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

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/AceIO.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/AceIO.py
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--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/AceIO.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 "ace" file format.
-
-You are expected to use this module via the Bio.SeqIO functions.
-See also the Bio.Sequencing.Ace module which offers more than just accessing
-the contig consensus sequences in an ACE file as SeqRecord objects."""
-
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
-from Bio.Alphabet import generic_nucleotide, generic_dna, generic_rna, Gapped
-from Bio.Sequencing import Ace
-    
-#This is a generator function!
-def AceIterator(handle) :
-    """Returns SeqRecord objects from an ACE file.
-
-    This uses the Bio.Sequencing.Ace module to do the hard work.  Note that
-    by iterating over the file in a single pass, we are forced to ignore any
-    WA, CT, RT or WR footer tags."""
-
-    for ace_contig in Ace.parse(handle) :
-        #Convert the ACE contig record into a SeqRecord...
-        consensus_seq_str = ace_contig.sequence
-        #Assume its DNA unless there is a U in it,
-        if "U" in consensus_seq_str :
-            if "T" in consensus_seq_str :
-                #Very odd! Error?
-                alpha = generic_ncleotide
-            else :
-                alpha = generic_rna
-        else :
-            alpha = generic_dna
-            
-        if "*" in consensus_seq_str :
-            #For consistency with most other file formats, map
-            #any * gaps into 0 gaps.
-            assert "-" not in consensus_seq_str
-            consensus_seq = Seq(consensus_seq_str.replace("*","-"),
-                                Gapped(alpha, gap_char="-"))
-        else :
-            consensus_seq = Seq(consensus_seq_str, alpha)
-
-        #TODO - Consensus base quality (BQ lines).  Note that any gaps
-        #(* character) in the consensus does not get a quality entry.
-        #This really needs Biopython support for per-letter-annotation.
-
-        #TODO? - Base segments (BS lines) which indicates which read
-        #phrap has chosen to be the consensus at a particular position.
-        #Perhaps as SeqFeature objects?
-
-        #TODO - Supporting reads (RD lines, plus perhaps QA and DS lines)
-        #Perhaps as SeqFeature objects?
-            
-        seq_record = SeqRecord(consensus_seq,
-                               id = ace_contig.name,
-                               name = ace_contig.name)
-        yield seq_record 
-    #All done