[Bioperl-l] parsing tblastn using BPlite

[Christoffels Alan]

> Hmm, which version of bioperl/BPlite are you using?

$Id: BPlite.pm,v 1.14.2.5 2001/04/08 21:28:44 lapp Exp $


Alan


> 
> % perldoc -m Bio::Tools::BPlite | grep Id
> 
> Will help us diagnose if this is a new or old bug.
> 
> -jason
> On Wed, 24 Oct 2001, Christoffels Alan wrote:
> 
> > Hi,
> >
> > I am using BPlite to parse a tblastn output file containing multiple
> > tblastn reports (~30K query sequences).
> >
> > WHen I count the actually reports being read by the script, I only get
> > about 16K. Can any tell me what I am doing wrong in this script?
> >
> > use Bio::Tools::BPlite;
> > use strict;
> > my $file = $ARGV[0];
> > my $cutoff = $ARGV[1];
> > my $total_rec = 0;
> > open(BLAST, "$file");
> > {
> > my $report = new Bio::Tools::BPlite(-fh=>\*BLAST);
> > $total_rec++;
> > my $QUERY = $report->query;
> > my $rec = 0;
> > GG:
> > while (my $sbjct = $report->nextSbjct) {
> > 	$rec++;
> > 	my $SUBJ = $sbjct->name;
> > 	while (my $hsp = $sbjct->nextHSP) {
> > 		my $HSP = $hsp->P;
> > 		if ($HSP < $cutoff) {
> > 		print "$QUERY\t$SUBJ\t$HSP\n";
> > 		last;
> > 		}
> > 	}
> > 	if ($rec ==1) {
> > 		last GG;
> > 	}
> > }
> > last if ($report->_parseHeader == -1);
> > redo;
> > }
> > close(BLAST);
> > print STDERR "total records .$total_rec.\n";
> >
> > Alan Christoffels
> > Institute of Molecular and Cell Biology
> > 30 Medical Drive
> > Singapore
> > 117609
> > Tel: 65-8741489
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 

Christoffels Alan
Institute of Molecular and Cell Biology
30 Medical Drive
Singapore
117609
Tel: 65-8741489