Mercurial > repos > davidmurphy > codonlogo

comparison corebio/seq_io/nexus_io.py @ 0:c55bdc2fb9fa

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidmurphy
date Thu, 27 Oct 2011 12:09:09 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c55bdc2fb9fa
1 #!/usr/bin/env python
2
3 # Copyright 2005 Gavin E. Crooks <gec@threeplusone.com>
4 # Copyright 2005-2006 The Regents of the University of California.
5 #
6 # This software is distributed under the MIT Open Source License.
7 # <http://www.opensource.org/licenses/mit-license.html>
8 #
9 # Permission is hereby granted, free of charge, to any person obtaining a
10 # copy of this software and associated documentation files (the "Software"),
11 # to deal in the Software without restriction, including without limitation
12 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
13 # and/or sell copies of the Software, and to permit persons to whom the
14 # Software is furnished to do so, subject to the following conditions:
15 #
16 # The above copyright notice and this permission notice shall be included
17 # in all copies or substantial portions of the Software.
18 #
19 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
20 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
21 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
22 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
23 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
24 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
25 # THE SOFTWARE.
26 #
27
28 """Read the sequence data from a nexus file.
29
30 This IO code only gives read access to the sequence data.
31
32 Reference:
33 'NEXUS: An extensible file format for systematic information'
34 Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
35 """
36
37 from corebio.seq import Seq, SeqList, Alphabet
38 from corebio.seq_io._nexus import Nexus, safename
39
40
41
42
43
44 names = ( 'nexus', 'paup')
45 extensions = ('nex', 'nexus', 'paup', 'nxs')
46
47 def iterseq(fin, alphabet=None):
48 """Iterate over the sequences in the file."""
49 # Default implementation
50 return iter(read(fin, alphabet) )
51
52
53 def read(fin, alphabet=None):
54 """ Extract sequence data from a nexus file."""
55 n = Nexus(fin)
56
57 seqs = []
58 for taxon in n.taxlabels:
59 name = safename(taxon)
60 r = n.matrix[taxon]
61 if alphabet is None :
62 s = Seq(r, name = name, alphabet=r.alphabet)
63 else :
64 s = Seq(r, name = name, alphabet=alphabet )
65 seqs.append(s)
66
67 if len(seqs) == 0 :
68 # Something went terrible wrong.
69 raise ValueError("Cannot parse file")
70
71 return SeqList(seqs)
72
73
74
75
76