biocommons.seqrepo 0.3.0a1

Python package for writing and reading a local collection of biological sequences. The repository is non-redundant, compressed, and journalled, making it efficient to store and transfer incremental snapshots.

biocommons.seqrepo

Python package for writing and reading a local collection of biological sequences. The repository is non-redundant, compressed, and journalled, making it efficient to store and transfer multiple snapshots.

Released under the Apache License, 2.0.

Features

• Timestamped snapshots of read-only sequence repository

• Space-efficient storage of sequences within a single snapshot and across snapshots

• Bandwidth-efficient transfer incremental updates

• Fast fetching of sequence slices on chromosome-scale sequences

• Precomputed digests that may be used as sequence aliases

• Mappings of external aliases (i.e., accessions or identifiers like NM_013305.4) to sequences

The above features are achieved by storing sequences non-redundantly and compressed, using an add-only journalled filesystem structure within a single snapshot, and by using hard links across snapshots. Each sequence is associated with a namespaced alias such as <seguid,rvvuhY0FxFLNwf10FXFIrSQ7AvQ>, <ncbi,NP_004009.1>, <gi,5032303>, <ensembl-75ENSP00000354464>, <ensembl-85,ENSP00000354464.4> (all of which refer to the same sequence). Block gzipped format (BGZF)) enables pysam to provide fast random access to compressed sequences.

For more information, see doc/design.rst.

Deployments Scenarios

• Available now: Local read-only archive, mirrored from public site, accessed via Python API (see Mirroring documentation)

• Available now: Local read-write archive, maintained with command line utility and/or API (see Command Line Interface documentation).

• Planned: Docker-based data-only container that may be linked to application container

• Planned: Docker image that provides REST interface for local or remote access

Requirements

Reading a sequence repository requires several packages, all of which are available from pypi. Installation should be as simple as pip install biocommons.seqrepo.

Writing sequence files also requires bgzip, which provided in the htslib repo. Ubuntu users should install the tabix package with sudo apt install tabix.

Development and deployments are on Ubuntu. Other systems may work but are not tested. Patches to get other systems working would be welcomed.

Quick Start

On Ubuntu 16.04:

$ sudo apt install -y python3-dev gcc zlib1g-dev tabix
$ pip install seqrepo
$ seqrepo pull -i 20160906
$ seqrepo show-status -i 20160906
seqrepo 0.2.3.post3.dev8+nb8298bd62283
root directory: /usr/local/share/seqrepo/20160906, 7.9 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 773587 sequences, 93051609959 residues, 192 files
aliases: 5579572 aliases, 5480085 current, 26 namespaces, 773587 sequences

$ seqrepo start-shell -i 20160906
In [1]: sr["NC_000001.11"][780000:780020]
Out[1]: 'TGGTGGCACGCGCTTGTAGT'

# N.B. The following output is edited
$ seqrepo export -i 20160906 | head -n100
>sha1:9a2acba3dd7603f... seguid:mirLo912A/MppLuS1cUyFMduLUQ ensembl-85:GENSCAN00000003538 sh:---7nAwbv5Fs2Ml2-k3X6Zvj-6ZcjeD3 ...
MDSPLREDDSQTCARLWEAEVKRHSLEGLTVFGTAVQIHNVQRRAIRAKGTQEAQAELLCRGPRLLDRFLEDACILKEGRGTDTGQHCRGDARISSHLEA
SGTHIQLLALFLVSSSDTPPSLLRFCHALEHDIRYNSSFDSYYPLSPHSRHNDDLQTPSSHLGYIITVPDPTLPLTFASLYLGMAPCTSMGSSSMGIFQS
QRIHAFMKGKNKWDEYEGRKESWKIRSNSQTGEPTF
>sha1:ca996b263102b1... seguid:yplrJjECsVqQufeYy0HkDD16z58 ncbi:XR_001733142.1 sh:---WkVUs3IT3_ZZM-ReDjypLo6d_vJx6 gi:1034683989
TTTACGTCTTTCTGGGAATTTATACTGGAAGTATACTTACCTCTGTGCAAAATTGCAAATATATAAGGTAATTCATTCCAGCATTGCTTATATTAGGTTG
AACTATGTAACATTGACATTGATGTGAATCAAAAATGGTTGAAGGCTGGCAGTTTCATATGATTCAGCCTATAATAGCAAAAGATTGAAAAAATCCATTA
ATACAGTGTGGTTCAAAAAAATTTGTTGTATCAAGGTAAAATAATAGCCTGAATATAATTAAGATAGTCTGTGTATACATCGATGAAAACATTGCCAATA

See Installation and Mirroring for more information.