is a code file:\n<|memory_start|>```python\nfrom sfsimodels import models\nimport sfsimodels as sm\nimport json\nimport numpy as np\n\n\ndef test_link_building_and_soil():\n number_of_storeys = 6\n interstorey_height = 3.4 # m\n n_bays = 3\n\n fb = models.FrameBuilding(number_of_... | ```python
from sfsimodels import models
import sfsimodels as sm
import json
import numpy as np
def test_link_building_and_soil():
number_of_storeys = 6
interstorey_height = 3.4 # m
n_bays = 3
fb = models.FrameBuilding(number_of_storeys, n_bays)
fb.id = 1
fb.interstorey_heights = interstorey_... |
[
{
"content": "Here is the code block:\n```python\n#!/usr/bin/python\n#\n# Copyright 2017 Google Inc.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache... | [
{
"content": "Here is the code block:\n<|memory_start|>```python\n#!/usr/bin/python\n#\n# Copyright 2017 Google Inc.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# h... | ```python
#!/usr/bin/python
#
# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
[
{
"content": "Return the code exactly, with no changes:\n```python\n#!/usr/bin/python\n\nimport sqlite3\n\nclass Database:\n def __init__(self):\n self.connect()\n\n def connect(self):\n self.conn = sqlite3.connect('lifebot.db')\n\n def get_cursor(self):\n # A bit weird for now but... | [
{
"content": "Return the code exactly, with no changes:\n<|memory_start|>```python\n#!/usr/bin/python\n\nimport sqlite3\n\nclass Database:\n def __init__(self):\n self.connect()\n\n def connect(self):\n self.conn = sqlite3.connect('lifebot.db')\n\n def get_cursor(self):\n # A bit w... | ```python
#!/usr/bin/python
import sqlite3
class Database:
def __init__(self):
self.connect()
def connect(self):
self.conn = sqlite3.connect('lifebot.db')
def get_cursor(self):
# A bit weird for now but trying to figure out SQLite
try:
return self.conn.cursor(... |
[
{
"content": "Provide a verbatim copy of the code:\n```python\nfrom citrination_client.models.design.constraints.base import BaseConstraint\nfrom citrination_client.base.errors import CitrinationClientError\n\nclass ElementalInclusionConstraint(BaseConstraint):\n \"\"\"\n Constraint class which allows the... | [
{
"content": "Provide a verbatim copy of the code:\n<|memory_start|>```python\nfrom citrination_client.models.design.constraints.base import BaseConstraint\nfrom citrination_client.base.errors import CitrinationClientError\n\nclass ElementalInclusionConstraint(BaseConstraint):\n \"\"\"\n Constraint class ... | ```python
from citrination_client.models.design.constraints.base import BaseConstraint
from citrination_client.base.errors import CitrinationClientError
class ElementalInclusionConstraint(BaseConstraint):
"""
Constraint class which allows the assertion that a set of
elements is included in the candidate c... |
[
{
"content": "Write the code verbatim:\n```python\nfrom datetime import date\n\nfrom cornflake.exceptions import ValidationError\nimport pytest\n\nfrom radar.api.serializers.salt_wasting import SaltWastingClinicalFeaturesSerializer\nfrom radar.models.patient_demographics import PatientDemographics\nfrom radar.m... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\nfrom datetime import date\n\nfrom cornflake.exceptions import ValidationError\nimport pytest\n\nfrom radar.api.serializers.salt_wasting import SaltWastingClinicalFeaturesSerializer\nfrom radar.models.patient_demographics import PatientDemographi... | ```python
from datetime import date
from cornflake.exceptions import ValidationError
import pytest
from radar.api.serializers.salt_wasting import SaltWastingClinicalFeaturesSerializer
from radar.models.patient_demographics import PatientDemographics
from radar.models.patients import Patient
from radar.models.users im... |
[
{
"content": "Here is a code snippet:\n```python\n# -*- coding: utf-8 -*-\n# This file is part of Shoop.\n#\n# Copyright (c) 2012-2015, Shoop Ltd. All rights reserved.\n#\n# This source code is licensed under the AGPLv3 license found in the\n# LICENSE file in the root directory of this source tree.\nimport os\n... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n# This file is part of Shoop.\n#\n# Copyright (c) 2012-2015, Shoop Ltd. All rights reserved.\n#\n# This source code is licensed under the AGPLv3 license found in the\n# LICENSE file in the root directory of this source tr... | ```python
# -*- coding: utf-8 -*-
# This file is part of Shoop.
#
# Copyright (c) 2012-2015, Shoop Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import os
from django.core.exceptions import ImproperlyConfigured... |
[
{
"content": "Here is some code:\n```python\n'''function [out] = imrotateFill(inp, angle)\n% function [out] = imrotateFill(inp)\n% Rotates an 2D image couterclockwise by angle in degrees\n% Output image has the same dimension as input.\n% Undefined regions are filled in by repeating the original image\n% Note:... | [
{
"content": "Here is some code:\n<|memory_start|>```python\n'''function [out] = imrotateFill(inp, angle)\n% function [out] = imrotateFill(inp)\n% Rotates an 2D image couterclockwise by angle in degrees\n% Output image has the same dimension as input.\n% Undefined regions are filled in by repeating the origina... | ```python
'''function [out] = imrotateFill(inp, angle)
% function [out] = imrotateFill(inp)
% Rotates an 2D image couterclockwise by angle in degrees
% Output image has the same dimension as input.
% Undefined regions are filled in by repeating the original image
% Note: input images must be square
%
% Copyright (c) U... |
[
{
"content": "Here is a code file:\n```python\n\"\"\"Settings that need to be set in order to run the tests.\"\"\"\nimport os\n\n\nDEBUG = True\nSITE_ID = 1\n\nAPP_ROOT = os.path.abspath(\n os.path.join(os.path.dirname(__file__), '..'))\n\n\nDATABASES = {\n 'default': {\n 'ENGINE': 'django.db.backe... | [
{
"content": "Here is a code file:\n<|memory_start|>```python\n\"\"\"Settings that need to be set in order to run the tests.\"\"\"\nimport os\n\n\nDEBUG = True\nSITE_ID = 1\n\nAPP_ROOT = os.path.abspath(\n os.path.join(os.path.dirname(__file__), '..'))\n\n\nDATABASES = {\n 'default': {\n 'ENGINE': ... | ```python
"""Settings that need to be set in order to run the tests."""
import os
DEBUG = True
SITE_ID = 1
APP_ROOT = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..'))
