idx int64 0 252k | question stringlengths 48 5.28k | target stringlengths 5 1.23k |
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2,600 | def count_lines_in_file ( self , fname = '' ) : i = 0 if fname == '' : fname = self . fullname try : with codecs . open ( fname , "r" , encoding = 'utf8' , errors = 'ignore' ) as f : for i , _ in enumerate ( f ) : pass return i + 1 except Exception as ex : print ( 'cant count lines in file in "' , fname , '":' , str ( ... | you wont believe what this method does |
2,601 | def count_lines_of_code ( self , fname = '' ) : if fname == '' : fname = self . fullname loc = 0 try : with open ( fname ) as f : for l in f : if l . strip ( ) != '' : loc += 1 return loc except Exception as ex : print ( 'cant count lines of code in "' , fname , '":' , str ( ex ) ) return 0 | counts non blank lines |
2,602 | def get_file_sample ( self , numLines = 10 ) : res = '' try : with open ( self . fullname , 'r' ) as f : for line_num , line in enumerate ( f ) : res += str ( line_num ) . zfill ( 5 ) + ' ' + line if line_num >= numLines - 1 : break return res except Exception as ex : print ( 'cant get_file_sample in "' , self . fullna... | retrieve a sample of the file |
2,603 | def append_text ( self , txt ) : with open ( self . fullname , "a" ) as myfile : myfile . write ( txt ) | adds a line of text to a file |
2,604 | def load_file_to_string ( self ) : try : with open ( self . fullname , 'r' ) as f : txt = f . read ( ) return txt except IOError : return '' | load a file to a string |
2,605 | def load_file_to_list ( self ) : lst = [ ] try : with open ( self . fullname , 'r' ) as f : for line in f : lst . append ( line ) return lst except IOError : return lst | load a file to a list |
2,606 | def get_program_list ( ) : colList = [ 'FileName' , 'FileSize' , 'Functions' , 'Imports' ] txt = '<TABLE width=90% border=0>' txt += format_file_table_header ( colList ) fl = web . GetFileList ( aikif_folder , [ '*.py' ] , 'N' ) for f in fl : if '__init__.py' in f : txt += '<TR><TD colspan=4><HR><H3>' + get_subfolder (... | get a HTML formatted view of all Python programs in all subfolders of AIKIF including imports and lists of functions and classes |
2,607 | def get_subfolder ( txt ) : root_folder = os . sep + 'aikif' + os . sep ndx = txt . find ( root_folder , 1 ) return txt [ ndx : ] . replace ( '__init__.py' , '' ) | extracts a displayable subfolder name from full filename |
2,608 | def get_functions ( fname ) : txt = '' with open ( fname , 'r' ) as f : for line in f : if line . strip ( ) [ 0 : 4 ] == 'def ' : txt += '<PRE>' + strip_text_after_string ( strip_text_after_string ( line , '#' ) [ 4 : ] , ':' ) + '</PRE>\n' if line [ 0 : 5 ] == 'class' : txt += '<PRE>' + strip_text_after_string ( strip... | get a list of functions from a Python program |
2,609 | def strip_text_after_string ( txt , junk ) : if junk in txt : return txt [ : txt . find ( junk ) ] else : return txt | used to strip any poorly documented comments at the end of function defs |
2,610 | def get_imports ( fname ) : txt = '' with open ( fname , 'r' ) as f : for line in f : if line [ 0 : 6 ] == 'import' : txt += '<PRE>' + strip_text_after_string ( line [ 7 : ] , ' as ' ) + '</PRE>\n' return txt + '<BR>' | get a list of imports from a Python program |
2,611 | def main ( arg1 = 55 , arg2 = 'test' , arg3 = None ) : print ( 'Starting dummy AI algorithm with :' , arg1 , arg2 , arg3 ) if arg3 is None : arg3 = [ 5 , 6 , 7 , 5 , 4 , ] result = arg1 + arg3 [ 0 ] * 7566.545 print ( 'Done - returning ' , result ) return result | This is a sample program to show how a learning agent can be logged using AIKIF . The idea is that this main function is your algorithm which will run until it finds a successful result . The result is returned and the time taken is logged . There can optionally be have additional functions to call to allow for easy lo... |
2,612 | def get ( self , key ) : res = self . connection . get ( key ) print ( res ) return res | get a set of keys from redis |
