1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
# 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 SAF formatted files.
This is a huge regular regular expression for Saf, built using
the 'regular expressiona on steroids' capabilities of Martel.
#http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html
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.Align.Generic import Alignment
import Bio.Alphabet
"""Hold SAF data in a straightforward format.
classes:
o Record - All of the information in an Saf record.
"""
class Record:
"""Hold Saf 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 Saf data.
Attributes:
alignment
"""
def __init__(self):
self.alignment = Alignment( Bio.Alphabet.generic_alphabet )
def __str__( self ):
output = ''
sequences = self.alignment.get_all_seqs()
for sequence_record in sequences:
output = output + '%s\n' % sequence_record.description
# output = output + out_sequence( sequence_record.seq.data )
output = output + out_sequence( sequence_record.seq.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
|