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.sqlite3',
'NAME': ':memory:',
}
}
ROOT_URLCONF ... |
[
{
"content": "Write the code verbatim:\n```python\nimport json\nimport jwt\nimport logging\nimport os\nimport uuid\nimport signal\nimport sys\nimport traceback\n\nfrom tornado import ioloop, web, auth, httpserver, gen, escape, log\nfrom tornado.options import options, parse_command_line, define\n\nfrom problem ... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\nimport json\nimport jwt\nimport logging\nimport os\nimport uuid\nimport signal\nimport sys\nimport traceback\n\nfrom tornado import ioloop, web, auth, httpserver, gen, escape, log\nfrom tornado.options import options, parse_command_line, define\... | ```python
import json
import jwt
import logging
import os
import uuid
import signal
import sys
import traceback
from tornado import ioloop, web, auth, httpserver, gen, escape, log
from tornado.options import options, parse_command_line, define
from problem import Problem
from contest import Contest
from judge import ... |
[
{
"content": "Recreate the entire code block with identical formatting:\n```python\n'''\r\nStrava club information is not publicly available. To get the club information\r\n the club owner needs to be logged in. This script takes the HTML file of the\r\n strava club page and extracts all the users/athletes.\r\n... | [
{
"content": "Recreate the entire code block with identical formatting:\n<|memory_start|>```python\n'''\r\nStrava club information is not publicly available. To get the club information\r\n the club owner needs to be logged in. This script takes the HTML file of the\r\n strava club page and extracts all the use... | ```python
'''
Strava club information is not publicly available. To get the club information
the club owner needs to be logged in. This script takes the HTML file of the
strava club page and extracts all the users/athletes.
'''
from bs4 import BeautifulSoup
import argparse
def get_group_members_from_html(h... |
[
{
"content": "```python\n#!/usr/bin/env python\n#************************************************************************\n# Codelet Tuning Infrastructure\n# Copyright (C) 2010-2015 Intel Corporation, CEA, GENCI, and UVSQ\n#\n# This program is free software: you can redistribute it and/or modify\n# it under the... | [
{
"content": "<|memory_start|>```python\n#!/usr/bin/env python\n#************************************************************************\n# Codelet Tuning Infrastructure\n# Copyright (C) 2010-2015 Intel Corporation, CEA, GENCI, and UVSQ\n#\n# This program is free software: you can redistribute it and/or modify... | ```python
#!/usr/bin/env python
#************************************************************************
# Codelet Tuning Infrastructure
# Copyright (C) 2010-2015 Intel Corporation, CEA, GENCI, and UVSQ
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Pub... |
[
{
"content": "Here is the code block:\n```python\n# Copyright (c) 2012 OpenStack Foundation.\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of the License at\n#\... | [
{
"content": "Here is the code block:\n<|memory_start|>```python\n# Copyright (c) 2012 OpenStack Foundation.\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of th... | ```python
# Copyright (c) 2012 OpenStack Foundation.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#... |
[
{
"content": "```python\n# Copyright 2019, The TensorFlow Authors. All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses... | [
{
"content": "<|memory_start|>```python\n# Copyright 2019, The TensorFlow Authors. All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apa... | ```python
# Copyright 2019, The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
[
{
"content": "Here is the source code:\n```python\nimport requests # Used to make HTTP requests\nimport json # Used to parse JSON\nimport os # Used to infer environment variables\n\nAPI_TAGO = os.environ.get('TAGO_API') or 'https://api.tago.io'\nREALTIME = os.environ.get('TAGO_REALTIME') or 'https://realtime... | [
{
"content": "Here is the source code:\n<|memory_start|>```python\nimport requests # Used to make HTTP requests\nimport json # Used to parse JSON\nimport os # Used to infer environment variables\n\nAPI_TAGO = os.environ.get('TAGO_API') or 'https://api.tago.io'\nREALTIME = os.environ.get('TAGO_REALTIME') or '... | ```python
import requests # Used to make HTTP requests
import json # Used to parse JSON
import os # Used to infer environment variables
API_TAGO = os.environ.get('TAGO_API') or 'https://api.tago.io'
REALTIME = os.environ.get('TAGO_REALTIME') or 'https://realtime.tago.io'
class Plan:
def __init__(self, acc_token... |
[
{
"content": "Provide an exact copy of the source code:\n```python\nimport _plotly_utils.basevalidators\n\n\nclass CaxisValidator(_plotly_utils.basevalidators.CompoundValidator):\n def __init__(self, plotly_name=\"caxis\", parent_name=\"layout.ternary\", **kwargs):\n super(CaxisValidator, self).__init... | [
{
"content": "Provide an exact copy of the source code:\n<|memory_start|>```python\nimport _plotly_utils.basevalidators\n\n\nclass CaxisValidator(_plotly_utils.basevalidators.CompoundValidator):\n def __init__(self, plotly_name=\"caxis\", parent_name=\"layout.ternary\", **kwargs):\n super(CaxisValidat... | ```python
import _plotly_utils.basevalidators
class CaxisValidator(_plotly_utils.basevalidators.CompoundValidator):
def __init__(self, plotly_name="caxis", parent_name="layout.ternary", **kwargs):
super(CaxisValidator, self).__init__(
plotly_name=plotly_name,
parent_name=parent_nam... |
[
{
"content": "Return the code unaltered:\n```python\n# -*- coding: utf-8 -*-\n'''\nQueries for experiments with ENDSEQ operator\n'''\n\nimport os\n\nfrom tool.attributes import get_move_attribute_list, get_place_attribute_list\nfrom tool.experiment import SLI, RAN, ALGORITHM, \\\n CQL_ALG, QUERY, Q_MOVE, Q_P... | [
{
"content": "Return the code unaltered:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n'''\nQueries for experiments with ENDSEQ operator\n'''\n\nimport os\n\nfrom tool.attributes import get_move_attribute_list, get_place_attribute_list\nfrom tool.experiment import SLI, RAN, ALGORITHM, \\\n CQL_ALG, QU... | ```python
# -*- coding: utf-8 -*-
'''
Queries for experiments with ENDSEQ operator
'''
import os
from tool.attributes import get_move_attribute_list, get_place_attribute_list
from tool.experiment import SLI, RAN, ALGORITHM, \
CQL_ALG, QUERY, Q_MOVE, Q_PLACE
from tool.io import get_query_dir, write_to_txt, get_out... |
[
{
"content": "Produce an exact reconstruction of the code:\n```python\nfrom __future__ import division, print_function\n\nimport operator\nfrom collections import OrderedDict\nimport numpy as np\nimport pandas as pd\nimport toolz\nfrom tornado.ioloop import IOLoop\nfrom tornado import gen\n\nfrom ..collection i... | [
