Source Code for Module Bio.SearchIO.ExonerateIO.exonerate_cigar

  1  # Copyright 2012 by Wibowo Arindrarto.  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.SearchIO parser for Exonerate cigar output format.""" 
  7   
  8  import re 
  9   
 10  from Bio._py3k import _as_bytes, _bytes_to_string 
 11   
 12  from _base import _BaseExonerateParser, _STRAND_MAP 
 13  from exonerate_vulgar import ExonerateVulgarIndexer 
 14   
 15   
 16  __all__ = ['ExonerateCigarParser', 'ExonerateCigarIndexer'] 
 17   
 18   
 19  # precompile regex 
 20  _RE_CIGAR = re.compile(r"""^cigar:\s+ 
 21          (\S+)\s+(\d+)\s+(\d+)\s+([\+-\.])\s+  # query: ID, start, end, strand 
 22          (\S+)\s+(\d+)\s+(\d+)\s+([\+-\.])\s+  # hit: ID, start, end, strand 
 23          (\d+)(\s+.*)$                         # score, vulgar components 
 24          """, re.VERBOSE) 
 25   
 26   
 27 -class ExonerateCigarParser(_BaseExonerateParser): 
 28   
 29      """Parser for Exonerate cigar strings.""" 
 30   
 31      _ALN_MARK = 'cigar' 
 32   
 33 -    def parse_alignment_block(self, header): 
 34          qresult = header['qresult'] 
 35          hit = header['hit'] 
 36          hsp = header['hsp'] 
 37          self.read_until(lambda line: line.startswith('cigar')) 
 38          cigars = re.search(_RE_CIGAR, self.line) 
 39          # if the file has c4 alignments 
 40          # check if cigar values match our previously parsed header values 
 41          if self.has_c4_alignment: 
 42              assert qresult['id'] == cigars.group(1) 
 43              assert hsp['query_start'] == cigars.group(2) 
 44              assert hsp['query_end'] == cigars.group(3) 
 45              assert hsp['query_strand'] == cigars.group(4) 
 46              assert hit['id'] == cigars.group(5) 
 47              assert hsp['hit_start'] == cigars.group(6) 
 48              assert hsp['hit_end'] == cigars.group(7) 
 49              assert hsp['hit_strand'] == cigars.group(8) 
 50              assert hsp['score'] == cigars.group(9) 
 51          else: 
 52              qresult['id'] = cigars.group(1) 
 53              hsp['query_start'] = cigars.group(2) 
 54              hsp['query_end'] = cigars.group(3) 
 55              hsp['query_strand'] = cigars.group(4) 
 56              hit['id'] = cigars.group(5) 
 57              hsp['hit_start'] = cigars.group(6) 
 58              hsp['hit_end'] = cigars.group(7) 
 59              hsp['hit_strand'] = cigars.group(8) 
 60              hsp['score'] = cigars.group(9) 
 61   
 62          # adjust strands 
 63          hsp['query_strand'] = _STRAND_MAP[hsp['query_strand']] 
 64          hsp['hit_strand'] = _STRAND_MAP[hsp['hit_strand']] 
 65          # cast coords into ints 
 66          qstart = int(hsp['query_start']) 
 67          qend = int(hsp['query_end']) 
 68          hstart = int(hsp['hit_start']) 
 69          hend = int(hsp['hit_end']) 
 70          # set coords (start <= end) 
 71          hsp['query_start'] = min(qstart, qend) 
 72          hsp['query_end'] = max(qstart, qend) 
 73          hsp['hit_start'] = min(hstart, hend) 
 74          hsp['hit_end'] = max(hstart, hend) 
 75          # cast score into int 
 76          hsp['score'] = int(hsp['score']) 
 77          # store cigar components 
 78          hsp['cigar_comp'] = cigars.group(10) 
 79          # HACK: since we can't really figure out exactly when a 
 80          # HSP starts or ends, we set the entire alignment as one HSP 
 81          hsp['query_ranges'] = [(hsp['query_start'], hsp['query_end'])] 
 82          hsp['hit_ranges'] = [(hsp['hit_start'], hsp['hit_end'])] 
 83   
 84          return {'qresult': qresult, 'hit': hit, 'hsp': hsp} 
 85   
 86   
 87 -class ExonerateCigarIndexer(ExonerateVulgarIndexer): 
 88   
 89      """Indexer class for exonerate cigar lines.""" 
 90   
 91      _parser = ExonerateCigarParser 
 92      _query_mark = _as_bytes('cigar') 
 93   
 94 -    def get_qresult_id(self, pos): 
 95          """Returns the query ID of the nearest cigar line.""" 
 96          handle = self._handle 
 97          handle.seek(pos) 
 98          # get line, check if it's a vulgar line, and get query ID 
 99          line = handle.readline() 
100          assert line.startswith(self._query_mark), line 
101          id = re.search(_RE_CIGAR, _bytes_to_string(line)) 
102          return id.group(1) 
103   
104   
105  # if not used as a module, run the doctest 
106  if __name__ == "__main__": 
107      from Bio._utils import run_doctest 
108      run_doctest() 
109