[Bioperl-l] blat module

[Jack Chen]

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
+++++++++++++++++++++++++++++++++++++++++++++