2,613 | def creator ( _ , config ) : packer_script = render ( config . script , model = config . model , env = config . env , variables = config . variables , item = config . item ) filename = "packer.dry.run.see.comment" if not config . dry_run : filename = write_temporary_file ( packer_script , 'packer-' , '.json' ) packer_s... | Creator function for creating an instance of a Packer image script . |
2,614 | def process_jpeg_bytes ( bytes_in , quality = DEFAULT_JPEG_QUALITY ) : bytes_out_p = ffi . new ( "char**" ) bytes_out_p_gc = ffi . gc ( bytes_out_p , lib . guetzli_free_bytes ) length = lib . guetzli_process_jpeg_bytes ( bytes_in , len ( bytes_in ) , bytes_out_p_gc , quality ) if length == 0 : raise ValueError ( "Inval... | Generates an optimized JPEG from JPEG - encoded bytes . |
2,615 | def process_rgb_bytes ( bytes_in , width , height , quality = DEFAULT_JPEG_QUALITY ) : if len ( bytes_in ) != width * height * 3 : raise ValueError ( "bytes_in length is not coherent with given width and height" ) bytes_out_p = ffi . new ( "char**" ) bytes_out_p_gc = ffi . gc ( bytes_out_p , lib . guetzli_free_bytes ) ... | Generates an optimized JPEG from RGB bytes . |
2,616 | def singleton ( the_class ) : class_instances = { } def get_instance ( * args , ** kwargs ) : key = ( the_class , args , str ( kwargs ) ) if key not in class_instances : class_instances [ key ] = the_class ( * args , ** kwargs ) return class_instances [ key ] return get_instance | Decorator for a class to make a singleton out of it . |
2,617 | def build_board_2048 ( ) : grd = Grid ( 4 , 4 , [ 2 , 4 ] ) grd . new_tile ( ) grd . new_tile ( ) print ( grd ) return grd | builds a 2048 starting board Printing Grid 0 0 0 2 0 0 4 0 0 0 0 0 0 0 0 0 |
2,618 | def build_board_checkers ( ) : grd = Grid ( 8 , 8 , [ "B" , "W" ] ) for c in range ( 4 ) : grd . set_tile ( 0 , ( c * 2 ) - 1 , "B" ) grd . set_tile ( 1 , ( c * 2 ) - 0 , "B" ) grd . set_tile ( 6 , ( c * 2 ) + 1 , "W" ) grd . set_tile ( 7 , ( c * 2 ) - 0 , "W" ) print ( grd ) return grd | builds a checkers starting board Printing Grid 0 B 0 B 0 B 0 B B 0 B 0 B 0 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 W 0 W 0 W 0 W W 0 W 0 W 0 W 0 |
2,619 | def TEST ( ) : grd = Grid ( 4 , 4 , [ 2 , 4 ] ) grd . new_tile ( ) grd . new_tile ( ) print ( grd ) print ( "There are " , grd . count_blank_positions ( ) , " blanks in grid 1\n" ) grd2 = Grid ( 5 , 5 , [ 'A' , 'B' ] ) grd2 . new_tile ( 26 ) print ( grd2 ) build_board_checkers ( ) print ( "There are " , grd2 . count_bl... | tests for this module |
2,620 | def url ( self , name ) : key = blobstore . create_gs_key ( '/gs' + name ) return images . get_serving_url ( key ) | Ask blobstore api for an url to directly serve the file |
2,621 | def process ( self , stage ) : self . logger . info ( "Processing pipeline stage '%s'" , self . title ) output = [ ] for entry in stage : key = list ( entry . keys ( ) ) [ 0 ] if key == "env" : self . pipeline . data . env_list [ 1 ] . update ( entry [ key ] ) self . logger . debug ( "Updating environment at level 1 wi... | Processing one stage . |
2,622 | def trading_fees ( self ) -> TradingFees : return self . _fetch ( 'trading fees' , self . market . code ) ( self . _trading_fees ) ( ) | Fetch trading fees . |
2,623 | def fetch_ticker ( self ) -> Ticker : return self . _fetch ( 'ticker' , self . market . code ) ( self . _ticker ) ( ) | Fetch the market ticker . |
2,624 | def fetch_order_book ( self ) -> OrderBook : return self . _fetch ( 'order book' , self . market . code ) ( self . _order_book ) ( ) | Fetch the order book . |
2,625 | def fetch_trades_since ( self , since : int ) -> List [ Trade ] : return self . _fetch_since ( 'trades' , self . market . code ) ( self . _trades_since ) ( since ) | Fetch trades since given timestamp . |
2,626 | def fetch_deposits ( self , limit : int ) -> List [ Deposit ] : return self . _transactions ( self . _deposits , 'deposits' , limit ) | Fetch latest deposits must provide a limit . |
2,627 | def fetch_deposits_since ( self , since : int ) -> List [ Deposit ] : return self . _transactions_since ( self . _deposits_since , 'deposits' , since ) | Fetch all deposits since the given timestamp . |
2,628 | def fetch_withdrawals ( self , limit : int ) -> List [ Withdrawal ] : return self . _transactions ( self . _withdrawals , 'withdrawals' , limit ) | Fetch latest withdrawals must provide a limit . |
