diff corebio/seq_io/nexus_io.py @ 7:8d676bbd1f2d

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/nexus_io.py	Mon Jan 16 07:03:36 2012 -0500
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+# Copyright 2005 Gavin E. Crooks <[e-mail]>
+# Copyright 2005-2006 The Regents of the University of California.
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+#
+
+"""Read the sequence data from a nexus file.
+
+This IO code only gives read access to the sequence data.
+
+Reference:
+'NEXUS: An extensible file format for systematic information'
+Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
+"""
+
+from corebio.seq import Seq, SeqList, Alphabet
+from corebio.seq_io._nexus import Nexus, safename
+
+
+
+
+
+names = ( 'nexus', 'paup')
+extensions = ('nex', 'nexus', 'paup', 'nxs')
+
+def iterseq(fin, alphabet=None):
+    """Iterate over the sequences in the file."""
+    # Default implementation
+    return iter(read(fin, alphabet) )
+
+
+def read(fin, alphabet=None):          
+    """ Extract sequence data from a nexus file."""
+    n = Nexus(fin)
+    
+    seqs = []
+    for taxon in n.taxlabels:   
+        name = safename(taxon)
+        r = n.matrix[taxon]
+        if alphabet is None  :
+            s = Seq(r, name = name, alphabet=r.alphabet)
+        else :
+            s = Seq(r, name = name, alphabet=alphabet )
+        seqs.append(s)
+
+    if len(seqs) == 0 :
+        # Something went terrible wrong.
+        raise ValueError("Cannot parse file")
+        
+    return SeqList(seqs)
+
+    
+    
+    
+