Metadata-Version: 2.4
Name: biodownloader
Version: 0.1.0
Summary: Python toolkit for fetching GEO / SRA / ENA metadata into structured tables.
Author: Kiarash Babaei
License: MIT
Keywords: ENA,GEO,NGS,RNA-seq,SRA,bioinformatics,metadata
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Requires-Dist: pandas>=2.0.0
Requires-Dist: requests>=2.31.0
Description-Content-Type: text/markdown

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.
