Mac binaries

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

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/IgIO.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/IgIO.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.
+#
+# This module is for reading and writing IntelliGenetics format files as
+# SeqRecord objects.  This file format appears to be the same as the MASE
+# multiple sequence alignment format.
+
+"""Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.
+
+You are expected to use this module via the Bio.SeqIO functions."""
+
+from Bio.Alphabet import single_letter_alphabet
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+#This is a generator function!
+def IgIterator(handle, alphabet = single_letter_alphabet) :
+    """Iterate over IntelliGenetics records (as SeqRecord objects).
+
+    handle - input file
+    alphabet - optional alphabet
+
+    The optional free format file header lines (which start with two
+    semi-colons) are ignored.
+
+    The free format commentary lines at the start of each record (which
+    start with a semi-colon) are recorded as a single string with embedded
+    new line characters in the SeqRecord's annotations dictionary under the
+    key 'comment'.
+    """
+    #Skip any file header text before the first record (;; lines)
+    while True :
+        line = handle.readline()
+        if not line : break #Premature end of file, or just empty?
+        if not line.startswith(";;") : break
+
+    while line :
+        #Now iterate over the records
+        if line[0]!=";" :
+            raise ValueError( \
+                  "Records should start with ';' and not:\n%s" % repr(line))
+
+        #Try and agree with SeqRecord convention from the GenBank parser,
+        #(and followed in the SwissProt parser) which stores the comments
+        #as a long string with newlines under annotations key 'comment'.
+
+        #Note some examples use "; ..." and others ";..."
+        comment_lines = []
+        while line.startswith(";") :
+            #TODO - Extract identifier from lines like "LOCUS\tB_SF2"?
+            comment_lines.append(line[1:].strip())
+            line = handle.readline()
+        title = line.rstrip()
+
+        seq_lines = []
+        while True:
+            line = handle.readline()
+            if not line : break
+            if line[0] == ";": break
+            #Remove trailing whitespace, and any internal spaces
+            seq_lines.append(line.rstrip().replace(" ",""))
+        seq_str = "".join(seq_lines)
+        if seq_str.endswith("1") :
+            #Remove the optional terminator (digit one)
+            seq_str = seq_str[:-1]
+        if "1" in seq_str :
+            raise ValueError("Potential terminator digit one found within sequence.")
+                
+        #Return the record and then continue...
+        record= SeqRecord(Seq(seq_str, alphabet),
+                          id = title, name = title)
+        record.annotations['comment'] = "\n".join(comment_lines)
+        yield record
+    
+    #We should be at the end of the file now
+    assert not line
+
+if __name__ == "__main__" :
+    print "Running quick self test"
+    
+    import os
+    path = "../../Tests/IntelliGenetics/"
+    if os.path.isdir(path) :
+        for filename in os.listdir(path) :
+            if os.path.splitext(filename)[-1] == ".txt" :
+                print
+                print filename
+                print "-"*len(filename)
+                handle = open(os.path.join(path, filename))
+                for record in IgIterator(handle) :
+                    print record.id, len(record)
+                handle.close()
+        print "Done"
+    else :
+        print "Could not find input files"