brentp/pyfaidx

Description

Samtools provides a function "faidx" (FAsta InDeX), which creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed fasta.

Pyfaidx provides an interface for creating and using this index for fast random access of subsequences in a "pythonic" manner. For example:

class Genome

>>> from pyfaidx import Genome
>>> genome = Genome('T7.fa')
>>> genome['EM_PHG:V01146'][0:10]
EM_PHG:V01146:1-10
TCTCACAGTG

It also provides a command-line script:

cli script: pyfaidx

$ pyfaidx /tmp/hg19.fa -r chr10:1000000-1000010
GGAGGGCTGCA

$ pyfaidx /tmp/hg19.fa -n -r chr10:1000000-1000010
chr10:1000000-1000010
GGAGGGCTGCA

A lower-level Faidx class is also exposed:

class Faidx

>>> from pyfaidx import Faidx
>>> fa = Faidx('T7.fa')
>>> fa.build('T7.fa', 'T7.fa.fai')
>>> fa.index
{'EM_PHG:V01146': {'lenc': 60, 'lenb': 61, 'rlen': 39937, 'offset': 40571}, 'EM_PHG:GU071091': {'lenc': 60, 'lenb': 61, 'rlen': 39778, 'offset': 74}}
>>> fa.fetch('EM_PHG:V01146', 1, 10)
EM_PHG:V01146
TCTCACAGTG
>>> x = fa.fetch('EM_PHG:V01146', 100, 120)
>>> x
EM_PHG:V01146
GGTTGGGGATGACCCTTGGGT
>>> x.name
EM_PHG:V01146
>>> x.seq
GGTTGGGGATGACCCTTGGGT

If the FASTA file is not indexed, when Faidx is initialized the build method will automatically run, producing "filename.fa.fai" where "filename.fa" is the original FASTA file.
Start and end coordinates are 1-based.

Installation

This package is tested under Python 3.3, 3.2, 2.7, 2.6, and pypy.

pip install -r requirements.txt
python setup.py install

CLI Usage

"samtools faidx" compatible FASTA indexing in pure python.

usage: pyfaidx [-h] [-r REGION] [-n] fasta

Fetch sequence from faidx-indexed FASTA

positional arguments:
  fasta                 faidx indexed FASTA file

optional arguments:
  -h, --help            show this help message and exit
  -r REGION, --region REGION
                        region of sequence to fetch e.g. chr1:1-1000
  -n, --name            print sequence names

Acknowledgements

This project is freely licensed by the author, Matthew Shirley, and was completed under the mentorship and financial support of Drs. Sarah Wheelan and Vasan Yegnasubramanian at the Sidney Kimmel Comprehensive Cancer Center in the Department of Oncology. Genome and Chromosome object implementations are influenced by the Counsyl HGVS module.

brentp / pyfaidx