{
"content": "Produce an exact reconstruction of the code:\n<|memory_start|>```python\nfrom __future__ import division, print_function\n\nimport operator\nfrom collections import OrderedDict\nimport numpy as np\nimport pandas as pd\nimport toolz\nfrom tornado.ioloop import IOLoop\nfrom tornado import gen\n\nfro... | ```python
from __future__ import division, print_function
import operator
from collections import OrderedDict
import numpy as np
import pandas as pd
import toolz
from tornado.ioloop import IOLoop
from tornado import gen
from ..collection import Streaming, _stream_types, OperatorMixin
from ..sources import Source
from... |
[
{
"content": "Here is the snippet:\n```python\n# -*- coding: utf8 -*-\n\n__author__ = 'sergey'\n\nimport hashlib\nfrom time import time\nfrom dedupsqlfs.db.mysql.table import Table\n\nclass TableSubvolume( Table ):\n\n _table_name = \"subvolume\"\n\n def create( self ):\n c = self.getCursor()\n\n ... | [
{
"content": "Here is the snippet:\n<|memory_start|>```python\n# -*- coding: utf8 -*-\n\n__author__ = 'sergey'\n\nimport hashlib\nfrom time import time\nfrom dedupsqlfs.db.mysql.table import Table\n\nclass TableSubvolume( Table ):\n\n _table_name = \"subvolume\"\n\n def create( self ):\n c = self.g... | ```python
# -*- coding: utf8 -*-
__author__ = 'sergey'
import hashlib
from time import time
from dedupsqlfs.db.mysql.table import Table
class TableSubvolume( Table ):
_table_name = "subvolume"
def create( self ):
c = self.getCursor()
# Create table
c.execute(
"CREATE TA... |
[
{
"content": "Recreate the original code text:\n```python\n# -*- coding: utf-8 -*-\n#\n# Tolk documentation build configuration file, created by\n# sphinx-quickstart on Wed Sep 30 13:15:07 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\n# Note that not all possi... | [
{
"content": "Recreate the original code text:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n#\n# Tolk documentation build configuration file, created by\n# sphinx-quickstart on Wed Sep 30 13:15:07 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\n# Note th... | ```python
# -*- coding: utf-8 -*-
#
# Tolk documentation build configuration file, created by
# sphinx-quickstart on Wed Sep 30 13:15:07 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file... |
[
{
"content": "Provide an exact copy of the source code:\n```python\n\"\"\"\nProvide container class for gas chemistry data.\n\"\"\"\nimport hashlib\nimport warnings\n\nimport numpy as np\nimport tables\nfrom tables.exceptions import NoSuchNodeError, NodeError\n\nfrom spectroscopy.class_factory import ResourceId... | [
{
"content": "Provide an exact copy of the source code:\n<|memory_start|>```python\n\"\"\"\nProvide container class for gas chemistry data.\n\"\"\"\nimport hashlib\nimport warnings\n\nimport numpy as np\nimport tables\nfrom tables.exceptions import NoSuchNodeError, NodeError\n\nfrom spectroscopy.class_factory i... | ```python
"""
Provide container class for gas chemistry data.
"""
import hashlib
import warnings
import numpy as np
import tables
from tables.exceptions import NoSuchNodeError, NodeError
from spectroscopy.class_factory import ResourceIdentifier
from spectroscopy.plugins import get_registered_plugins
from spectroscopy... |
[
{
"content": "Replicate the source code:\n```python\n#\n# Licensed to the Apache Software Foundation (ASF) under one or more\n# contributor license agreements. See the NOTICE file distributed with\n# this work for additional information regarding copyright ownership.\n# The ASF licenses this file to You under ... | [
{
"content": "Replicate the source code:\n<|memory_start|>```python\n#\n# Licensed to the Apache Software Foundation (ASF) under one or more\n# contributor license agreements. See the NOTICE file distributed with\n# this work for additional information regarding copyright ownership.\n# The ASF licenses this fi... | ```python
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you ... |
[
{
"content": "```python\n\"\"\"\nWSGI config for Creamas project.\n\nThis module contains the WSGI application used by Django's development server\nand any production WSGI deployments. It should expose a module-level variable\nnamed ``application``. Django's ``runserver`` and ``runfcgi`` commands discover\nthis... | [
{
"content": "<|memory_start|>```python\n\"\"\"\nWSGI config for Creamas project.\n\nThis module contains the WSGI application used by Django's development server\nand any production WSGI deployments. It should expose a module-level variable\nnamed ``application``. Django's ``runserver`` and ``runfcgi`` command... | ```python
"""
WSGI config for Creamas project.
This module contains the WSGI application used by Django's development server
and any production WSGI deployments. It should expose a module-level variable
named ``application``. Django's ``runserver`` and ``runfcgi`` commands discover
this application via the ``WSGI_APPL... |
[
{
"content": "Repeat the following code:\n```python\nimport os\nimport urlparse\nimport subprocess\nimport smtplib\nimport getpass\nimport re\nfrom email.mime.text import MIMEText\n\nimport pyrax\n\n\nenv_file = '/home/ubuntu/blimp.env'\n\n\ndef run():\n print('---> Getting latest backup of {}...'.format(her... | [
{
"content": "Repeat the following code:\n<|memory_start|>```python\nimport os\nimport urlparse\nimport subprocess\nimport smtplib\nimport getpass\nimport re\nfrom email.mime.text import MIMEText\n\nimport pyrax\n\n\nenv_file = '/home/ubuntu/blimp.env'\n\n\ndef run():\n print('---> Getting latest backup of {... | ```python
import os
import urlparse
import subprocess
import smtplib
import getpass
import re
from email.mime.text import MIMEText
import pyrax
env_file = '/home/ubuntu/blimp.env'
def run():
print('---> Getting latest backup of {}...'.format(heroku_app_name))
latest_backup_url = subprocess.check_output(
... |
[
{
"content": "Reproduce the code exactly as provided (keep formatting):\n```python\n#!/usr/bin/python\n\n#run as array job\n#if files are bzipped -> copy to local disk and unzip there\n\n\nimport os,sys\n\ndb_dir = sys.argv[1]\n\nzipped = sys.argv[2] #are files bzipped?\n\nif zipped == 'True':\n\tzipped = True\... | [
{
"content": "Reproduce the code exactly as provided (keep formatting):\n<|memory_start|>```python\n#!/usr/bin/python\n\n#run as array job\n#if files are bzipped -> copy to local disk and unzip there\n\n\nimport os,sys\n\ndb_dir = sys.argv[1]\n\nzipped = sys.argv[2] #are files bzipped?\n\nif zipped == 'True':\n... | ```python
#!/usr/bin/python
#run as array job
#if files are bzipped -> copy to local disk and unzip there
import os,sys
db_dir = sys.argv[1]
zipped = sys.argv[2] #are files bzipped?