2,629 | def fetch_withdrawals_since ( self , since : int ) -> List [ Withdrawal ] : return self . _transactions_since ( self . _withdrawals_since , 'withdrawals' , since ) | Fetch all withdrawals since the given timestamp . |
2,630 | def request_withdrawal ( self , amount : Number , address : str , subtract_fee : bool = False , ** params ) -> Withdrawal : self . log . debug ( f'Requesting {self.currency} withdrawal from {self.name} to {address}' ) amount = self . _parse_money ( amount ) if self . dry_run : withdrawal = Withdrawal . create_default (... | Request a withdrawal . |
2,631 | def fetch_order ( self , order_id : str ) -> Order : return self . _fetch ( f'order id={order_id}' , exc = OrderNotFound ) ( self . _order ) ( order_id ) | Fetch an order by ID . |
2,632 | def fetch_open_orders ( self , limit : int ) -> List [ Order ] : return self . _fetch_orders_limit ( self . _open_orders , limit ) | Fetch latest open orders must provide a limit . |
2,633 | def fetch_closed_orders ( self , limit : int ) -> List [ Order ] : return self . _fetch_orders_limit ( self . _closed_orders , limit ) | Fetch latest closed orders must provide a limit . |
2,634 | def fetch_closed_orders_since ( self , since : int ) -> List [ Order ] : return self . _fetch_orders_since ( self . _closed_orders_since , since ) | Fetch closed orders since the given timestamp . |
2,635 | def cancel_order ( self , order_id : str ) -> str : self . log . debug ( f'Canceling order id={order_id} on {self.name}' ) if self . dry_run : self . log . warning ( f'DRY RUN: Order cancelled on {self.name}: id={order_id}' ) return order_id try : self . _cancel_order ( order_id ) except Exception as e : raise self . e... | Cancel an order by ID . |
2,636 | def cancel_orders ( self , order_ids : List [ str ] ) -> List [ str ] : orders_to_cancel = order_ids self . log . debug ( f'Canceling orders on {self.name}: ids={orders_to_cancel}' ) cancelled_orders = [ ] if self . dry_run : self . log . warning ( f'DRY RUN: Orders cancelled on {self.name}: {orders_to_cancel}' ) retur... | Cancel multiple orders by a list of IDs . |
2,637 | def cancel_all_orders ( self ) -> List [ str ] : order_ids = [ o . id for o in self . fetch_all_open_orders ( ) ] return self . cancel_orders ( order_ids ) | Cancel all open orders . |
2,638 | def min_order_amount ( self ) -> Money : return self . _fetch ( 'minimum order amount' , self . market . code ) ( self . _min_order_amount ) ( ) | Minimum amount to place an order . |
2,639 | def place_market_order ( self , side : Side , amount : Number ) -> Order : return self . place_order ( side , OrderType . MARKET , amount ) | Place a market order . |
2,640 | def main ( ) : parser = argparse . ArgumentParser ( description = main . __doc__ , add_help = True ) parser . add_argument ( '-M' , '--master_key' , dest = 'master_key' , help = 'Path to the master key ' + 'used for the encryption. Data is transferred without encryption if this' + 'is not provided.' , type = str , re... | This is the main module for the script . The script will accept a file or a directory and then encrypt it with a provided key before pushing it to S3 into a specified bucket . |
2,641 | def _get_bucket_endpoint ( self ) : conn = S3Connection ( ) bucket = conn . lookup ( self . bucket_name ) if not bucket : raise InputParameterError ( 'The provided bucket %s doesn\'t exist' % self . bucket_name ) endpoint = str ( bucket . get_location ( ) ) return endpoint | Queries S3 to identify the region hosting the provided bucket . |
2,642 | def align_rna ( job , fastqs , univ_options , star_options ) : star = job . wrapJobFn ( run_star , fastqs , univ_options , star_options , cores = star_options [ 'n' ] , memory = PromisedRequirement ( lambda x : int ( 1.85 * x . size ) , star_options [ 'index' ] ) , disk = PromisedRequirement ( star_disk , fastqs , star... | A wrapper for the entire rna alignment subgraph . |
2,643 | def run_star ( job , fastqs , univ_options , star_options ) : assert star_options [ 'type' ] in ( 'star' , 'starlong' ) work_dir = os . getcwd ( ) input_files = { 'rna_cutadapt_1.fastq' : fastqs [ 0 ] , 'rna_cutadapt_2.fastq' : fastqs [ 1 ] , 'star_index.tar.gz' : star_options [ 'index' ] } input_files = get_files_from... | Align a pair of fastqs with STAR . |
