Source Code for Module Bio.SeqIO.AceIO

  1  # Copyright 2008-2010 by Peter Cock.  All rights reserved. 
  2  # 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6   
  7  """Bio.SeqIO support for the "ace" file format. 
  8   
  9  You are expected to use this module via the Bio.SeqIO functions. 
 10  See also the Bio.Sequencing.Ace module which offers more than just accessing 
 11  the contig consensus sequences in an ACE file as SeqRecord objects. 
 12  """ 
 13   
 14  from Bio.Seq import Seq 
 15  from Bio.SeqRecord import SeqRecord 
 16  from Bio.Alphabet import generic_nucleotide, generic_dna, generic_rna, Gapped 
 17  from Bio.Sequencing import Ace 
 18   
 19   
 20 -def AceIterator(handle): 
 21      """Returns SeqRecord objects from an ACE file. 
 22   
 23      This uses the Bio.Sequencing.Ace module to do the hard work.  Note that 
 24      by iterating over the file in a single pass, we are forced to ignore any 
 25      WA, CT, RT or WR footer tags. 
 26   
 27      Ace files include the base quality for each position, which are taken 
 28      to be PHRED style scores. Just as if you had read in a FASTQ or QUAL file 
 29      using PHRED scores using Bio.SeqIO, these are stored in the SeqRecord's 
 30      letter_annotations dictionary under the "phred_quality" key. 
 31   
 32      >>> from Bio import SeqIO 
 33      >>> handle = open("Ace/consed_sample.ace", "rU") 
 34      >>> for record in SeqIO.parse(handle, "ace"): 
 35      ...     print record.id, record.seq[:10]+"...", len(record) 
 36      ...     print max(record.letter_annotations["phred_quality"]) 
 37      Contig1 agccccgggc... 1475 
 38      90 
 39   
 40      However, ACE files do not include a base quality for any gaps in the 
 41      consensus sequence, and these are represented in Biopython with a quality 
 42      of zero. Using zero is perhaps misleading as there may be very strong 
 43      evidence to support the gap in the consensus. Previous versions of 
 44      Biopython therefore used None instead, but this complicated usage, and 
 45      prevented output of the gapped sequence as FASTQ format. 
 46   
 47      >>> from Bio import SeqIO 
 48      >>> handle = open("Ace/contig1.ace", "rU") 
 49      >>> for record in SeqIO.parse(handle, "ace"): 
 50      ...     print record.id, "..." + record.seq[85:95]+"..." 
 51      ...     print record.letter_annotations["phred_quality"][85:95] 
 52      ...     print max(record.letter_annotations["phred_quality"]) 
 53      Contig1 ...AGAGG-ATGC... 
 54      [57, 57, 54, 57, 57, 0, 57, 72, 72, 72] 
 55      90 
 56      Contig2 ...GAATTACTAT... 
 57      [68, 68, 68, 68, 68, 68, 68, 68, 68, 68] 
 58      90 
 59   
 60      """ 
 61      for ace_contig in Ace.parse(handle): 
 62          #Convert the ACE contig record into a SeqRecord... 
 63          consensus_seq_str = ace_contig.sequence 
 64          #Assume its DNA unless there is a U in it, 
 65          if "U" in consensus_seq_str: 
 66              if "T" in consensus_seq_str: 
 67                  #Very odd! Error? 
 68                  alpha = generic_nucleotide 
 69              else: 
 70                  alpha = generic_rna 
 71          else: 
 72              alpha = generic_dna 
 73   
 74          if "*" in consensus_seq_str: 
 75              #For consistency with most other file formats, map 
 76              #any * gaps into - gaps. 
 77              assert "-" not in consensus_seq_str 
 78              consensus_seq = Seq(consensus_seq_str.replace("*", "-"), 
 79                                  Gapped(alpha, gap_char="-")) 
 80          else: 
 81              consensus_seq = Seq(consensus_seq_str, alpha) 
 82   
 83          #TODO? - Base segments (BS lines) which indicates which read 
 84          #phrap has chosen to be the consensus at a particular position. 
 85          #Perhaps as SeqFeature objects? 
 86   
 87          #TODO - Supporting reads (RD lines, plus perhaps QA and DS lines) 
 88          #Perhaps as SeqFeature objects? 
 89   
 90          seq_record = SeqRecord(consensus_seq, 
 91                                 id=ace_contig.name, 
 92                                 name=ace_contig.name) 
 93   
 94          #Consensus base quality (BQ lines).  Note that any gaps (originally 
 95          #as * characters) in the consensus do not get a quality entry, so 
 96          #we assign a quality of None (zero would be missleading as there may 
 97          #be excelent support for having a gap here). 
 98          quals = [] 
 99          i = 0 
100          for base in consensus_seq: 
101              if base == "-": 
102                  quals.append(0) 
103              else: 
104                  quals.append(ace_contig.quality[i]) 
105                  i += 1 
106          assert i == len(ace_contig.quality) 
107          seq_record.letter_annotations["phred_quality"] = quals 
108   
109          yield seq_record 
110      #All done 
111   
112   
113  if __name__ == "__main__": 
114      from Bio._utils import run_doctest 
115      run_doctest() 
116