if zipped == 'True':
zipped = True
else:
zipped = False
files = os.listdir(db_dir)
file = '#$ -S /bin/tcsh\n#$ -cwd\n#$ -V\n'
p... |
[
{
"content": "```python\nfrom random import uniform\nimport numpy\n\ndef sigmoidFunction(x):\n try:\n ret = 1 / (1 + numpy.exp(-x))\n except OverflowError:\n ret = 0\n return ret\n\ndef softMax(array):\n exp = [numpy.exp(x) for x in array]\n return numpy.array([x / sum(exp) for x in... | [
{
"content": "<|memory_start|>```python\nfrom random import uniform\nimport numpy\n\ndef sigmoidFunction(x):\n try:\n ret = 1 / (1 + numpy.exp(-x))\n except OverflowError:\n ret = 0\n return ret\n\ndef softMax(array):\n exp = [numpy.exp(x) for x in array]\n return numpy.array([x / s... | ```python
from random import uniform
import numpy
def sigmoidFunction(x):
try:
ret = 1 / (1 + numpy.exp(-x))
except OverflowError:
ret = 0
return ret
def softMax(array):
exp = [numpy.exp(x) for x in array]
return numpy.array([x / sum(exp) for x in exp])
global sigmoid
sigm... |
[
{
"content": "```python\n# Written by Nicolas Neubauer, Arno Bakker\r\n# see LICENSE.txt for license information\r\n#\r\n# Test case for BuddyCast overlay version 12 (and 8). To be integrated into\r\n# test_buddycast_msg.py\r\n#\r\n# Very sensitive to the order in which things are put into DB,\r\n# so not a rob... | [
{
"content": "<|memory_start|>```python\n# Written by Nicolas Neubauer, Arno Bakker\r\n# see LICENSE.txt for license information\r\n#\r\n# Test case for BuddyCast overlay version 12 (and 8). To be integrated into\r\n# test_buddycast_msg.py\r\n#\r\n# Very sensitive to the order in which things are put into DB,\r... | ```python
# Written by Nicolas Neubauer, Arno Bakker
# see LICENSE.txt for license information
#
# Test case for BuddyCast overlay version 12 (and 8). To be integrated into
# test_buddycast_msg.py
#
# Very sensitive to the order in which things are put into DB,
# so not a robust test
import unittest
import... |
[
{
"content": "Repeat the code precisely:\n```python\n#!/bin/python\n#\n# Hacking together tutorials from deeplearning.net to make\n# a MLP model\n\nimport numpy\nimport theano\nimport theano.tensor as T\nimport sklearn.cross_validation\n\nclass LogisticRegression(object):\n \"\"\"Multi-class Logistic Regress... | [
{
"content": "Repeat the code precisely:\n<|memory_start|>```python\n#!/bin/python\n#\n# Hacking together tutorials from deeplearning.net to make\n# a MLP model\n\nimport numpy\nimport theano\nimport theano.tensor as T\nimport sklearn.cross_validation\n\nclass LogisticRegression(object):\n \"\"\"Multi-class ... | ```python
#!/bin/python
#
# Hacking together tutorials from deeplearning.net to make
# a MLP model
import numpy
import theano
import theano.tensor as T
import sklearn.cross_validation
class LogisticRegression(object):
"""Multi-class Logistic Regression Class
The logistic regression is fully described by a we... |
[
{
"content": "Output the full code verbatim (no extra comments):\n```python\nfrom eden.model import _CrontabPattern, _ParsedSpec, Task, User\nfrom datetime import datetime, timedelta\nimport unittest\n\nclass TaskTest(unittest.TestCase):\n\n def test_new(self):\n task = Task(1, 'task_id', 'name', 'job... | [
{
"content": "Output the full code verbatim (no extra comments):\n<|memory_start|>```python\nfrom eden.model import _CrontabPattern, _ParsedSpec, Task, User\nfrom datetime import datetime, timedelta\nimport unittest\n\nclass TaskTest(unittest.TestCase):\n\n def test_new(self):\n task = Task(1, 'task_i... | ```python
from eden.model import _CrontabPattern, _ParsedSpec, Task, User
from datetime import datetime, timedelta
import unittest
class TaskTest(unittest.TestCase):
def test_new(self):
task = Task(1, 'task_id', 'name', 'job.test', {'args':(), 'kw':{}}, 'every 5')
self.assertEquals((task.name, tas... |
[
{
"content": "Replicate the source code:\n```python\nfrom rest_framework import serializers\nfrom django.contrib.auth.hashers import make_password\nfrom rest_framework.exceptions import ValidationError\nfrom django.contrib.auth import get_user_model\nfrom common.serializers import JobSerializer\nfrom job_auth.s... | [
{
"content": "Replicate the source code:\n<|memory_start|>```python\nfrom rest_framework import serializers\nfrom django.contrib.auth.hashers import make_password\nfrom rest_framework.exceptions import ValidationError\nfrom django.contrib.auth import get_user_model\nfrom common.serializers import JobSerializer\... | ```python
from rest_framework import serializers
from django.contrib.auth.hashers import make_password
from rest_framework.exceptions import ValidationError
from django.contrib.auth import get_user_model
from common.serializers import JobSerializer
from job_auth.serializers import UserSerializer
from .models import(
... |
[
{
"content": "Here is a code snippet:\n```python\n#!/usr/bin/env python\n# -*- coding: ascii -*-\n\nr\"\"\"\nSupport routines for exhaustive equation search in curve fit routines.\n\nUses itertools to find all combinations.\n\"\"\"\nfrom __future__ import print_function\nfrom builtins import str\n\n\nfrom itert... | [
{
"content": "Here is a code snippet:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: ascii -*-\n\nr\"\"\"\nSupport routines for exhaustive equation search in curve fit routines.\n\nUses itertools to find all combinations.\n\"\"\"\nfrom __future__ import print_function\nfrom builtins import str... | ```python
#!/usr/bin/env python
# -*- coding: ascii -*-
r"""
Support routines for exhaustive equation search in curve fit routines.
