Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / SeqIO / SwissIO.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqIO/SwissIO.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqIO/SwissIO.py
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+# Copyright 2006 by Peter Cock.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format.
+
+You are expected to use this module via the Bio.SeqIO functions.
+See also the Bio.SwissProt module which offers more than just accessing
+the sequences as SeqRecord objects."""
+
+from Bio.SwissProt import SProt
+import cStringIO
+    
+#This is a generator function!
+def SwissIterator(handle) :
+    """Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.
+
+    Every section from the ID line to the terminating // becomes
+    a single SeqRecord with associated annotation and features.
+
+    This parser is for the flat file "swiss" format as used by:
+     * Swiss-Prot aka SwissProt
+     * TrEMBL
+     * UniProtKB aka UniProt Knowledgebase
+
+    It does NOT read their new XML file format.
+    http://www.expasy.org/sprot/
+
+    For consistency with BioPerl and EMBOSS we call this the "swiss"
+    format.
+    """
+    parser = SProt.SequenceParser()
+    lines = []
+    for line in handle:
+        lines.append(line)
+        if line[:2]=='//':
+            handle = cStringIO.StringIO("".join(lines))
+            record = parser.parse(handle)
+            lines = []
+            yield record
+    #If there are more lines, it could only be a partial record.
+    #Should we try and parse them anyway?
+ 
+
+if __name__ == "__main__" :
+    print "Quick self test..."
+
+    example_filename = "../../Tests/SwissProt/sp008"
+
+    import os
+    if not os.path.isfile(example_filename):
+        print "Missing test file %s" % example_filename
+    else :
+        #Try parsing it!
+        handle = open(example_filename)
+        records = SwissIterator(handle)
+        for record in records:
+            print record.name
+            print record.id
+            print record.annotations['keywords']
+            print repr(record.annotations['organism'])
+            print record.seq.tostring()[:20] + "..."
+        handle.close()