pysradb

library2.5.1pypypi✓ verified 82d ago

pysradb is a Python tool for querying and downloading metadata and data from NCBI SRA (Sequence Read Archive), ENA (European Nucleotide Archive), and GEO (Gene Expression Omnibus). It provides CLI and Python interfaces to search experiments, samples, runs, and download FASTQ/SRA files. Current version 2.5.1 (released 2025, active development).

data

pip install pysradb

package ↗homepage ↗

INSTALL

IMPORT

SIG · PYSRADB

pysradb

datapythonv2.5.1

Install

9.2s avg

Import

—

Disk

182MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.5.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.000s · 183.8MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 9.2s · import 0.000s · 176MB

182MB installed

● package 182MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

SRAweb

✓ from pysradb import SRAweb

✗ from pysradb import SRA database

SRAdb

✓ from pysradb import SRAdb

GEOdb

✓ from pysradb import GEOdb

Initialize the SRA database and search for studies related to a gene/term.

from pysradb import SRA database db = SRA database() df = db.search('SMAD4', n=5) print(df[['study_accession', 'experiment_title', 'sample_accession']].head())

pysradb --version

Debug

Known issues

breakingIn v2.0.0, the API was completely rewritten. The old SRA class and CLI commands are replaced. Scripts using pysradb <2.0.0 will break.

fix

Migrate to new API: use 'from pysradb import SRA database' and new method signatures.

affects: <2.0.0

gotchaThe '.search()' method may return empty results if the query is too specific or server timeout. Always check if the returned DataFrame is empty.

fix

Wrap search in a try-except or check df.empty after calling search.

affects: all

deprecatedThe 'sradb' command-line entry point is deprecated in favor of 'pysradb' CLI. Using 'sradb' will emit a warning and may be removed in future.

fix

Use 'pysradb' instead of 'sradb' for CLI commands.

affects: >=2.3.0

Upgrade

Version history

2.5.1latest on PyPI · released Oct 20, 2025

Audit

Dependencies

pandasrequiredData manipulation for metadata tables

requestsrequiredHTTP requests to NCBI/ENA APIs

tqdmrequiredProgress bars for downloads

Agent activity

13 hits · last 30 days

node

Resources

packagehttps://pypi.org/project/pysradb/ ↗

homepagehttps://saket-choudhary.me/pysradb ↗