Uses itertools to find all combinations.
"""
from __future__ import print_function
from builtins import str
from itertools import combinations
from math import factorial
full_funcL = ... |
[
{
"content": "```python\nfrom django.conf.urls import url, patterns, include\nfrom django.contrib.auth.decorators import login_required\nfrom django.views.decorators.cache import cache_page\nfrom common.views import APIRoot, root_redirect_view\n\nfrom rest_auth.views import (\n Login, Logout, UserDetails, Pa... | [
{
"content": "<|memory_start|>```python\nfrom django.conf.urls import url, patterns, include\nfrom django.contrib.auth.decorators import login_required\nfrom django.views.decorators.cache import cache_page\nfrom common.views import APIRoot, root_redirect_view\n\nfrom rest_auth.views import (\n Login, Logout,... | ```python
from django.conf.urls import url, patterns, include
from django.contrib.auth.decorators import login_required
from django.views.decorators.cache import cache_page
from common.views import APIRoot, root_redirect_view
from rest_auth.views import (
Login, Logout, UserDetails, PasswordChange,
PasswordRes... |
[
{
"content": "Recreate the entire code block with identical formatting:\n```python\n# -*- coding: utf-8 -*-\nimport re\nfrom traceback import format_exc\n\nimport pytest\nfrom wrapanapi.utils import eval_strings\n\nfrom cfme.containers.provider import ContainersProvider\nfrom cfme.utils.appliance.implementation... | [
{
"content": "Recreate the entire code block with identical formatting:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\nimport re\nfrom traceback import format_exc\n\nimport pytest\nfrom wrapanapi.utils import eval_strings\n\nfrom cfme.containers.provider import ContainersProvider\nfrom cfme.utils.applianc... | ```python
# -*- coding: utf-8 -*-
import re
from traceback import format_exc
import pytest
from wrapanapi.utils import eval_strings
from cfme.containers.provider import ContainersProvider
from cfme.utils.appliance.implementations.ui import navigate_to
from cfme.utils.wait import TimedOutError
pytestmark = [
pyt... |
[
{
"content": "Here is the source code:\n```python\n# -*- coding: utf-8 -*-\n\n#+---------------------------------------------------------------------------+\n#| 01001110 01100101 01110100 01111010 01101111 01100010 |\n#| ... | [
{
"content": "Here is the source code:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n#+---------------------------------------------------------------------------+\n#| 01001110 01100101 01110100 01111010 01101111 01100010 |\n#| ... | ```python
# -*- coding: utf-8 -*-
#+---------------------------------------------------------------------------+
#| 01001110 01100101 01110100 01111010 01101111 01100010 |
#| |
#| Netzob : Inferring communicatio... |
[
{
"content": "Return the code exactly, with no changes:\n```python\n#!/usr/bin/env python\n# encoding: utf-8\n\nimport asyncio\nimport logging\nfrom functools import singledispatch\nfrom bson.objectid import ObjectId\nfrom bson.errors import InvalidId\nfrom tbone.data.fields.mongo import DBRefField\nfrom tbone.... | [
{
"content": "Return the code exactly, with no changes:\n<|memory_start|>```python\n#!/usr/bin/env python\n# encoding: utf-8\n\nimport asyncio\nimport logging\nfrom functools import singledispatch\nfrom bson.objectid import ObjectId\nfrom bson.errors import InvalidId\nfrom tbone.data.fields.mongo import DBRefFi... | ```python
#!/usr/bin/env python
# encoding: utf-8
import asyncio
import logging
from functools import singledispatch
from bson.objectid import ObjectId
from bson.errors import InvalidId
from tbone.data.fields.mongo import DBRefField
from tbone.db.models import MongoCollectionMixin, post_save
from tbone.dispatch.channe... |
[
{
"content": "```python\n# -*- coding: utf-8 -*-\n# Copyright (c) 2014 Metaswitch Networks\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of the License at\n#\n#... | [
{
"content": "<|memory_start|>```python\n# -*- coding: utf-8 -*-\n# Copyright (c) 2014 Metaswitch Networks\n# All Rights Reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of the ... | ```python
# -*- coding: utf-8 -*-
# Copyright (c) 2014 Metaswitch Networks
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/li... |
[
{
"content": "Repeat the code exactly as the original, including blank lines:\n```python\n# -*- coding: utf-8 -*-\n# Copyright (c) Vispy Development Team. All Rights Reserved.\n# Distributed under the (new) BSD License. See LICENSE.txt for more info.\n\"\"\"\nForce-Directed Graph Layout\n=======================... | [
{
"content": "Repeat the code exactly as the original, including blank lines:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n# Copyright (c) Vispy Development Team. All Rights Reserved.\n# Distributed under the (new) BSD License. See LICENSE.txt for more info.\n\"\"\"\nForce-Directed Graph Layout\n=======... | ```python
# -*- coding: utf-8 -*-
# Copyright (c) Vispy Development Team. All Rights Reserved.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
"""
Force-Directed Graph Layout
===========================
This module contains implementations for a force-directed layout, where the
graph is model... |
[
{
"content": "Replicate the source code:\n```python\n\"\"\"\nDjango settings for financeiro project.\n\nGenerated by 'django-admin startproject' using Django 1.9.5.\n\nFor more information on this file, see\nhttps://docs.djangoproject.com/en/1.9/topics/settings/\n\nFor the full list of settings and their values... | [
{
"content": "Replicate the source code:\n<|memory_start|>```python\n\"\"\"\nDjango settings for financeiro project.\n\nGenerated by 'django-admin startproject' using Django 1.9.5.\n\nFor more information on this file, see\nhttps://docs.djangoproject.com/en/1.9/topics/settings/\n\nFor the full list of settings ... | ```python
"""
Django settings for financeiro project.
Generated by 'django-admin startproject' using Django 1.9.5.
