Search FDA adverse event reports (FAERS). Args: drug: Drug name to search for reaction: Adverse reaction term to search for

Validate that required dependencies are installed.

Append to with automatic attribute injection.

Get OncoKB annotation for a specific variant. Fetches clinical annotation including oncogenicity, mutation effect, and therapeutic implicatio

Get OncoKB summary for multiple genes. Fetches gene annotations from the curated genes list and aggregates results into a markdown table show

Make API call with error handling and exponential backoff retry. Args: url: API endpoint URL params: Query parameters

Print verbose logging messages.

Analyze protein interaction network using ToolUniverse tools. This function implements a 4-phase workflow: 1. Identifier mapping (STRING

Calculate delay for the next retry attempt. Args: attempt: Current attempt number (0-based) config: Retry configuration Retu

Interpret a SNP by aggregating GWAS evidence from multiple sources. Args: rs_id: dbSNP rs identifier (e.g., 'rs7903146') inc

Make a request to the OpenFDA API with retry logic and caching. Args: endpoint: Full URL to the OpenFDA endpoint params: Que

Search variants using the MyVariant.info API with optional cBioPortal and OncoKB summaries.

Make an API request with error handling and retries. Args: endpoint: API endpoint path params: Query paramet

Run PCA on a genotype matrix (0/1/2/-1 encoding). Missing values (-1) are mean-imputed per variant. Returns: coords: (n_samples, n_c

Get clinical annotation for a specific variant. Provides variant-level therapeutic, diagnostic, and prognostic information with evide

Make a request to the NCI CTS API with proper authentication. Args: url: Full URL to the CTS API endpoint method: HTTP metho

Helper function to get reverse complement of a sequence.

Run a test function and capture result.

Sanitize user input to prevent injection attacks. Args: value: Input string to sanitize max_length: Maximum allowed length

Search FDA device adverse event reports (MAUDE). Args: device: Device name to search for manufacturer: Manufacturer name

Search FDA drug product labels (SPL). Args: name: Drug name to search for indication: Search for drugs indicated for this co

Safely traverse nested dicts, returning None if any key is missing.

Check if request is allowed under rate limit. Args: key: Identifier for rate limit bucket Returns: Tuple of

Classify variant type based on ref/alt alleles.

Convert PDF to images using PyMuPDF.

Helper to create a JSON stream from data

Convert EMUs (English Metric Units) to inches.

Get comprehensive annotation for a specific gene. Provides gene-level information including: - Oncogene/TSG classification -

Predicts mean and variance for a new set of points X using the GP.

Sanitize a gene symbol for API calls. Args: gene: The gene symbol to sanitize Returns: Sanitized gene symbol in uppercase wi

Validate input parameters for variant prediction. Args: chromosome: Chromosome identifier position: Genomic position refe

Compute comprehensive statistics for a list of variants.

Format DICOM values for display.

Generate synthetic scRNA-seq count data with known cell types and conditions. Returns: adata: AnnData object with counts, cell_type, and

Get drug information from MyChem.info. Args: drug_id_or_name: Drug ID (DrugBank, ChEMBL, etc.) or name output_json: Return JSON i

Get detailed shortage information for a specific drug. Args: drug: Generic or brand name of the drug api_key: Optional OpenF

Fetch and aggregate variant annotations from external sources. Args: variant_id: The variant identifier (rsID or HGVS)

Get summary statistics for a gene across cBioPortal. Args: gene: Gene symbol (e.g., "BRAF") max_studies: Maximum numb

Get summary statistics for a metric. Args: name: Metric name Returns: Summary statistics or None if metric not found

Fetch variant data from TCGA/GDC. Args: variant_id: Can be gene AA change (e.g., "BRAF V600E") or genomic coordinates

Load a medical image using SimpleITK. Args: image_path: Path to the image file Returns: SimpleITK I

Merge all API results into a unified structure. api_results keys: gwas_catalog, open_targets, open_targets_credsets, p

Search ClinicalTrials.gov for clinical trials.

Convert to dictionary for JSON serialization.

Validate that required dependencies are installed.

Compute IBS (0, 1, or 2) between two diploid genotype calls. Handles haploid calls on X/Y/MT (single character).

Import scanpy lazily with a clear user-facing error.

Load demo VCF + map for reuse.

Return an RDKit Mol object or an error string.

Extract local name from an IRI (after last # or /).

Convert a value to float, returning None on failure.

Update report file with new section.

Update report file with new section.

Append a line to 'lines', avoiding consecutive blank lines. :param lines: The running list of lines to which we add. :param line: The line to

Calculate ICI Response Score.

Compare all GWAS studies for a specific trait. Args: tu: ToolUniverse instance trait: Disease or trait name (e.g., "type 2 d

Complete text using the specified model with appropriate API.

Format with specific number of decimal places.

Generate synthetic RNA-seq count data with known DE genes.

Get user-friendly instructions for obtaining and setting the API key. Returns: Formatted string with instructions

Get the appropriate handler class for a domain. Args: domain: The domain name ('article', 'trial', 'variant', 'gene', 'drug', 'disease',

Get detailed drug approval information for a specific application. Args: application_number: NDA or BLA application number

Get detailed drug recall information for a specific recall. Args: recall_number: FDA recall number api_key: Optional OpenFD

Get a DOM element by tag and identifier. Finds an element by either its line number in the original file or by matching attr

Check if an HTTP status code should trigger a retry. Args: status_code: HTTP status code config: Retry configuration Returns

Metabolomics research analysis pipeline. Args: metabolite_list: List of metabolite names (e.g., ["glucose", "lactate"]) stud

Parse a genetic data file and extract PGx-relevant SNPs. Uses the shared parser from clawbio.common.parsers for file reading and format detec

Convert various input formats to lists. Handles: - JSON arrays: '["item1", "item2"]' -> ['item1', 'item2'] - Comma-separated:

Truncate text to a maximum length with ellipsis.

Validate API key format. Args: api_key: API key string Returns: Validated API key or None

Validate that required dependencies are installed.

Inject RSID, author, and date attributes into DOM nodes where applicable. Adds attributes to elements that support them: - w:r: gets

Build a complete gene result dict for report testing.

Given a request of biotype and query, returns the best matching Entity. If API call fails or returns 0 results, then None is returned. Exampl

Calculate similarity metrics between two images. Args: image1: First image image2: Second image Ret

Compute the composite HEIM Equity Score (0-100).

Compute Identity By State between two genotype dictionaries. Returns: ibs_score: float in [0, 1] n_overlap: number of shared rsID

Discover genes associated with a trait/disease from GWAS data. This function: 1. Searches GWAS Catalog for trait associations 2. Fil

Execute a GraphQL query against the Open Targets Platform API. Args: query: GraphQL query string variables: Optional diction

Extract a row from a clinical annotation.

Filter a list of mutations. Args: mutations: List of mutation objects with protein_change attribute Returns:

Format as integer count (no decimals).