test.jsonl

{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"在只读夹具 PX-41 里精确查找人工基因 fxg01，不要跳转当前视图。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_gene_by_name","arguments":{"name":"fxg01","navigate_to_gene":false}}}]}],"tools":[{"type":"function","function":{"name":"find_gene_by_name","description":"Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_available_tools","description":"List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.","parameters":{"type":"object","properties":{"category":{"type":"string","default":null},"include_details":{"type":"boolean","default":false},"format":{"type":"string","enum":["summary","detailed"],"default":"summary"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_annotation_file","description":"Load annotation files (GFF/BED/GTF) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","gff","bed","gtf"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_sequence","description":"Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to_position instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"+"},"format":{"type":"string","enum":["raw","fasta","genbank"],"default":"raw"},"include_annotations":{"type":"boolean","default":false},"max_length":{"type":"number","default":1000000,"maximum":10000000},"clientId":{"type":"string","default":"default"}},"required":["start","end"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-0def6eec6d4d1fd526bb","scenario_family_id":"fixture:v2:single:find_gene_by_name:holdout:0:5","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"核对 PX-72：列出 px_core_B:6007-6099 内的 CDS 注释，最多 7 条。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_annotations","arguments":{"chromosome":"px_core_B","start":6007,"end":6099,"type":"CDS","limit":7}}}]}],"tools":[{"type":"function","function":{"name":"list_annotations","description":"List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_annotation_history","description":"Retrieve change history for a specific annotation or the entire genome","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"limit":{"type":"number","default":50},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"export_protein_fasta","description":"Export protein sequences translated from CDS in FASTA format","parameters":{"type":"object","properties":{"filename":{"type":"string","default":"proteins.fasta"},"auto_save":{"type":"boolean","default":false},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","yeast_mitochondrial","mold_mitochondrial","bacterial"],"default":"standard"},"include_gene_names":{"type":"boolean","default":true},"include_locus_tags":{"type":"boolean","default":true},"include_products":{"type":"boolean","default":true},"include_ec_numbers":{"type":"boolean","default":true},"selection_type":{"type":"string","enum":["all","selected","current_view","by_gene_name","by_locus_tag","by_function"],"default":"all"},"gene_names":{"type":"array","items":{"type":"string"}},"locus_tags":{"type":"array","items":{"type":"string"}},"function_keywords":{"type":"array","items":{"type":"string"}},"wrap_length":{"type":"integer","minimum":0,"maximum":200,"default":80}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_coding_sequence","description":"Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.","parameters":{"type":"object","properties":{"gene_name":{"type":"string"},"include_upstream":{"type":"number","default":0,"minimum":0},"include_downstream":{"type":"number","default":0,"minimum":0},"format":{"type":"string","enum":["raw","fasta","genbank"],"default":"raw"},"clientId":{"type":"string","default":"default"}},"required":["gene_name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_operons","description":"Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"export_cds_fasta","description":"Export coding sequences (CDS) in FASTA format","parameters":{"type":"object","properties":{"filename":{"type":"string","default":"cds_sequences.fasta"},"auto_save":{"type":"boolean","default":false},"include_gene_names":{"type":"boolean","default":true},"include_locus_tags":{"type":"boolean","default":true},"include_products":{"type":"boolean","default":true},"selection_type":{"type":"string","enum":["all","selected","current_view","by_gene_name","by_locus_tag"],"default":"all"},"gene_names":{"type":"array","items":{"type":"string"}},"locus_tags":{"type":"array","items":{"type":"string"}},"wrap_length":{"type":"integer","minimum":0,"maximum":200,"default":80}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-7f1f63536f04f547bc6d","scenario_family_id":"fixture:v2:single:list_annotations:holdout:0:27","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"请从 undefined 的固定数据中取回 px003 的完整注释记录（样本 PX-103）。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"get_annotation","arguments":{"identifier":"px003","full_details":true}}}]}],"tools":[{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_annotations","description":"Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.","parameters":{"type":"object","properties":{"query":{"type":"string"},"chromosome":{"type":"string"},"type":{"type":"string"},"fields":{"type":"array","items":{"type":"string"}},"limit":{"type":"number","default":50},"clientId":{"type":"string","default":"default"}},"required":["query"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"create_annotation","description":"Create a new user-defined annotation","parameters":{"type":"object","properties":{"type":{"type":"string","enum":["gene","CDS","mRNA","tRNA","rRNA","promoter","regulatory","terminator","ribosome_binding_site","primer","other"]},"name":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"integer"},"end":{"type":"integer"},"strand":{"type":"integer","enum":[1,-1],"default":1},"description":{"type":"string"},"product":{"type":"string"},"codonStart":{"type":"integer","enum":[1,2,3],"default":1},"translTable":{"type":"integer","default":11},"translation":{"type":"string"},"anticodon":{"type":"string"},"regulatoryClass":{"type":"string"},"sequence":{"type":"string"},"direction":{"type":"string","enum":["forward","reverse"]},"qualifiers":{"type":"object"},"clientId":{"type":"string","default":"default"}},"required":["type","name","chromosome","start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_annotations","description":"List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_nearby_features","description":"Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position, genes around a location, or what is nearby a genomic coordinate. NOT the same as navigate_to_position which moves the view, or list_annotations which lists all annotations in a region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"distance":{"type":"number","default":5000},"featureTypes":{"type":"array","items":{"type":"string"},"default":[]},"clientId":{"type":"string","default":"default"}},"required":["position"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_gene_details","description":"Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"chromosome":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-463439b81c24cf90099b","scenario_family_id":"fixture:v2:single:get_annotation:holdout:0:12","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"为固定寡核苷酸 PX-196 生成反向互补序列，并校验碱基：CGTCCCAGGTATTGTTTCCCGCTCCTTGTG。