For more information on this file, see
https://docs.djangoproject.com/en/1.9/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.9/ref/settings/
"""
... |
[
{
"content": "Here is the source code:\n```python\nfrom . import FixtureTest\n\n\nclass EarlyStep(FixtureTest):\n def test_steps_with_regional_route(self):\n self.load_fixtures([\n 'https://www.openstreetmap.org/way/24655593',\n 'https://www.openstreetmap.org/relation/2260059',\n... | [
{
"content": "Here is the source code:\n<|memory_start|>```python\nfrom . import FixtureTest\n\n\nclass EarlyStep(FixtureTest):\n def test_steps_with_regional_route(self):\n self.load_fixtures([\n 'https://www.openstreetmap.org/way/24655593',\n 'https://www.openstreetmap.org/rela... | ```python
from . import FixtureTest
class EarlyStep(FixtureTest):
def test_steps_with_regional_route(self):
self.load_fixtures([
'https://www.openstreetmap.org/way/24655593',
'https://www.openstreetmap.org/relation/2260059',
], clip=self.tile_bbox(12, 653, 1582))
s... |
[
{
"content": "```python\n# -*- coding: utf-8 -*-\n\n\"\"\"\n***************************************************************************\n Union.py\n ---------------------\n Date : August 2012\n Copyright : (C) 2012 by Victor Olaya\n Email : volayaf at gma... | [
{
"content": "<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n\"\"\"\n***************************************************************************\n Union.py\n ---------------------\n Date : August 2012\n Copyright : (C) 2012 by Victor Olaya\n Email ... | ```python
# -*- coding: utf-8 -*-
"""
***************************************************************************
Union.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
***********************... |
[
{
"content": "Replicate the source code:\n```python\n#===========================================================================\n# This library is free software; you can redistribute it and/or\n# modify it under the terms of version 2.1 of the GNU Lesser General Public\n# License as published by the Free Soft... | [
{
"content": "Replicate the source code:\n<|memory_start|>```python\n#===========================================================================\n# This library is free software; you can redistribute it and/or\n# modify it under the terms of version 2.1 of the GNU Lesser General Public\n# License as published ... | ```python
#===========================================================================
# This library is free software; you can redistribute it and/or
# modify it under the terms of version 2.1 of the GNU Lesser General Public
# License as published by the Free Software Foundation.
#
# This library is distributed in th... |
[
{
"content": "Repeat the full code snippet:\n```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n#\n# h5features documentation build configuration file, created by\n# sphinx-quickstart on Mon Nov 2 16:02:53 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\... | [
{
"content": "Repeat the full code snippet:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n#\n# h5features documentation build configuration file, created by\n# sphinx-quickstart on Mon Nov 2 16:02:53 2015.\n#\n# This file is execfile()d with the current directory set to its\n# con... | ```python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# h5features documentation build configuration file, created by
# sphinx-quickstart on Mon Nov 2 16:02:53 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present ... |
[
{
"content": "Output the full code verbatim (no extra comments):\n```python\n#!/usr/bin/env python\n\"\"\"A module with utilities for dealing with context managers.\"\"\"\n\nfrom typing import ContextManager\nfrom typing import Generic\nfrom typing import Sequence\nfrom typing import TypeVar\n\n_T = TypeVar(\"_... | [
{
"content": "Output the full code verbatim (no extra comments):\n<|memory_start|>```python\n#!/usr/bin/env python\n\"\"\"A module with utilities for dealing with context managers.\"\"\"\n\nfrom typing import ContextManager\nfrom typing import Generic\nfrom typing import Sequence\nfrom typing import TypeVar\n\n... | ```python
#!/usr/bin/env python
"""A module with utilities for dealing with context managers."""
from typing import ContextManager
from typing import Generic
from typing import Sequence
from typing import TypeVar
_T = TypeVar("_T")
class NullContext(ContextManager[_T], Generic[_T]):
"""A context manager that alwa... |
[
{
"content": "Recreate the entire code block with identical formatting:\n```python\ndef succ(x):\n return x + 1\n\nsuccessor = succ\ndel succ\nprint(successor(10))\n\n\n# functions inside functions\ndef f1():\n def g1():\n print(\"hi, it's me 'g'\")\n print(\"Thanks for calling me\")\n\n ... | [
{
"content": "Recreate the entire code block with identical formatting:\n<|memory_start|>```python\ndef succ(x):\n return x + 1\n\nsuccessor = succ\ndel succ\nprint(successor(10))\n\n\n# functions inside functions\ndef f1():\n def g1():\n print(\"hi, it's me 'g'\")\n print(\"Thanks for calli... | ```python
def succ(x):
return x + 1
successor = succ
del succ
print(successor(10))
# functions inside functions
def f1():
def g1():
print("hi, it's me 'g'")
print("Thanks for calling me")
print("This is the function 'f'")
print("I am calling 'g' now")
g1()
def temperature(t):
... |
[
{
"content": "Here is a code file:\n```python\n# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:\n\n# Copyright 2014-2015 Florian Bruhin (The Compiler) <mail@qutebrowser.org>\n#\n# This file is part of qutebrowser.\n#\n# qutebrowser is free software: you can redistribute it and/or modify\n# it under the terms ... | [
{
"content": "Here is a code file:\n<|memory_start|>```python\n# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:\n\n# Copyright 2014-2015 Florian Bruhin (The Compiler) <mail@qutebrowser.org>\n#\n# This file is part of qutebrowser.\n#\n# qutebrowser is free software: you can redistribute it and/or modify\n# it ... | ```python
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2015 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# ... |
[
{
"content": "Repeat the following code:\n```python\n\"\"\"\nThis is a module to read in an HDF5 file with CCFs.\nUse this to determine the best parameters, and plot the best CCF for each star/date\n\"\"\"\nfrom collections import defaultdict\nimport logging\n\nimport h5py\nimport numpy as np\nimport pandas as ... | [
{
"content": "Repeat the following code:\n<|memory_start|>```python\n\"\"\"\nThis is a module to read in an HDF5 file with CCFs.\nUse this to determine the best parameters, and plot the best CCF for each star/date\n\"\"\"\nfrom collections import defaultdict\nimport logging\n\nimport h5py\nimport numpy as np\ni... | ```python
"""
This is a module to read in an HDF5 file with CCFs.
