biocommons.seqrepo

0.6.11 verified Fri May 01 auth: no python

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.

pip install biocommons-seqrepo

Common errors

error ModuleNotFoundError: No module named 'biocommons.seqrepo' ↓

cause Package not installed or installed under a different name.

fix

pip install biocommons-seqrepo

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

cause Outdated version (<0.6.0) or incorrect import path.

fix

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

error ValueError: no sequence found for 'NM_000558' ↓

cause 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.

Warnings

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

fix Upgrade to Python 3.10 or later.

deprecated The 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'.

gotcha SeqRepo 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.

gotcha Accession lookup is case-sensitive. 'NM_000558.4' works, 'nm_000558.4' does not. ↓

fix Ensure correct case for accessions.

gotcha When 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.

Imports

SeqRepo

wrong

from seqrepo import SeqRepo

correct

from biocommons.seqrepo import SeqRepo

top-level package is biocommons.seqrepo, not seqrepo

SeqRepo
wrong
```
from biocommons_seqrepo import SeqRepo
```
correct
```
from biocommons.seqrepo import SeqRepo
```
hyphenated package name maps to biocommons.seqrepo, not underscore

Quickstart

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))