Generate the ancestry PCA markdown report.

Get a language model instance based on the specified model name and source. This function supports models from OpenAI, Azure OpenAI, Anthropi

Get the global endpoint registry.

Get variant details from MyVariant.info using the variant identifier. The identifier can be a full HGVS-style string (e.g. "chr7:g.140453136

Get variant information by ID. Args: species: Species name variant_id: Variant identifier (e.g., 'rs699')

Fetch variant data from cBioPortal. Args: gene_aa: Gene and AA change format (e.g., "BRAF V600E")

Load alignment with auto-format detection.

Parse a CSV/TSV population map or infer from sample ID prefixes. Accepts files with columns like sample_id/population (flexible naming).

Perform a research lookup for the given query.

Parse a VCF file into a genotype matrix. Delegates to ``clawbio.common.parsers.parse_vcf_matrix``. Returns: samples: list of sample

Map phenotype description to GUIDELINES rec key.

Preprocess an image with denoising and normalization. Args: image: Input SimpleITK image denoise: Whether to

Record a metric to the global collector. Note: This is a no-op if BIOMCP_METRICS_ENABLED is not set to true. Args: name: Metric name

Set item in cache with TTL.

SHA-256 checksum — delegates to shared checksums module.

Comprehensive systems biology and pathway analysis pipeline. Args: gene_list: List of gene symbols for pathway enrichment pr

Count alt alleles in a diploid genotype given ref/alt annotation. Returns 0 (hom ref), 1 (het), 2 (hom alt), or None if ambiguous. Skips ambi

Generate random 8-character hex ID for para/durable IDs. Values are constrained to be less than 0x7FFFFFFF per OOXML spec: - paraId must be <

Get rdf:about attribute from an element.

Standardize drug names using fuzzy matching against DDInter database. Parameters ---------- drug_name : str Original drug na

Standardize drug names for FDA API queries.

Update report with new section.

Update report with new section.

Compute a metric across all genes in a group. Args: gene_files: list from discover_gene_files() metric_func: function that takes

Build a polygenic risk score by extracting genome-wide significant SNPs. This function queries GWAS databases to find all variants significa

Format a count with appropriate singular/plural label.

Format file size in human-readable format.

Generate synthetic BED DataFrame (narrowPeak format).

Generate a full markdown report.

Generate a concise text summary for stdout.

Get detailed drug label information by set ID. Args: set_id: Label set ID sections: Specific sections to retrieve (default:

Get shape of nested list.

Get a session by ID or the current session.

Generate a human-readable summary of the results.

Inject database links into variant data. Args: variants: List of variant dictionaries from MyVariant.info API Returns:

Insert after with automatic attribute injection.

Check if an exception should trigger a retry. Args: exc: The exception that occurred config: Retry configuration Returns:

Validate if a string is a valid gene symbol. Args: gene: The gene symbol to validate Returns: True if the gene symbol appear

Load AIMs panel. Returns (markers, population_names).

Load tree from file.

Perform meta-analysis for a specific locus across studies. Args: tu: ToolUniverse instance rs_id: SNP rs identifier (e.g., "

Record a metric sample. Args: name: Metric name duration: Duration in seconds success: Whether operation

Full ancestry PCA pipeline with report output.

Search for diseases in the NCI CTS database. This provides access to NCI's controlled vocabulary of cancer conditions used in clinical t

Search for interventions in the NCI CTS database. Args: name: Intervention name to search for (partial match) intervention_t

Search for patents. Args: query: Query dictionary (see PatentSearch API docs for syntax) fields: Fields to r

Convert a JSON string or already-parsed data (dict or list) into a simple Markdown representation. :param data: The input data, either as a J

Validate date string format. Args: date_str: Date string in YYYY-MM-DD format Returns: Validated date string or None

Validate and sanitize drug name input. Args: drug: Drug name to validate Returns: Validated drug name or None

Verify the result has expected structure.

Use LLM to repair and format JSON strings Parameters: - json_string: JSON string to format - api_key: OpenAI API key - base_

Retrieves details for a single article given its identifier. Parameters: - call_benefit: Define and summarize why this function is being

Searches for articles across PubMed and preprint servers. Parameters: - call_benefit: Define and summarize why this function is being ca

Create the final test result dictionary.

Get rdf:resource attribute from an element.

Parse a genetic data file via the shared parser. Returns: genotypes: {rsid: genotype_str} positions: {rsid: {"chrom": str, "pos":

Enforce minimum interval between API requests.

Update report with new section.

Update report with new section.

Acquire tokens from the bucket.

MCP Endpoint: Execute a tool.

Compute pairwise FST between all population pairs. Uses Nei's GST approach (robust with small samples): Per-site: FST = (HT - HS) / HT

Configure the agent with the initial system prompt and workflow. Args: self_critic: Whether to enable self-critic mode

Detect technique from ASM structure.

Displays a message from the user or assistant with different styling. Supports displaying both text and image URLs for the user.

Displays a message from the user or assistant with different styling. Supports displaying both text and image URLs for the user.

Displays a message from the user or assistant with different styling. Supports displaying both text and image URLs for the user.

Displays a message from the user or assistant with different styling. Supports displaying both text and image URLs for the user.

Estimate ancestry composition using maximum likelihood + EM. For each AIM, computes P(genotype | population freq) using binomial genotype mod

Extract a row from a drug label.

Extract text content from all slides in a PowerPoint presentation. Args: pptx_path: Path to the PowerPoint file prs: Optional Pre

Fetch a single article from Europe PMC by DOI.

Fetch SRA run information for all samples in a GEO study. Args: geo_id: GEO accession (e.g., 'GSE110004') bioproject: Option

Format as percentage. Args: value: Float value (0-1 or 0-100) n_decimals: Decimal places include_sign: Include % sign in

Generate synthetic probe manifest with chromosome and position.

Generate a full markdown report from resolved variant + merged results.

Get detailed information for a specific adverse event report. Args: report_id: Safety report ID api_key: Optional OpenFDA AP

Get all registered endpoints. Returns: Dictionary mapping endpoint keys to their metadata

Get a value from cache if not expired.