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
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
|
# 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.
"""Hold CDD data in a straightforward format.
classes:
o Record - All of the information in a CDD record.
"""
# standard library
import string
from Bio.Seq import Seq
class Record( dict ):
"""Hold CDD 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 CDD data.
Attributes:
cd
description
status
source
date
reference
taxonomy
aligned
representative
range
sequence
"""
def __init__(self):
dict.__init__( self )
self[ 'references' ] = []
self[ 'alignment_lookup' ] = {}
def __str__( self ):
output = ''
keys = self.keys()
keys.sort()
for key in keys:
output = output + '%s:\n\n' % key.upper()
contents = self[ key ]
if( type( contents ) == type( '' ) ):
if( key == 'Sequence' ):
output = output + out_multiline( contents )
else:
output = output + '%s\n' % contents
elif( type( contents ) == type( {} ) ):
output = output + output_dict( contents, 1 )
elif( type( contents ) == type( [] ) ):
output = output + output_list( contents, 1 )
elif( isinstance( contents, Seq ) ):
output = output + out_multiline( contents.data )
output = output + '\n\n'
return output
def output_dict( dict, level = 0 ):
output = ''
prefix = ''
for j in range( 0, level ):
prefix = prefix + ' '
keys = dict.keys()
keys.sort()
for key in keys:
contents = dict[ key ]
if( type( contents ) == type( '' ) ):
output = output + '%s%s = %s\n' % ( prefix, key, contents )
elif( type( contents ) == type( {} ) ):
output = output + output_dict( contents, level + 1 )
elif( type( contents ) == type( [] ) ):
output = output + output_list( contents, level + 1 )
output = output + '\n'
return output
def output_list( items, level = 0 ):
output = ''
prefix = ''
for j in range( 0, level ):
prefix = prefix + ' '
for item in items:
if( type( item ) == type( '' ) ):
output = output + '%s%s\n' % ( prefix, item )
elif( type( item ) == type( {} ) ):
output = output + output_dict( item, level + 1 )
elif( type( item ) == type( [] ) ):
output = output + output_list( item, level + 1 )
output = output + '\n'
return output
def out_multiline( multiline ):
output = ''
for j in range( 0, len( multiline ), 80 ):
output = output + '%s\n' % multiline[ j: j + 80 ]
output = output + '\n'
return output
|
