Name
Smash::Utils::WUBLAST - A light-weight parser for WU-BLAST tabular output
Synopsis
my $blast = Smash::Utils::WUBLAST->new("file.blastp");
while (my $report = $blast->nextReport) {
print "Report for Query: ".$report->queryName."\n";
while (my $sbjct = $report->nextSbjct) {
print "Subject: ".$sbjct->sbjctName."\n";
while (my $group = $sbjct->nextGroup) {
print "HSP Group: ".$group->groupId."\n";
while (my $hsp = $group->nextHSP) {
print $hsp->line."\n";
$hsp->query;
$hsp->sbjct;
$hsp->qb;
$hsp->qe;
$hsp->sb;
$hsp->se;
$hsp->strand;
$hsp->percent;
$hsp->positive;
}
}
}
}
Description
Smash::Utils::WUBLAST is a light-weight parser for WU-BLAST tabular output, designed after the BPlite parser from Ian Korf. It provides most of the functionalities (except the sequences and alignments) using the same interfaces.
The group functionality is useful when you specify topComboN or topComboE together with links to WU-BLAST. It will then link groups using a given id, and that can be used to track the groups. If you do not specify this option, a default group will be created for all HSPs between the query and a subject.