2,644 | def sort_and_index_star ( job , star_bams , univ_options , star_options ) : star_options [ 'samtools' ] [ 'n' ] = star_options [ 'n' ] sort = job . wrapJobFn ( sort_bamfile , star_bams [ 'rnaAligned.out.bam' ] , 'rna' , univ_options , samtools_options = star_options [ 'samtools' ] , disk = PromisedRequirement ( sort_di... | A wrapper for sorting and indexing the genomic star bam generated by run_star . It is required since run_star returns a dict of 2 bams |
2,645 | def reset ( self ) : self . expr = [ ] self . matcher = None self . last_matcher = None self . description = None | Resets the state of the expression |
2,646 | def clone ( self ) : from copy import copy clone = copy ( self ) clone . expr = copy ( self . expr ) clone . factory = False return clone | Clone this expression |
2,647 | def resolve ( self , value = None ) : if self . matcher : self . _init_matcher ( ) matcher = self . evaluate ( ) try : value = self . _transform ( value ) self . _assertion ( matcher , value ) except AssertionError as ex : raise ex finally : if self . deferred : self . reset ( ) | Resolve the current expression against the supplied value |
2,648 | def _assertion ( self , matcher , value ) : if isinstance ( value , Expectation ) : assertion = value . _assertion . __get__ ( self , Expectation ) assertion ( matcher , value . value ) else : hc . assert_that ( value , matcher ) | Perform the actual assertion for the given matcher and value . Override this method to apply a special configuration when performing the assertion . If the assertion fails it should raise an AssertionError . |
2,649 | def _transform ( self , value ) : if self . transform : try : value = self . transform ( value ) except : import sys exc_type , exc_obj , exc_tb = sys . exc_info ( ) raise AssertionError ( 'Error applying transformation <{0}>: {2}: {3}' . format ( self . transform . __name__ , value , exc_type . __name__ , exc_obj ) ) ... | Applies any defined transformation to the given value |
2,650 | def evaluate ( self ) : ops = [ ] rpn = [ ] for token in self . expr : if isinstance ( token , int ) : while len ( ops ) and token <= ops [ - 1 ] : rpn . append ( ops . pop ( ) ) ops . append ( token ) else : rpn . append ( token ) while len ( ops ) : rpn . append ( ops . pop ( ) ) stack = [ ] for token in rpn : if isi... | Converts the current expression into a single matcher applying coordination operators to operands according to their binding rules |
2,651 | def _find_matcher ( self , alias ) : matcher = lookup ( alias ) if not matcher : msg = 'Matcher "%s" not found' % alias similar = suggest ( alias , max = 3 , cutoff = 0.5 ) if len ( similar ) > 1 : last = similar . pop ( ) msg += '. Perhaps you meant to use %s or %s?' % ( ', ' . join ( similar ) , last ) elif len ( sim... | Finds a matcher based on the given alias or raises an error if no matcher could be found . |
2,652 | def _init_matcher ( self , * args , ** kwargs ) : fn = lambda x : x . evaluate ( ) if isinstance ( x , Expectation ) else x args = [ fn ( x ) for x in args ] kwargs = dict ( ( k , fn ( v ) ) for k , v in kwargs . items ( ) ) matcher = self . matcher ( * args , ** kwargs ) self . expr . append ( matcher ) self . matcher... | Executes the current matcher appending it to the expression |
2,653 | def described_as ( self , description , * args ) : if len ( args ) : description = description . format ( * args ) self . description = description return self | Specify a custom message for the matcher |
2,654 | def make_dbsource ( ** kwargs ) : if 'spatialite' in connection . settings_dict . get ( 'ENGINE' ) : kwargs . setdefault ( 'file' , connection . settings_dict [ 'NAME' ] ) return mapnik . SQLite ( wkb_format = 'spatialite' , ** kwargs ) names = ( ( 'dbname' , 'NAME' ) , ( 'user' , 'USER' ) , ( 'password' , 'PASSWORD' )... | Returns a mapnik PostGIS or SQLite Datasource . |
