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# Copyright 2001 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Martel based parser to read NBRF formatted files.
This is a huge regular regular expression for NBRF, built using
the 'regular expressiona on steroids' capabilities of Martel.
http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "\n|\r\n?"
[\R] means "[\n\r]"
This helps us have endlines be consistent across platforms.
"""
# standard library
import string
from Bio.Seq import Seq
from Bio.NBRF.ValSeq import valid_sequence_dict
"""Hold NBRF data in a straightforward format.
classes:
o Record - All of the information in an NBRF record.
"""
class Record:
"""Hold NBRF information in a format similar to the original record.
The Record class is meant to make data easy to get to when you are
just interested in looking at NBRF data.
Attributes:
sequence_type
sequence_name
comment
sequence
"""
def __init__(self):
self.sequence_type = ''
self.sequence_name = ''
self.comment = ''
self.sequence = Seq('')
def __str__( self ):
sequence_type = valid_sequence_dict[ self.sequence_type ]
output = 'Sequence type %s\n' % sequence_type
output = output + 'Sequence name %s\n' % self.sequence_name
output = output + '%s\n' % self.comment
output = output + out_sequence( self.sequence.data )
return output
def out_sequence( seq ):
output = ''
for j in range( 0, len( seq ), 80 ):
output = output + '%s\n' % seq[ j: j + 80 ]
output = output + '\n'
return output
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