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

  1  # Copyright 2008 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  """Bio.SeqIO support for the "tab" (simple tab separated) file format. 
  7   
  8  You are expected to use this module via the Bio.SeqIO functions. 
  9   
 10  The "tab" format is an ad-hoc plain text file format where each sequence is 
 11  on one (long) line.  Each line contains the identifier/description, followed 
 12  by a tab, followed by the sequence.  For example, consider the following 
 13  short FASTA format file: 
 14   
 15  >ID123456 possible binding site? 
 16  CATCNAGATGACACTACGACTACGACTCAGACTAC 
 17  >ID123457 random sequence 
 18  ACACTACGACTACGACTCAGACTACAAN 
 19   
 20  Apart from the descriptions, this can be represented in the simple two column 
 21  tab separated format as follows: 
 22   
 23  ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC 
 24  ID123457(tab)ACACTACGACTACGACTCAGACTACAAN 
 25   
 26  When reading this file, "ID123456" or "ID123457" will be taken as the record's 
 27  .id and .name property.  There is no other information to record. 
 28   
 29  Similarly, when writing to this format, Biopython will ONLY record the record's 
 30  .id and .seq (and not the description or any other information) as in the example 
 31  above. 
 32  """ 
 33   
 34  from Bio.Alphabet import single_letter_alphabet 
 35  from Bio.Seq import Seq 
 36  from Bio.SeqRecord import SeqRecord 
 37  from Interfaces import SequentialSequenceWriter 
 38   
 39  #This is a generator function! 
40 -def TabIterator(handle, alphabet = single_letter_alphabet) :
41 """Iterates over tab separated lines (as SeqRecord objects). 42 43 Each line of the file should contain one tab only, dividing the line 44 into an identifier and the full sequence. 45 46 handle - input file 47 alphabet - optional alphabet 48 49 The first field is taken as the record's .id and .name (regardless of 50 any spaces within the text) and the second field is the sequence. 51 52 Any blank lines are ignored. 53 """ 54 for line in handle : 55 try : 56 title, seq = line.split("\t") #will fail if more than one tab! 57 except : 58 if line.strip() == "" : 59 #It's a blank line, ignore it 60 continue 61 raise ValueError("Each line should have one tab separating the" + \ 62 " title and sequence, this line has %i tabs: %s" \ 63 % (line.count("\t"), repr(line))) 64 title = title.strip() 65 seq = seq.strip() #removes the trailing new line 66 yield SeqRecord(Seq(seq, alphabet), id = title, name = title)
67
68 -class TabWriter(SequentialSequenceWriter):
69 """Class to write simple tab separated format files. 70 71 Each line consists of "id(tab)sequence" only. 72 73 Any description, name or other annotation is not recorded. 74 """
75 - def write_record(self, record):
76 """Write a single tab line to the file.""" 77 assert self._header_written 78 assert not self._footer_written 79 self._record_written = True 80 81 title = self.clean(record.id) 82 seq = self._get_seq_string(record) #Catches sequence being None 83 assert "\t" not in title 84 assert "\n" not in title 85 assert "\r" not in title 86 assert "\t" not in seq 87 assert "\n" not in seq 88 assert "\r" not in seq 89 self.handle.write("%s\t%s\n" % (title, seq))
90 91 92 if __name__ == "__main__" : 93 print "Running quick self test" 94 from StringIO import StringIO 95 96 #This example has a trailing blank line which should be ignored 97 handle = StringIO("Alpha\tAAAAAAA\nBeta\tCCCCCCC\n\n") 98 records = list(TabIterator(handle)) 99 assert len(records) == 2 100 101 handle = StringIO("Alpha\tAAAAAAA\tExtra\nBeta\tCCCCCCC\n") 102 try : 103 records = list(TabIterator(handle)) 104 assert False, "Should have reject this invalid example!" 105 except ValueError : 106 #Good! 107 pass 108 109 print "Done" 110