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"reverse_complement","arguments":{"sequence":"CGTCCCAGGTATTGTTTCCCGCTCCTTGTG"}}}]}],"tools":[{"type":"function","function":{"name":"reverse_complement","description":"Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).","parameters":{"type":"object","properties":{"sequence":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"preserve_case":{"type":"boolean","default":false},"validate_sequence":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_current_state","description":"Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"include_tracks":{"type":"boolean","default":true},"include_data_summary":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"find_gene_by_name","description":"Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"navigate_to_position","description":"Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to \"show\", \"display\", or \"view\" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"position":{"type":"number","minimum":1},"clientId":{"type":"string","default":"default"}},"anyOf":[{"required":["start","end"]},{"required":["position"]},{"required":["start"]}],"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-58c09cc5bdafbde5abe0","scenario_family_id":"fixture:v2:single:reverse_complement:holdout:0:20","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"使用 standard 密码表和第 1 阅读框翻译样本 PX-227：ATGTATAAACTGACCGACGCTTAA；保留终止符。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"translate_dna","arguments":{"dna":"ATGTATAAACTGACCGACGCTTAA","reading_frame":1,"genetic_code":"standard","include_stop_codons":true}}}]}],"tools":[{"type":"function","function":{"name":"translate_dna","description":"Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.","parameters":{"type":"object","properties":{"dna":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","bacterial","archaeal"],"default":"standard"},"include_stop_codons":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["dna"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_sequence","description":"Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to_position instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"+"},"format":{"type":"string","enum":["raw","fasta","genbank"],"default":"raw"},"include_annotations":{"type":"boolean","default":false},"max_length":{"type":"number","default":1000000,"maximum":10000000},"clientId":{"type":"string","default":"default"}},"required":["start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"navigate_to_position","description":"Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to \"show\", \"display\", or \"view\" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"position":{"type":"number","minimum":1},"clientId":{"type":"string","default":"default"}},"anyOf":[{"required":["start","end"]},{"required":["position"]},{"required":["start"]}],"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_annotation_file","description":"Load annotation files (GFF/BED/GTF) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","gff","bed","gtf"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_current_state","description":"Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"include_tracks":{"type":"boolean","default":true},"include_data_summary":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"find_gene_by_name","description":"Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-4e5bda19256b046ee260","scenario_family_id":"fixture:v2:single:translate_dna:holdout:0:1","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"Run the GC quality metric for pinned sequence PX-249, with case normalization enabled: TTTCGGGAGACGCTTGCCCAACCCCGTAT."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"compute_gc","arguments":{"sequence":"TTTCGGGAGACGCTTGCCCAACCCCGTAT","normalize_case":true}}}]}],"tools":[{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_detect_sequence_type","description":"Detect whether a sequence is DNA, RNA, or protein","parameters":{"type":"object","properties":{"sequence":{"type":"string"}},"required":["sequence"],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"search_sequence_motif","description":"Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.","parameters":{"type":"object","properties":{"motif":{"type":"string"},"pattern":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"both"},"max_mismatches":{"type":"number","minimum":0,"default":0},"case_sensitive":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["motif"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"replace_sequence","description":"Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"sequence":{"type":"string"},"strand":{"type":"string","enum":["+","-"],"default":"+"}},"required":["chromosome","start","end","sequence"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-62770589e1252679a92c","scenario_family_id":"fixture:v2:single:compute_gc:train:0:1","supervised_target":"tool_call","turn_index":2}}
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{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."},{"role":"user","content":"Run the GC quality metric for pinned sequence PX-251, with case normalization enabled: CGCCGAGATGCTAATTCTTCACAACCTCAGG."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"compute_gc","arguments":{"sequence":"CGCCGAGATGCTAATTCTTCACAACCTCAGG","normalize_case":true}}}]}],"tools":[{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence","description":"Perform BLAST search on a DNA sequence","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"sequence":{"type":"string"},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"]},"database":{"type":"string","default":"nr"}},"required":["sequence","blastType","database"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_sequence_motif","description":"Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.","parameters":{"type":"object","properties":{"motif":{"type":"string"},"pattern":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"both"},"max_mismatches":{"type":"number","minimum":0,"default":0},"case_sensitive":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["motif"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"replace_sequence","description":"Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"sequence":{"type":"string"},"strand":{"type":"string","enum":["+","-"],"default":"+"}},"required":["chromosome","start","end","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-414957d01ac343bcb50c","scenario_family_id":"fixture:v2:single:compute_gc:train:2:0","supervised_target":"tool_call","turn_index":2}}
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