biodownloader 0.1.0

Python toolkit for fetching GEO / SRA / ENA metadata into structured tables.

BioDownloader Lightweight Python tools for retrieving structured metadata from GEO, SRA, and ENA.

Features • Fetch GEO metadata (GSE/GSM) • Retrieve SRA RunInfo via NCBI API • Access ENA run‑level metadata • Optional automated GEO–SRA merging • Includes a command‑line client (biofetch)

Installation pip install biodownloader

Usage Examples GEO from biodownloader import fetch_geo_series geo = fetch_geo_series("GSE181294") SRA from biodownloader import fetch_sra_bioproject sra = fetch_sra_bioproject("PRJNA730495") ENA from biodownloader import fetch_ena_accession ena = fetch_ena_accession("SRR23080510") GEO–SRA merge from biodownloader import fetch_and_merge_geo_sra merged = fetch_and_merge_geo_sra("GSE181294", "PRJNA730495")

CLI biofetch --source geo --id GSE181294 --out output.csv biofetch --source sra --id PRJNA730495 --out sra.csv biofetch --source ena --id SRR23080510 --out ena.tsv

Limitations • When GSM identifiers do not match between GEO and SRA, merged tables may be empty. • GEO HTML structures may evolve and require parser updates.

License MIT License.