2,655 | def layer ( self , queryset , stylename = None ) : cls = RasterLayer if hasattr ( queryset , 'image' ) else VectorLayer layer = cls ( queryset , style = stylename ) try : style = self . map . find_style ( layer . stylename ) except KeyError : self . map . append_style ( layer . stylename , layer . style ( ) ) layer . s... | Returns a map Layer . |
2,656 | def zoom_bbox ( self , bbox ) : try : bbox . transform ( self . map . srs ) except gdal . GDALException : pass else : self . map . zoom_to_box ( mapnik . Box2d ( * bbox . extent ) ) | Zoom map to geometry extent . |
2,657 | def style ( self ) : style = mapnik . Style ( ) rule = mapnik . Rule ( ) self . _symbolizer = self . symbolizer ( ) rule . symbols . append ( self . _symbolizer ) style . rules . append ( rule ) return style | Returns a default Style . |
2,658 | def wrap_fusion ( job , fastqs , star_output , univ_options , star_fusion_options , fusion_inspector_options ) : if not star_fusion_options [ 'run' ] : job . fileStore . logToMaster ( 'Skipping STAR-Fusion on %s' % univ_options [ 'patient' ] ) return fusion = job . wrapJobFn ( run_fusion , fastqs , star_output [ 'rnaCh... | A wrapper for run_fusion using the results from cutadapt and star as input . |
2,659 | def parse_star_fusion ( infile ) : reader = csv . reader ( infile , delimiter = '\t' ) header = reader . next ( ) header = { key : index for index , key in enumerate ( header ) } features = [ 'LeftGene' , 'LeftLocalBreakpoint' , 'LeftBreakpoint' , 'RightGene' , 'RightLocalBreakpoint' , 'RightBreakpoint' , 'LargeAnchorS... | Parses STAR - Fusion format and returns an Expando object with basic features |
2,660 | def get_transcripts ( transcript_file ) : with open ( transcript_file , 'r' ) as fa : transcripts = { } regex_s = r"(?P<ID>TRINITY.*)\s(?P<fusion>.*--.*):(?P<left_start>\d+)-(?P<right_start>\d+)" regex = re . compile ( regex_s ) while True : try : info = fa . next ( ) seq = fa . next ( ) assert info . startswith ( '>' ... | Parses FusionInspector transcript file and returns dictionary of sequences |
2,661 | def split_fusion_transcript ( annotation_path , transcripts ) : annotation = collections . defaultdict ( dict ) forward = 'ACGTN' reverse = 'TGCAN' trans = string . maketrans ( forward , reverse ) five_pr_splits = collections . defaultdict ( dict ) three_pr_splits = collections . defaultdict ( dict ) regex = re . compi... | Finds the breakpoint in the fusion transcript and splits the 5 donor from the 3 acceptor |
2,662 | def get_gene_ids ( fusion_bed ) : with open ( fusion_bed , 'r' ) as f : gene_to_id = { } regex = re . compile ( r'(?P<gene>ENSG\d*)' ) for line in f : line = line . split ( '\t' ) transcript , gene_bit , name = line [ 3 ] . split ( ';' ) m = regex . search ( gene_bit ) if m : gene_to_id [ name ] = m . group ( 'gene' ) ... | Parses FusionInspector bed file to ascertain the ENSEMBL gene ids |
2,663 | def reformat_star_fusion_output ( job , fusion_annot , fusion_file , transcript_file , transcript_gff_file , univ_options ) : input_files = { 'results.tsv' : fusion_file , 'fusion.bed' : fusion_annot } if transcript_file and transcript_gff_file : input_files [ 'transcripts.fa' ] = transcript_file input_files [ 'transcr... | Writes STAR - Fusion results in Transgene BEDPE format |
2,664 | def _ensure_patient_group_is_ok ( patient_object , patient_name = None ) : from protect . addons . common import TCGAToGTEx assert isinstance ( patient_object , ( set , dict ) ) , '%s,%s' % ( patient_object , patient_name ) test_set = set ( patient_object ) if 'tumor_type' not in patient_object : raise ParameterError (... | Ensure that the provided entries for the patient groups is formatted properly . |
2,665 | def _add_default_entries ( input_dict , defaults_dict ) : for key , value in defaults_dict . iteritems ( ) : if key == 'patients' : print ( 'Cannot default `patients`.' ) continue if isinstance ( value , dict ) : if key not in input_dict or input_dict [ key ] is None : input_dict [ key ] = value else : r = _add_default... | Add the entries in defaults dict into input_dict if they don t exist in input_dict |
