Delete unneeded directory

[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
deleted file mode 100644 (file)
index 57b7aa1..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqIO/IgIO.py
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@@ -1,97 +0,0 @@
-# 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"