Source Code for Module Bio.SeqIO.NexusIO

 1  # Copyright 2006 by Peter Cock.  All rights reserved. 
 2  # 
 3  # This code is part of the Biopython distribution and governed by its 
 4  # license.  Please see the LICENSE file that should have been included 
 5  # as part of this package. 
 6  """Bio.SeqIO support for the "nexus" file format. 
 7   
 8  You were expected to use this module via the Bio.SeqIO functions. 
 9  This module has now been replaced by Bio.AlignIO.NexusIO, and is 
10  deprecated.""" 
11   
12  import warnings 
13  warnings.warn("Bio.SeqIO.NexusIO is deprecated.  You can continue to read" \ 
14                + " 'nexus' files with Bio.SeqIO, but this is now" \ 
15                + " handled via Bio.AlignIO internally.", 
16                DeprecationWarning) 
17   
18  from Bio.Seq import Seq 
19  from Bio.SeqRecord import SeqRecord 
20  from Bio.Nexus import Nexus 
21   
22  #You can get a couple of example files here: 
23  #http://www.molecularevolution.org/resources/fileformats/ 
24       
25  #This is a generator function! 
26 -def NexusIterator(handle) : 
27      """Returns SeqRecord objects from a Nexus file. 
28   
29      Thus uses the Bio.Nexus module to do the hard work.""" 
30      n = Nexus.Nexus(handle) 
31      for id in n.original_taxon_order : 
32          if id in n.matrix : 
33              seq = n.matrix[id] 
34          else : 
35              #Missing the sequence? 
36              seq = Seq("", n.alphabet) 
37          #ToDo - Can we extract any annotation too? 
38          yield SeqRecord(seq, id=id, name=id, description="") 
39      #All done 
40      return 
41