/usr/lib/python2.7/dist-packages/cogent/parse/macsim.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 2007-2016, The Cogent Project"
__credits__ = ["Raymond Sammut", "Peter Maxwell", "Gavin Huttley",
"Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__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)
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