Use this to determine the best parameters, and plot the best CCF for each star/date
"""
from collections import defaultdict
import logging
import h5py
import numpy as np
import pandas as pd
from scipy.interpolate import InterpolatedUnivariateSpline as s... |
[
{
"content": "Replicate the code snippet exactly, without paraphrasing or reformatting:\n```python\n#!/usr/bin/env python\n#\n# A library that provides a Python interface to the Telegram Bot API\n# Copyright (C) 2015-2021\n# Leandro Toledo de Souza <devs@python-telegram-bot.org>\n#\n# This program is free softw... | [
{
"content": "Replicate the code snippet exactly, without paraphrasing or reformatting:\n<|memory_start|>```python\n#!/usr/bin/env python\n#\n# A library that provides a Python interface to the Telegram Bot API\n# Copyright (C) 2015-2021\n# Leandro Toledo de Souza <devs@python-telegram-bot.org>\n#\n# This progr... | ```python
#!/usr/bin/env python
#
# A library that provides a Python interface to the Telegram Bot API
# Copyright (C) 2015-2021
# Leandro Toledo de Souza <devs@python-telegram-bot.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser Public License as publ... |
[
{
"content": "Write out the code verbatim, preserving indentation and whitespace:\n```python\n# Copyright (C) 2004-2016 by\n# Aric Hagberg <hagberg@lanl.gov>\n# Dan Schult <dschult@colgate.edu>\n# Pieter Swart <swart@lanl.gov>\n# All rights reserved.\n# BSD license.\n\"\"\"\nGenerators for som... | [
{
"content": "Write out the code verbatim, preserving indentation and whitespace:\n<|memory_start|>```python\n# Copyright (C) 2004-2016 by\n# Aric Hagberg <hagberg@lanl.gov>\n# Dan Schult <dschult@colgate.edu>\n# Pieter Swart <swart@lanl.gov>\n# All rights reserved.\n# BSD license.\n\"\"\"\nGe... | ```python
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
"""
Generators for some classic graphs.
The typical graph generator is called as follows:
>>> G=nx.complete_graph(100)
re... |
[
{
"content": "Repeat the code precisely:\n```python\n#!/usr/bin/env python\nfrom __future__ import absolute_import, division, print_function, \\\n unicode_literals\nimport os\nimport sys\nimport time\nimport socket\ntry:\n import urllib.request as urllib\nexcept ImportError:\n import urllib\nimport has... | [
{
"content": "Repeat the code precisely:\n<|memory_start|>```python\n#!/usr/bin/env python\nfrom __future__ import absolute_import, division, print_function, \\\n unicode_literals\nimport os\nimport sys\nimport time\nimport socket\ntry:\n import urllib.request as urllib\nexcept ImportError:\n import ur... | ```python
#!/usr/bin/env python
from __future__ import absolute_import, division, print_function, \
unicode_literals
import os
import sys
import time
import socket
try:
import urllib.request as urllib
except ImportError:
import urllib
import hashlib
import argparse
import logging
from zeroconf import Servi... |
[
{
"content": "Write the code verbatim:\n```python\n# -*- coding: utf-8 -*-\n\n__author__ = 'meanwhile'\n\nimport ssl\nimport time\nimport socket\nimport sys\nimport logging\n\nimport vkontakte\nimport ProvaderStorage\nimport Constants\nimport FileWriter\nimport ProccessingResponce\nimport daemon\n\n\nclass VkPa... | [
{
"content": "Write the code verbatim:\n<|memory_start|>```python\n# -*- coding: utf-8 -*-\n\n__author__ = 'meanwhile'\n\nimport ssl\nimport time\nimport socket\nimport sys\nimport logging\n\nimport vkontakte\nimport ProvaderStorage\nimport Constants\nimport FileWriter\nimport ProccessingResponce\nimport daemon... | ```python
# -*- coding: utf-8 -*-
__author__ = 'meanwhile'
import ssl
import time
import socket
import sys
import logging
import vkontakte
import ProvaderStorage
import Constants
import FileWriter
import ProccessingResponce
import daemon
class VkParserDemon(daemon.Daemon):
def run(self):
#read code for... |
[
{
"content": "Repeat the following code:\n```python\n# Copyright 2010 OpenStack Foundation\n# Copyright 2012 University Of Minho\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\n# a copy of ... | [
{
"content": "Repeat the following code:\n<|memory_start|>```python\n# Copyright 2010 OpenStack Foundation\n# Copyright 2012 University Of Minho\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\"); you may\n# not use this file except in compliance with the License. You may obtain\... | ```python
# Copyright 2010 OpenStack Foundation
# Copyright 2012 University Of Minho
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/... |
[
{
"content": "Here is the snippet:\n```python\n\"\"\"Dirac notation for states.\"\"\"\n\n\nfrom sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,\n Tuple)\nfrom sympy.printing.pretty.stringpict import prettyForm, stringPict\nfrom sympy.physics.quantum.qexpr import QExpr, d... | [
{
"content": "Here is the snippet:\n<|memory_start|>```python\n\"\"\"Dirac notation for states.\"\"\"\n\n\nfrom sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,\n Tuple)\nfrom sympy.printing.pretty.stringpict import prettyForm, stringPict\nfrom sympy.physics.quantum.qexpr... | ```python
"""Dirac notation for states."""
from sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,
Tuple)
from sympy.printing.pretty.stringpict import prettyForm, stringPict
from sympy.physics.quantum.qexpr import QExpr, dispatch_method
__all__ = [
'KetBase',
'BraBase',... |
[
{
"content": "```python\nimport pytz\nfrom pytz import timezone\nfrom datetime import timedelta, datetime, date, time\nimport re\nfrom corehq.apps.casegroups.models import CommCareCaseGroup\nfrom corehq.apps.hqcase.dbaccessors import get_case_ids_in_domain\nfrom corehq.apps.reminders.dbaccessors import get_surv... | [
{
"content": "<|memory_start|>```python\nimport pytz\nfrom pytz import timezone\nfrom datetime import timedelta, datetime, date, time\nimport re\nfrom corehq.apps.casegroups.models import CommCareCaseGroup\nfrom corehq.apps.hqcase.dbaccessors import get_case_ids_in_domain\nfrom corehq.apps.reminders.dbaccessors... | ```python
import pytz
from pytz import timezone
from datetime import timedelta, datetime, date, time
import re
from corehq.apps.casegroups.models import CommCareCaseGroup
from corehq.apps.hqcase.dbaccessors import get_case_ids_in_domain
from corehq.apps.reminders.dbaccessors import get_surveys_in_domain
from dimagi.ext... |
[
{
"content": "Repeat the code exactly as the original, including blank lines:\n```python\n# Copyright 2016 Casey Jaymes\n\n# This file is part of PySCAP.\n#\n# PySCAP is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Softw... | [
{
"content": "Repeat the code exactly as the original, including blank lines:\n<|memory_start|>```python\n# Copyright 2016 Casey Jaymes\n\n# This file is part of PySCAP.\n#\n# PySCAP is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n... | ```python
