biocommons.seqrepo 0.2.1

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.

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.

Features

• Space-efficient storage of sequences within a release and across releases

• Bandwidth-efficient transfer incremental updates

• Fast fetching of sequence slices on chromosome-scale sequences

• Provenance data regarding sequence sources and accessions

• Precomputed digests that may be used as sequence aliases

For more information, see doc/design.rst.

Expected deployment cases

• Local access via Python package, using a repo rsync’d from a remote source or loaded locally

• Docker image with REST interface

Installation

seqrepo has been tested only on Ubuntu 14.04 and 16.04. It requires separate installation of the tabix package. It requires sqlite3 >= 3.8.0, which likely precludes early Ubuntu distributions.

On Ubuntu 16.04:

sudo apt install tabix
pip install seqrepo

Command line usage

seqrepo includes a command line interface for loading, fetching, and exporting sequences.

Loading

$ SEQREPO_ROOT=/opt/seqrepo/data/2016/0818

$ seqrepo -d $SEQREPO_ROOT init

$ seqrepo -v -d $SEQREPO_ROOT load-fasta -n me fasta1.gz fasta2.gz fasta3.gz

$ seqrepo -v -d $SEQREPO_ROOT status
seqrepo 0.1.0
root directory: /opt/seqrepo/data/2016/0818, 0.2 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 3 files, 33080 sequences, 110419437 residues
aliases: 165481 aliases, 165481 current, 5 namespaces, 33080 sequences

Exporting all sequences

$ seqrepo -v -d $SEQREPO_ROOT export | head
>me:sequence1 seguid:EqjiLe... md5:04e8c3c75... sha512:000a70c470f6... sha1:12a8e22d...
GTACGCCCCCTCCCCCCGTCCCTATCGGCAGAACCGGAGGCCAACCTTCGCGATCCCTTGCTGCGGGCCCGGAGATCAAACGTGGCCCGCCCCCGGCAGG
GCACAGCGCGCTGGGCAACCGCGATCCGGCGCCGGACTGGAGGGGTCGATGCGCGGCGCGCTGGGGCGCACAGGGGACGGAGCCCGGGTCTTGCTCCCCA

API Usage

$ seqrepo -v -d $SEQREPO_ROOT shell

In [10]: %time sr.fetch("NC_000001.10", start=6000000, end=6000200)
CPU times: user 4 ms, sys: 0 ns, total: 4 ms
Wall time: 492 µs
Out[10]: 'GGACAACAGAGGATGAGGTGGGGCCAGCAGAGGGACAGAGAAGAGCTGCCTGCCCTGGAACAGGCAGAAAGCATCCCACGTGCAAGAAAAAGTAGGCCAGCTAGACTTAAAATCAGAACTACCGCTCATCAAAAGATAGTGTAACATTTGGGGTGCTATAATTTTAACATGTCCCCCAAAAGGCATGTGTTGGAAATTTA'


# iterate over unique sequences:
for srec, arec in sr:
    pprint.pprint(srec)
    pprint.pprint(arec)

# results in records like:
{'added': '2016-08-18 17:40:49',
 'alpha': 'ACGT',
 'len': 2627,
 'relpath': '2016/08/18/1740/1471542046.008535.fa.bgz',
 'seq': 'GTACGCCC...',
 'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518'}

and

[{'added': '2016-08-18 17:40:49',
  'alias': '04e8c3c753dad9c19741cdf81ec2b3d5',
  'is_current': 1,
  'namespace': 'md5',
  'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'seqalias_id': 144388},
 {'added': '2016-08-18 17:40:49',
  'alias': 'EqjiLeXFeeBT6LIMnbCFQxNqHD8',
  'is_current': 1,
  'namespace': 'seguid',
  'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'seqalias_id': 144389},
 {'added': '2016-08-18 17:40:49',
  'alias': '12a8e22de5c579e053e8b20c9db08543136a1c3f',
  'is_current': 1,
  'namespace': 'sha1',
  'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'seqalias_id': 144387},
 {'added': '2016-08-18 17:40:49',
  'alias': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'is_current': 1,
  'namespace': 'sha512',
  'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'seqalias_id': 144386},
 {'added': '2016-08-18 17:40:49',
  'alias': 'NM_013305.4',
  'is_current': 1,
  'namespace': 'ncbi',
  'seq_id': '000a70c470f637d6e3a76497aac3eabc4f7816be8fe03d15bdbd3504655fd3f6ddb2609aeef5e0edfbea16ae8ab181b704c4bfb3cd4328c57a895e02fe5ab518',
  'seqalias_id': 144390}]

Fetching existing sequence repositories

TO BE WRITTEN

(General idea: Distribute repository with snapshots via rsync server from public site for manual installation, and use the same source to seed a docker container.)