2,666 | def _process_group ( input_group , required_group , groupname , append_subgroups = None ) : if append_subgroups is None : append_subgroups = [ ] tool_options = { } for key in input_group : _ensure_set_contains ( input_group [ key ] , required_group . get ( key , { } ) , groupname + '::' + key ) if key in append_subgrou... | Process one group from the input yaml . Ensure it has the required entries . If there is a subgroup that should be processed and then appended to the rest of the subgroups in that group handle it accordingly . |
2,667 | def get_fastq_2 ( job , patient_id , sample_type , fastq_1 ) : prefix , extn = fastq_1 , 'temp' final_extn = '' while extn : prefix , extn = os . path . splitext ( prefix ) final_extn = extn + final_extn if prefix . endswith ( '1' ) : prefix = prefix [ : - 1 ] job . fileStore . logToMaster ( '"%s" prefix for "%s" deter... | For a path to a fastq_1 file return a fastq_2 file with the same prefix and naming scheme . |
2,668 | def parse_config_file ( job , config_file , max_cores = None ) : sample_set , univ_options , processed_tool_inputs = _parse_config_file ( job , config_file , max_cores ) for patient_id in sample_set . keys ( ) : job . addFollowOnJobFn ( launch_protect , sample_set [ patient_id ] , univ_options , processed_tool_inputs )... | Parse the config file and spawn a ProTECT job for every input sample . |
2,669 | def get_all_tool_inputs ( job , tools , outer_key = '' , mutation_caller_list = None ) : for tool in tools : for option in tools [ tool ] : if isinstance ( tools [ tool ] [ option ] , dict ) : tools [ tool ] [ option ] = get_all_tool_inputs ( job , { option : tools [ tool ] [ option ] } , outer_key = ':' . join ( [ out... | Iterate through all the tool options and download required files from their remote locations . |
2,670 | def get_pipeline_inputs ( job , input_flag , input_file , encryption_key = None , per_file_encryption = False , gdc_download_token = None ) : work_dir = os . getcwd ( ) job . fileStore . logToMaster ( 'Obtaining file (%s) to the file job store' % input_flag ) if input_file . startswith ( ( 'http' , 'https' , 'ftp' ) ) ... | Get the input file from s3 or disk and write to file store . |
2,671 | def prepare_samples ( job , patient_dict , univ_options ) : job . fileStore . logToMaster ( 'Downloading Inputs for %s' % univ_options [ 'patient' ] ) output_dict = { } for input_file in patient_dict : if not input_file . endswith ( ( 'bam' , 'bai' , '_1' , '_2' , 'files' , 'vcf' , 'bedpe' ) ) : output_dict [ input_fil... | Obtain the input files for the patient and write them to the file store . |
2,672 | def get_patient_bams ( job , patient_dict , sample_type , univ_options , bwa_options , mutect_options ) : output_dict = { } if 'dna' in sample_type : sample_info = 'fix_pg_sorted' prefix = sample_type + '_' + sample_info else : sample_info = 'genome_sorted' prefix = 'rna_' + sample_info if sample_type + '_bam' in patie... | Convenience function to return the bam and its index in the correct format for a sample type . |
2,673 | def get_patient_vcf ( job , patient_dict ) : temp = job . fileStore . readGlobalFile ( patient_dict [ 'mutation_vcf' ] , os . path . join ( os . getcwd ( ) , 'temp.gz' ) ) if is_gzipfile ( temp ) : outfile = job . fileStore . writeGlobalFile ( gunzip ( temp ) ) job . fileStore . deleteGlobalFile ( patient_dict [ 'mutat... | Convenience function to get the vcf from the patient dict |
2,674 | def get_patient_mhc_haplotype ( job , patient_dict ) : haplotype_archive = job . fileStore . readGlobalFile ( patient_dict [ 'hla_haplotype_files' ] ) haplotype_archive = untargz ( haplotype_archive , os . getcwd ( ) ) output_dict = { } for filename in 'mhci_alleles.list' , 'mhcii_alleles.list' : output_dict [ filename... | Convenience function to get the mhc haplotype from the patient dict |
2,675 | def get_patient_expression ( job , patient_dict ) : expression_archive = job . fileStore . readGlobalFile ( patient_dict [ 'expression_files' ] ) expression_archive = untargz ( expression_archive , os . getcwd ( ) ) output_dict = { } for filename in 'rsem.genes.results' , 'rsem.isoforms.results' : output_dict [ filenam... | Convenience function to get the expression from the patient dict |
