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 2007-2009, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
rfam_base='http://www.sanger.ac.uk/cgi-bin/Rfam/getalignment.pl?'
rfam_formats = dict.fromkeys('link mul stock fal msf download belvu jalview'.split())
rfam_types = dict.fromkeys(['seed','full'])
class Rfam(UrlGetter):
"""Returns a pdb file."""
Defaults={'type':'seed','format':'stock', 'acc':None}
PrintedFields=dict.fromkeys('acc type format'.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
|
