pyfasta 0.2.5

pythonic access to fasta sequence files

Author:

Brent Pedersen (brentp)

Email:

[e-mail]

License:

MIT

Implementation

Requires Python >= 2.5. Stores a flattened version of the fasta file without spaces or headers. And a pickle of the start, stop (for fseek) locations of each header in the fasta file for internal use. Now supports the numpy array interface.

Usage

>>> from pyfasta import Fasta

>>> f = Fasta('tests/data/three_chrs.fasta')
>>> sorted(f.keys())
['chr1', 'chr2', 'chr3']

>>> f['chr1']
FastaRecord('tests/data/three_chrs.fasta.flat', 0..80)

Slicing

>>> f['chr1'][:10]
'ACTGACTGAC'

# get the 1st basepair in every codon (it's python yo)
>>> f['chr1'][::3]
'AGTCAGTCAGTCAGTCAGTCAGTCAGT'


# the index stores the start and stop of each header from the fasta file.
# (you should never need this)
>>> f.index
{'chr3': (160, 3760), 'chr2': (80, 160), 'chr1': (0, 80)}


# can query by a 'feature' dictionary
>>> f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9})
'CTGACTGA'

# with reverse complement for - strand
>>> f.sequence({'chr': 'chr1', 'start': 2, 'stop': 9, 'strand': '-'})
'TCAGTCAG'

Numpy Array Interface

# FastaRecords support the numpy array interface.
>>> import numpy as np
>>> a = np.array(f['chr2'])
>>> a.shape[0] == len(f['chr2'])
True

>>> a[10:14]
array(['A', 'A', 'A', 'A'],
      dtype='|S1')


# cleanup (though for real use these will remain for faster access)
>>> import os
>>> os.unlink('tests/data/three_chrs.fasta.gdx')
>>> os.unlink('tests/data/three_chrs.fasta.flat')