[Bioperl-l] parsing tblastn using BPlite

[Jason Eric Stajich]

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

% 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