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

       Apuã Paquola <apua@iq.usp.br>, Abimael Machado <abimael@iq.usp.br> IQ-USP Bioinformatics
       Lab

       Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany

SEE ALSO

       Zerg

POD ERRORS

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