# Copyright 2016 Casey Jaymes
# This file is part of PySCAP.
#
# PySCAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ... |
[
{
"content": "Repeat the full code snippet:\n```python\n\"\"\"\n2.2.2: If `onFulfilled` is a function\nhttps://github.com/promises-aplus/promises-tests/blob/2.1.1/lib/tests/2.2.2.js\n\"\"\"\nimport threading\n\nfrom sleekxmpp.test import SleekTest\n\n\nclass Promise_2_2_2_1_TestCase(SleekTest):\n \"\"\"\n ... | [
{
"content": "Repeat the full code snippet:\n<|memory_start|>```python\n\"\"\"\n2.2.2: If `onFulfilled` is a function\nhttps://github.com/promises-aplus/promises-tests/blob/2.1.1/lib/tests/2.2.2.js\n\"\"\"\nimport threading\n\nfrom sleekxmpp.test import SleekTest\n\n\nclass Promise_2_2_2_1_TestCase(SleekTest):\... | ```python
"""
2.2.2: If `onFulfilled` is a function
https://github.com/promises-aplus/promises-tests/blob/2.1.1/lib/tests/2.2.2.js
"""
import threading
from sleekxmpp.test import SleekTest
class Promise_2_2_2_1_TestCase(SleekTest):
"""
2.2.2.1: it must be called after `promise` is fulfilled, with `promise`'s... |
[
{
"content": "Return the code unaltered:\n```python\n#!/usr/bin/env python\n\nimport sys\nimport json\nfrom types import SimpleNamespace\nfrom argparse import ArgumentParser, ArgumentDefaultsHelpFormatter\nfrom webbrowser import open_new_tab\n\nimport tornado.ioloop\nimport tornado.web\n\nfrom .console import s... | [
{
"content": "Return the code unaltered:\n<|memory_start|>```python\n#!/usr/bin/env python\n\nimport sys\nimport json\nfrom types import SimpleNamespace\nfrom argparse import ArgumentParser, ArgumentDefaultsHelpFormatter\nfrom webbrowser import open_new_tab\n\nimport tornado.ioloop\nimport tornado.web\n\nfrom .... | ```python
#!/usr/bin/env python
import sys
import json
from types import SimpleNamespace
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from webbrowser import open_new_tab
import tornado.ioloop
import tornado.web
from .console import start_message, append_message, print_message
from .infos import... |
[
{
"content": "Repeat the full code snippet:\n```python\n# -*- coding: UTF-8 -*-\n\n\"\"\"\ntitlecase.py v0.2\nOriginal Perl version by: John Gruber http://daringfireball.net/ 10 May 2008\nPython version by Stuart Colville http://muffinresearch.co.uk\nLicense: http://www.opensource.org/licenses/mit-license.php\n... | [
{
"content": "Repeat the full code snippet:\n<|memory_start|>```python\n# -*- coding: UTF-8 -*-\n\n\"\"\"\ntitlecase.py v0.2\nOriginal Perl version by: John Gruber http://daringfireball.net/ 10 May 2008\nPython version by Stuart Colville http://muffinresearch.co.uk\nLicense: http://www.opensource.org/licenses/m... | ```python
# -*- coding: UTF-8 -*-
"""
titlecase.py v0.2
Original Perl version by: John Gruber http://daringfireball.net/ 10 May 2008
Python version by Stuart Colville http://muffinresearch.co.uk
License: http://www.opensource.org/licenses/mit-license.php
"""
import unittest
import sys
import re
SMALL = 'a|an|and|as... |
[
{
"content": "Replicate the source code:\n```python\n#!/usr/bin/env python\n\nfrom datetime import datetime\nfrom itertools import chain\nimport re\n\nimport numpy as np\nimport click\n\nfrom labman.db.process import (\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,\n LibraryPr... | [
{
"content": "Replicate the source code:\n<|memory_start|>```python\n#!/usr/bin/env python\n\nfrom datetime import datetime\nfrom itertools import chain\nimport re\n\nimport numpy as np\nimport click\n\nfrom labman.db.process import (\n SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess... | ```python
#!/usr/bin/env python
from datetime import datetime
from itertools import chain
import re
import numpy as np
import click
from labman.db.process import (
SamplePlatingProcess, GDNAExtractionProcess, GDNAPlateCompressionProcess,
LibraryPrep16SProcess, NormalizationProcess, QuantificationProcess,
... |
[
{
"content": "Here is the code content:\n```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n\n# Import smtplib for the actual sending function\nimport sys, os\nimport smtplib\nimport email\n# Import the email modules we'll need\nfrom email.mime.text import MIMEText\nfrom email.mime.multipart import MIME... | [
{
"content": "Here is the code content:\n<|memory_start|>```python\n#!/usr/bin/env python\n# -*- coding: utf-8 -*-\n\n# Import smtplib for the actual sending function\nimport sys, os\nimport smtplib\nimport email\n# Import the email modules we'll need\nfrom email.mime.text import MIMEText\nfrom email.mime.multi... | ```python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Import smtplib for the actual sending function
import sys, os
import smtplib
import email
# Import the email modules we'll need
from email.mime.text import MIMEText
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.h... |
[
{
"content": "Here is the snippet:\n```python\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\nimport package_file\nimport copy\n\n\ndef extract_checker_info(name_string):\n package_file.list_of_detection_info_sa0[name_string] = []\n package_file.list_of_detection_info_sa1[name_string] = []\n... | [
{
"content": "Here is the snippet:\n<|memory_start|>```python\n# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand\nimport package_file\nimport copy\n\n\ndef extract_checker_info(name_string):\n package_file.list_of_detection_info_sa0[name_string] = []\n package_file.list_of_detection_info_sa1[nam... | ```python
# copyright 2016 Siavoosh Payandeh Azad and Behrad Niazmand
import package_file
import copy
def extract_checker_info(name_string):
package_file.list_of_detection_info_sa0[name_string] = []
package_file.list_of_detection_info_sa1[name_string] = []
package_file.list_of_true_misses_sa0[name_string... |
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