Mac binaries

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

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqIO/AceIO.py b/website/archive/binaries/mac/src/disembl/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