[Bioperl-l] parsing tblastn using BPlite

[Jason Eric Stajich]

you can run the test individually by typing

% perl -I. -w t/BPlite.t

This will tell you what is failing wrt to test 30 as well as the line
number in the test.   If you can send us this output we may be able to
diagnose the problem.

-jason

 On Thu, 25 Oct 2001, Christoffels Alan wrote:

>
> > Pretty sure that some form of this bug is fixed in current versions - we
> > are trying to get 1.0 finished by the end of the year, you could
> > alternatively run off the CVS head or download a developer's release to
> > get a fix for  this.
>
> I downloaded the developer's release. One test for BPlite failed when I
> installed it (Test 30).
>
>
> t/BPlite............FAILED test 30
> 	Failed 1/97 tests, 98.97% okay
>
> What is test 30?? COuld this have contributed to the problem I am
> encountering with BPlite?  I get the same error as before when parsing my
> tblastn results (processing 16K records instead of 33K).
>
> Alan
>
>
> >
> >
> >
> > On Thu, 25 Oct 2001, Christoffels Alan wrote:
> >
> > > > 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
> > >
> >
> > --
> > 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu