[Bioperl-l] blat module

[Jason Stajich]

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
> +++++++++++++++++++++++++++++++++++++++++++++
>
>
>
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>

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