Ejemplo n.º 1
0
def getnib( nibdir ):
    seqs = {}
    for nibf in os.listdir( nibdir ):
        if not nibf.endswith('.nib'): continue
        chr = nibf.replace('.nib','')
        file = os.path.join( nibdir, nibf )
        seqs[chr] = nib.NibFile( open(file) )

    return seqs
Ejemplo n.º 2
0
#!/afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7
"""
Print the number of bases in a nib file.

usage: %prog nib_file
"""

from bx.seq import nib as seq_nib
import sys

nib = seq_nib.NibFile(file(sys.argv[1]))
print nib.length
Ejemplo n.º 3
0
#!/usr/bin/env python

"""
Print the number of bases in a nib file.

usage: %prog nib_file
"""
from __future__ import print_function

import sys

from bx.seq import nib as seq_nib

with open(sys.argv[1]) as f:
    nib = seq_nib.NibFile(f)
print(nib.length)