/usr/lib/python2.7/dist-packages/cogent/db/rfam.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 | #!/usr/bin/env python
"""Retrieves records by id from RFAM, the RNA families database."""
from cogent.db.util import UrlGetter
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight","Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
rfam_base='http://rfam.sanger.ac.uk/family/alignment/download/format?'
rfam_formats = dict.fromkeys('stockholm pfam fasta fastau')
rfam_types = dict.fromkeys(['seed','full'])
class Rfam(UrlGetter):
"""Returns a pdb file."""
Defaults={'alnType':'seed','format':'stockholm','acc':None,'nseLabels':'1',
'download':'0'}
PrintedFields=dict.fromkeys('acc alnType nseLabels format download'.split())
BaseUrl = rfam_base
def __getitem__(self, item):
"""Returns handle to file containing aln of specified rfam id."""
orig_acc = self.acc
item = str(item).upper()
if not item.startswith('RF'):
item = 'RF'+item
self.acc = item
result = self.open()
self.acc = orig_acc
return result
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