Bio::Tools::BPlite::HSP Bio::Tools::BPlite::HSP is a blast report High Scoring Pair (HSP).
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Perl module scoring bioperl blast report High Scoring Pair HSP

Bio::Tools::BPlite::HSP Description

Bio::Tools::BPlite::HSP is a blast report High Scoring Pair (HSP). Bio::Tools::BPlite::HSP is a blast report High Scoring Pair (HSP).SYNOPSIS use Bio::Tools::BPlite; my $report = new Bio::Tools::BPlite(-fh=>*STDIN); { while(my $sbjct = $report->nextSbjct) { while (my $hsp = $sbjct->nextHSP) { $hsp->score; $hsp->bits; $hsp->percent; $hsp->P; $hsp->match; $hsp->positive; $hsp->length; $hsp->querySeq; $hsp->sbjctSeq; $hsp->homologySeq; $hsp->query->start; $hsp->query->end; $hsp->hit->start; $hsp->hit->end; $hsp->hit->seq_id; $hsp->hit->overlaps($exon); } } # the following line takes you to the next report in the stream/file # it will return 0 if that report is empty, # but that is valid for an empty blast report. # Returns -1 for EOF. last if $report->_parseHeader == -1; redo }This object handles the High Scoring Pair data for a Blast report. This is where the percent identity, query and hit sequence length, P value, etc are stored and where most of the necessary information is located when building logic around parsing a Blast report. Requirements: · Perl

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