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[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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--- a/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()