Reference

Zerg::Report(3pm)

get attributes from a BLAST file in a data structure

NAME

Zerg::Report - get attributes from a BLAST file in a data structure

SYNOPSIS

  use Zerg::Report;
  
  my $zerg_report = new Zerg::Report("output.blastn");
  
  while($r=$zerg_report->getReport())
  { 
    foreach my $hit (@{$r->{hits}})
    {
      foreach my $hsp (@{$hit->{hsps}})
      {
        print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n";
      }
    }
  }
  $zerg_report->closeFile();

DESCRIPTION

  Zerg::Report uses Zerg to parse a file - or STDIN if file is not given -
  containing one or multiple BLAST reports and, for each report, stores
  the obtained fields in a data structure made of arrays and hashes.
  Please consult the Zerg man page to see which fields are extracted.
  The method getReport() reads a BLAST report from the input file and
  returns a reference to a data structure like the one in the example
  below. When no report is found, it returns undef. It dies from
  syntax errors in BLAST reports with a stack backtrace.
  Example of a data structure returned by getReport():
  
  $r = {
          'query_name' => 'ME1-0081T-R227-B12-U.G',
          'blast_version' => 'BLASTX 1.3.6 [2002-03-05]',
          'byte_offset' => 4981,
          'query_length' => '444',
          'query_annotation' => ''
          'round_begins' => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
          'hits' => [
                      {
                        'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]',
                        'hsps' => [
                                    {
                                      'query_end' => '82',
                                      'subject_ali' => 'ASELEIFAALIECEA-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA',
                                      'query_ali' => 'DAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK-TVDGLLAADPNYTYAVKDG-NQRYAKLMKATEAAIAADP',
                                      'subject_end' => '328',
                                      'identities' => '15',
                                      'score' => '87',
                                      'percent_positives' => '41',
                                      'gaps' => '3',
                                      'score_bits' => '37.9',
                                      'alignment_length' => '81',
                                      'evalue' => '0.40',
                                      'percent_identities' => '18',
                                      'positives' => '34',
                                      'query_start' => '4',
                                      'subject_start' => '249'
                                    }
                                  ],
                        'subject_length' => '880',
                        'subject_name' => 'gi|16802882|ref|NP_464367.1|'
                      },
                    ],
        };

AUTHORS

Apu� Paquola <[email protected]>, Abimael Machado <[email protected]> IQ-USP Bioinformatics Lab

Laszlo Kajan <[email protected]>, Technical University of Munich, Germany

SEE ALSO

Zerg

History