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biocommons-seqrepo

library0.6.11pypypi✓ verified 84d ago

Non-redundant, compressed, journalled, file-based storage for biological sequences. Current version 0.6.11, requires Python >=3.10. Released under Apache 2.0, maintained primarily by the biocommons community. Updates are occasional, with bug fixes and dependency updates.

data

pip install biocommons-seqrepo

github ↗package ↗

INSTALL

IMPORT

SIG · BIOCOMMONS-SEQREPO

biocommons-seqrepo

datapythonv0.6.11

Install

7.0s avg

Import

489ms

Disk

159MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.6.11 · 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 0.504s · 146MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 7.0s · import 0.474s · 160MB

159MB installed

● package 159MB

Code

Verified usage

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

SeqRepo

✓ from biocommons.seqrepo import SeqRepo

✗ from seqrepo import SeqRepo

top-level package is biocommons.seqrepo, not seqrepo

SeqRepo

✓ from biocommons.seqrepo import SeqRepo

✗ from biocommons_seqrepo import SeqRepo

hyphenated package name maps to biocommons.seqrepo, not underscore

Basic usage: create a SeqRepo instance pointing to a local seqrepo data directory and fetch sequences by accession.

from biocommons.seqrepo import SeqRepo # Use a local directory (or set SEQREPO_ROOT_DIR env var) sr = SeqRepo(root_dir="/path/to/seqrepo", writeable=True) # Fetch a sequence by NCBI accession (e.g., NM_000558.4) seq = sr.fetch("NM_000558.4") # returns a SeqRecord print(seq.id, len(seq.seq))

seqrepo --version

Debug

Known issues

breakingPython 3.9 and older are no longer supported since v0.6.11. Requires Python >=3.10.

fix

Upgrade to Python 3.10 or later.

affects: >=0.6.11

deprecatedThe old 'seqrepo' CLI (installed via setup.py) was replaced by a new entry point in v0.6.8. Use 'seqrepo' command directly (installed via pip).

fix

Use 'seqrepo --help' to see CLI commands; no more 'python -m seqrepo'.

affects: >=0.6.8

gotchaSeqRepo instances are read-only by default. To write or update, you must pass writeable=True to the constructor.

fix

Explicitly set writeable=True when creating a SeqRepo for writing.

affects: all

gotchaAccession lookup is case-sensitive. 'NM_000558.4' works, 'nm_000558.4' does not.

fix

Ensure correct case for accessions.

affects: all

gotchaWhen using a remote seqrepo instance (e.g., via rsync), ensure you have proper network access and the remote path is correctly configured via environment variables or constructor arguments.

fix

Set SEQREPO_ROOT_DIR or use the root_dir parameter with the correct path.

affects: all

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'biocommons.seqrepo'

Package not installed or installed under a different name.

fix

pip install biocommons-seqrepo

AttributeError: module 'biocommons.seqrepo' has no attribute 'SeqRepo'

Outdated version (<0.6.0) or incorrect import path.

fix

Upgrade: pip install --upgrade biocommons-seqrepo, then use 'from biocommons.seqrepo import SeqRepo'

ValueError: no sequence found for 'NM_000558'

Accession not present in the local seqrepo data or incorrect version.

fix

Check if the accession exists, include version (e.g., 'NM_000558.4'), and ensure the data directory is up-to-date.

Upgrade

Version history

0.6.11latest on PyPI · released Mar 19, 2025

Audit

Dependencies

psycopg2-binaryoptionalRequired for PostgreSQL-based seqrepo instances (optional if using directory mode only)

biocommons-commonrequiredShared utilities used by seqrepo

typing_extensionsrequiredRequired for type annotations in Python <3.11

Agent activity

12 hits · last 30 days

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OpenAI (training)

Resources

githubhttps://github.com/biocommons/biocommons.seqrepo ↗

packagehttps://pypi.org/project/biocommons-seqrepo/ ↗