This package is tested under Python 3.3.
To install the pyfaidx module and pyfaidx cli script, simply run python setup.py install.
A pure python implementation of samtools faidx FASTA indexing.
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
$ pyfaidx /tmp/hg19.fa -r chr10:1000000-1000010
GGAGGGCTGCA
$ pyfaidx /tmp/hg19.fa -n -r chr10:1000000-1000010
chr10:1000000-1000010
GGAGGGCTGCA
>>> from pyfaidx import Genome
>>> genome = Genome('T7.fa')
>>> genome['EM_PHG:V01146'][0:10]
EM_PHG:V01146:1-10
TCTCACAGTG
>>> 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
faidxis initialized thebuildmethod will automatically run, producing "filename.fa.fai" where "filename.fa" is the original FASTA file. - Start and end coordinates are 1-based.
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.