[Bioperl-l] blat module

[Jack Chen]

Thanks for your prompt reply!

I think the Bio::Tools::Blat documentation should be correct accordingly.

I got an error message like this:

Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blat.pm line 126, <GEN0> line 2.

the line read: 

unless ( $matches =~/^\d+$/ ){

Thanks,

jack



On Wed, 17 Sep 2003, Jason Stajich wrote:

> You want:
>   my $blat_parser = new Bio::Tools::Blat(-file => "./temp");
> 
> Otherwise, in absence of any arguments that Root::IO knows about, it will
> try and read from STDIN.
> 
> The new - more experimental Bio::SearchIO::blast is in CVS on the main
> trunk if you want to give that whirl too.  It *might* require you to have
> stripped out the header line ahead of time, can't remember if I added in
> a check to remove that or not.
> 
> -jason
> On Wed, 17 Sep 2003, Jack Chen wrote:
> 
> > Hi All,
> >
> > I am trying to use the Blat.pm module. I have a simple script like this:
> >
> > #!/usr/bin/perl -w
> > use strict;
> > use Bio::Tools::Blat;
> >
> > my @bllat_feat;
> >
> > my $blat_parser = new Bio::Tools::Blat(-filename => "./temp");
> >
> > while( my $blat_feat = $blat_parser->next_result() ) {
> >   warn "here...\n";
> >   push @bllat_feat, $blat_feat;
> > }
> >
> >
> > In the script, temp is a blat result file, sitting in the current
> > directory. The content of the file is (sorry that the lines in the file
> > are wrapped). The probelm I have is that the program never runs. It gets
> > stuck right after I execute the command. Any suggestion?
> >
> > Jack
> >
> > psLayout version 3
> >
> > match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap   strand  Q
> > Q       Q       Q       T               T       T       T       blockSizes
> > qStarts  tStarts
> >         match   match           count   bases   count   bases
> > name            size    start   end     name            size    start
> > end
> > ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> > 80      0       0       0       0       0       0       0       +
> > origi   80      0       80      CHROMOSOME_III  13783268        13703494
> > 13703574        1       80,     0,      13703494,
> >
> >
> >
> >
> > ++++++++++++++++++++++++++++++++++++++++++++
> >     o-o     Jack Chen, Stein Laboratory
> >     o---o   Cold Spring Harbor Laboratory
> >   o----o    #5 Williams, 1 Bungtown Road
> >  O----O     Cold Spring Harbor, NY, 11724
> >  0--o       Tel: 1 516 367 8394
> >    O        e-mail: chenn at cshl.org
> >   o-o       Website: http://www.wormbase.org
> > +++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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