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
|
#!/usr/bin/env python
from cogent.core import annotation, moltype
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Raymond Sammut", "Peter Maxwell", "Gavin Huttley",
"Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
#<?xml version="1.0"?>
#<!DOCTYPE macsim SYSTEM "http://www-bio3d-igbmc.u-strasbg.fr/macsim.dtd">
# As used by BAliBASE
def MacsimParser(doc):
doc = doc.getElementsByTagName('macsim')[0]
align = doc.getElementsByTagName('alignment')[0]
for record in align.getElementsByTagName('sequence'):
name = record.getElementsByTagName(
'seq-name')[0].childNodes[0].nodeValue
raw_seq = record.getElementsByTagName(
'seq-data')[0].childNodes[0].nodeValue
#cast as string to de-unicode
raw_string = ''.join(str(raw_seq).upper().split())
name=str(name).strip()
if str(record.getAttribute('seq-type')).lower() == 'protein':
alphabet = moltype.PROTEIN
else:
alphabet = moltype.DNA
seq = alphabet.makeSequence(raw_string, Name=name)
yield (name, seq)
|