2,676 | def generate_config_file ( ) : shutil . copy ( os . path . join ( os . path . dirname ( __file__ ) , 'input_parameters.yaml' ) , os . path . join ( os . getcwd ( ) , 'ProTECT_config.yaml' ) ) | Generate a config file for a ProTECT run on hg19 . |
2,677 | def main ( ) : parser = argparse . ArgumentParser ( prog = 'ProTECT' , description = 'Prediction of T-Cell Epitopes for Cancer Therapy' , epilog = 'Contact Arjun Rao (aarao@ucsc.edu) if you encounter ' 'any problems while running ProTECT' ) inputs = parser . add_mutually_exclusive_group ( required = True ) inputs . add... | This is the main function for ProTECT . |
2,678 | def poll ( self ) : if select . select ( [ self . tn ] , [ ] , [ ] , 0 ) == ( [ self . tn ] , [ ] , [ ] ) : response = urllib . unquote ( self . tn . read_until ( b"\n" ) . decode ( ) ) if self . debug : print "Telnet Poll: %s" % ( response [ : - 1 ] ) return response else : return None | Poll Check for a non - response string generated by LCDd and return any string read . LCDd generates strings for key presses menu events & screen visibility changes . |
2,679 | def module_to_dict ( module , omittable = lambda k : k . startswith ( '_' ) ) : return dict ( [ ( k , repr ( v ) ) for k , v in module . __dict__ . items ( ) if not omittable ( k ) ] ) | Converts a module namespace to a Python dictionary . Used by get_settings_diff . |
2,680 | def run_snpeff ( job , merged_mutation_file , univ_options , snpeff_options ) : work_dir = os . getcwd ( ) input_files = { 'merged_mutations.vcf' : merged_mutation_file , 'snpeff_index.tar.gz' : snpeff_options [ 'index' ] } input_files = get_files_from_filestore ( job , input_files , work_dir , docker = False ) input_f... | Run snpeff on an input vcf . |
2,681 | def paths_in_directory ( input_directory ) : paths = [ ] for base_path , directories , filenames in os . walk ( input_directory ) : relative_path = os . path . relpath ( base_path , input_directory ) path_components = relative_path . split ( os . sep ) if path_components [ 0 ] == "." : path_components = path_components... | Generate a list of all files in input_directory each as a list containing path components . |
2,682 | def run_car_t_validity_assessment ( job , rsem_files , univ_options , reports_options ) : return job . addChildJobFn ( assess_car_t_validity , rsem_files [ 'rsem.genes.results' ] , univ_options , reports_options ) . rv ( ) | A wrapper for assess_car_t_validity . |
2,683 | def align_dna ( job , fastqs , sample_type , univ_options , bwa_options ) : bwa = job . wrapJobFn ( run_bwa , fastqs , sample_type , univ_options , bwa_options , disk = PromisedRequirement ( bwa_disk , fastqs , bwa_options [ 'index' ] ) , memory = univ_options [ 'java_Xmx' ] , cores = bwa_options [ 'n' ] ) sam2bam = jo... | A wrapper for the entire dna alignment subgraph . |
2,684 | def run_bwa ( job , fastqs , sample_type , univ_options , bwa_options ) : work_dir = os . getcwd ( ) input_files = { 'dna_1.fastq' : fastqs [ 0 ] , 'dna_2.fastq' : fastqs [ 1 ] , 'bwa_index.tar.gz' : bwa_options [ 'index' ] } input_files = get_files_from_filestore ( job , input_files , work_dir , docker = False ) gz = ... | Align a pair of fastqs with bwa . |
2,685 | def bam_conversion ( job , samfile , sample_type , univ_options , samtools_options ) : work_dir = os . getcwd ( ) input_files = { sample_type + '.sam' : samfile } input_files = get_files_from_filestore ( job , input_files , work_dir , docker = True ) bamfile = '/' . join ( [ work_dir , sample_type + '.bam' ] ) paramete... | Convert a sam to a bam . |
2,686 | def fix_bam_header ( job , bamfile , sample_type , univ_options , samtools_options , retained_chroms = None ) : if retained_chroms is None : retained_chroms = [ ] work_dir = os . getcwd ( ) input_files = { sample_type + '.bam' : bamfile } input_files = get_files_from_filestore ( job , input_files , work_dir , docker = ... | Fix the bam header to remove the command line call . Failing to do this causes Picard to reject the bam . |
2,687 | def add_readgroups ( job , bamfile , sample_type , univ_options , picard_options ) : work_dir = os . getcwd ( ) input_files = { sample_type + '.bam' : bamfile } get_files_from_filestore ( job , input_files , work_dir , docker = True ) parameters = [ 'AddOrReplaceReadGroups' , 'CREATE_INDEX=false' , 'I=/data/' + sample_... | Add read groups to the bam . |
