pyfasta 0.4.1

Pythonic access to fasta sequence files<br /><br />pyfasta is a library that offers Pythonic access to fasta sequence files.<br />Usage:<br /><br /><br />.. sourcecode:: python<br /><br />>>> from pyfasta import Fasta<br /><br />>>> f = Fasta('tests/data/three_chrs.fasta')<br />>>> sorted(f.keys())<br />['chr1', 'chr2', 'chr3']<br /><br />>>> f['chr1']<br />FastaGz('tests/data/three_chrs.fasta.gz', 0..80)<br /><br />>>> f['chr1'][:10]<br />'ACTGACTGAC'<br /><br /># the index stores the start and stop of each header from teh fasta file<br />>>> f.index<br />{'chr3': (160, 3760), 'chr2': (80, 160), 'chr1': (0, 80)}<br /><br /><br /># can query by a 'feature' dictionary<br />>>> f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9})<br />'CTGACTGA'<br /><br /># with reverse complement for - strand<br />>>> f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9, 'strand': '-'})<br />'TCAGTCAG'<br /><br /><br /># creates a .gz and a .gdx pickle of the fasta and the index.<br />>>> import os<br />>>> sorted(os.listdir('tests/data/'))[1:]<br />['three_chrs.fasta', 'three_chrs.fasta.gdx', 'three_chrs.fasta.gz']<br /><br /># cleanup (though for real use these will remain for faster access)<br />>>> os.unlink('tests/data/three_chrs.fasta.gdx')<br />>>> os.unlink('tests/data/three_chrs.fasta.gz')

Requirements:	No special requirements
Platforms:	*nix, Linux
Keyword:	Access,  Complement,  Creates,  Fasta,  Import,  Pickle,  Python,  Pythonic,  Reverse,  Sequence,  Strandgtgtgt
Users rating:	0/10