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

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/PhdIO.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/PhdIO.py
deleted file mode 100644 (file)
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--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/PhdIO.py
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-# Copyright 2008 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 "phd" file format.
-
-PHD files are output by PHRED and used by PHRAP and CONSED.
-
-You are expected to use this module via the Bio.SeqIO functions.
-See also the underlying Bio.Sequencing.Phd module."""
-
-from Bio.SeqRecord import SeqRecord
-from Bio.Sequencing import Phd
-    
-#This is a generator function!
-def PhdIterator(handle) :
-    """Returns SeqRecord objects from a PHD file.
-
-    This uses the Bio.Sequencing.Phy module to do the hard work.
-    """
-
-    phd_records = Phd.parse(handle)
-    for phd_record in phd_records:
-        #Convert the PHY record into a SeqRecord...
-        seq_record = SeqRecord(phd_record.seq,
-                               id = phd_record.file_name,
-                               name = phd_record.file_name)
-        #Just re-use the comments dictionary as the SeqRecord's annotations
-        seq_record.annotations = phd_record.comments
-        yield seq_record 
-    #All done
-
-if __name__ == "__main__" :
-    print "Quick self test"
-    handle = open("../../Tests/Phd/Phd1")
-    for record in PhdIterator(handle) :
-        print record
-    handle.close()
-    print "Done"
-        
-