2,688 | def weekday ( cls , year , month , day ) : return NepDate . from_bs_date ( year , month , day ) . weekday ( ) | Returns the weekday of the date . 0 = aaitabar |
2,689 | def monthrange ( cls , year , month ) : functions . check_valid_bs_range ( NepDate ( year , month , 1 ) ) return values . NEPALI_MONTH_DAY_DATA [ year ] [ month - 1 ] | Returns the number of days in a month |
2,690 | def itermonthdays ( cls , year , month ) : for day in NepCal . itermonthdates ( year , month ) : if day . month == month : yield day . day else : yield 0 | Similar to itermonthdates but returns day number instead of NepDate object |
2,691 | def itermonthdays2 ( cls , year , month ) : for day in NepCal . itermonthdates ( year , month ) : if day . month == month : yield ( day . day , day . weekday ( ) ) else : yield ( 0 , day . weekday ( ) ) | Similar to itermonthdays2 but returns tuples of day and weekday . |
2,692 | def monthdatescalendar ( cls , year , month ) : weeks = [ ] week = [ ] for day in NepCal . itermonthdates ( year , month ) : week . append ( day ) if len ( week ) == 7 : weeks . append ( week ) week = [ ] if len ( week ) > 0 : weeks . append ( week ) return weeks | Returns a list of week in a month . A week is a list of NepDate objects |
2,693 | def monthdayscalendar ( cls , year , month ) : weeks = [ ] week = [ ] for day in NepCal . itermonthdays ( year , month ) : week . append ( day ) if len ( week ) == 7 : weeks . append ( week ) week = [ ] if len ( week ) > 0 : weeks . append ( week ) return weeks | Return a list of the weeks in the month month of the year as full weeks . Weeks are lists of seven day numbers . |
2,694 | def monthdays2calendar ( cls , year , month ) : weeks = [ ] week = [ ] for day in NepCal . itermonthdays2 ( year , month ) : week . append ( day ) if len ( week ) == 7 : weeks . append ( week ) week = [ ] if len ( week ) > 0 : weeks . append ( week ) return weeks | Return a list of the weeks in the month month of the year as full weeks . Weeks are lists of seven tuples of day numbers and weekday numbers . |
2,695 | def run_somaticsniper_with_merge ( job , tumor_bam , normal_bam , univ_options , somaticsniper_options ) : spawn = job . wrapJobFn ( run_somaticsniper , tumor_bam , normal_bam , univ_options , somaticsniper_options , split = False ) . encapsulate ( ) job . addChild ( spawn ) return spawn . rv ( ) | A wrapper for the the entire SomaticSniper sub - graph . |
2,696 | def run_somaticsniper ( job , tumor_bam , normal_bam , univ_options , somaticsniper_options , split = True ) : if somaticsniper_options [ 'chromosomes' ] : chromosomes = somaticsniper_options [ 'chromosomes' ] else : chromosomes = sample_chromosomes ( job , somaticsniper_options [ 'genome_fai' ] ) perchrom_somaticsnipe... | Run the SomaticSniper subgraph on the DNA bams . Optionally split the results into per - chromosome vcfs . |
2,697 | def run_somaticsniper_full ( job , tumor_bam , normal_bam , univ_options , somaticsniper_options ) : work_dir = os . getcwd ( ) input_files = { 'tumor.bam' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam' ] , 'tumor.bam.bai' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam.bai' ] , 'normal.bam' : normal_bam [ 'normal_dna_fix_pg_s... | Run SomaticSniper on the DNA bams . |
2,698 | def filter_somaticsniper ( job , tumor_bam , somaticsniper_output , tumor_pileup , univ_options , somaticsniper_options ) : work_dir = os . getcwd ( ) input_files = { 'tumor.bam' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam' ] , 'tumor.bam.bai' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam.bai' ] , 'input.vcf' : somaticsnip... | Filter SomaticSniper calls . |
2,699 | def run_pileup ( job , tumor_bam , univ_options , somaticsniper_options ) : work_dir = os . getcwd ( ) input_files = { 'tumor.bam' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam' ] , 'tumor.bam.bai' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam.bai' ] , 'genome.fa.tar.gz' : somaticsniper_options [ 'genome_fasta' ] , 'genome.f... | Runs a samtools pileup on the tumor bam . |
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