[Bioperl-l] parsing tblastn using BPlite

[Christoffels Alan]

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Jason,

I have attached the output from the BPlite test.

alan

> 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
> 

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

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