Package Bio :: Package SeqIO :: Module IgIO
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Source Code for Module Bio.SeqIO.IgIO

  1  # Copyright 2008-2010 by Peter Cock.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  # 
  6  # This module is for reading and writing IntelliGenetics format files as 
  7  # SeqRecord objects.  This file format appears to be the same as the MASE 
  8  # multiple sequence alignment format. 
  9   
 10  """Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format. 
 11   
 12  You are expected to use this module via the Bio.SeqIO functions.""" 
 13   
 14  from Bio.Alphabet import single_letter_alphabet 
 15  from Bio.Seq import Seq 
 16  from Bio.SeqRecord import SeqRecord 
 17   
 18  #This is a generator function! 
19 -def IgIterator(handle, alphabet = single_letter_alphabet):
20 """Iterate over IntelliGenetics records (as SeqRecord objects). 21 22 handle - input file 23 alphabet - optional alphabet 24 25 The optional free format file header lines (which start with two 26 semi-colons) are ignored. 27 28 The free format commentary lines at the start of each record (which 29 start with a semi-colon) are recorded as a single string with embedded 30 new line characters in the SeqRecord's annotations dictionary under the 31 key 'comment'. 32 """ 33 #Skip any file header text before the first record (;; lines) 34 while True: 35 line = handle.readline() 36 if not line : break #Premature end of file, or just empty? 37 if not line.startswith(";;") : break 38 39 while line: 40 #Now iterate over the records 41 if line[0] != ";": 42 raise ValueError( \ 43 "Records should start with ';' and not:\n%s" % repr(line)) 44 45 #Try and agree with SeqRecord convention from the GenBank parser, 46 #(and followed in the SwissProt parser) which stores the comments 47 #as a long string with newlines under annotations key 'comment'. 48 49 #Note some examples use "; ..." and others ";..." 50 comment_lines = [] 51 while line.startswith(";"): 52 #TODO - Extract identifier from lines like "LOCUS\tB_SF2"? 53 comment_lines.append(line[1:].strip()) 54 line = handle.readline() 55 title = line.rstrip() 56 57 seq_lines = [] 58 while True: 59 line = handle.readline() 60 if not line: 61 break 62 if line[0] == ";": 63 break 64 #Remove trailing whitespace, and any internal spaces 65 seq_lines.append(line.rstrip().replace(" ","")) 66 seq_str = "".join(seq_lines) 67 if seq_str.endswith("1"): 68 #Remove the optional terminator (digit one) 69 seq_str = seq_str[:-1] 70 if "1" in seq_str: 71 raise ValueError(\ 72 "Potential terminator digit one found within sequence.") 73 74 #Return the record and then continue... 75 record = SeqRecord(Seq(seq_str, alphabet), 76 id = title, name = title) 77 record.annotations['comment'] = "\n".join(comment_lines) 78 yield record 79 80 #We should be at the end of the file now 81 assert not line
82 83 if __name__ == "__main__": 84 print "Running quick self test" 85 86 import os 87 path = "../../Tests/IntelliGenetics/" 88 if os.path.isdir(path): 89 for filename in os.listdir(path): 90 if os.path.splitext(filename)[-1] == ".txt": 91 print 92 print filename 93 print "-"*len(filename) 94 handle = open(os.path.join(path, filename)) 95 for record in IgIterator(handle): 96 print record.id, len(record) 97 handle.close() 98 print "Done" 99 else: 100 print "Could not find input files" 101