[Bioperl-l] $query in Bio::Tools::Run::Alignment

John M.C. Ma manchunjohn-ma at uiowa.edu
Thu Jul 31 12:46:41 EDT 2008


Hi again,

Sorry to come again and ask: is the $DB in Bio::Tools::Run::Alignment->run()
accept the same things as the database argument in command line Blat? I
tried to run this:

use Bio::Seq;
use Bio::Tools::Run::Primer3;
use Bio::Tools::Primer3;
use Bio::Seq::PrimedSeq;
use Bio::SeqFeature::Primer;
use Bio::Tools::Run::Alignment::Blat;

my %gene_info;
$gene_info{seq}=Bio::Seq->new(-seq=>'[snip sequence]',
-id=>'Akr1c6',);
my $primer3_handle=Bio::Tools::Run::Primer3->new(-seq=>$gene_info{seq},
-path=>'/home/johnma/primer3-1.1.4/src/primer3_core');
my $primer3_results=$primer3_handle->run();
for my $primer($primer=$primer3_results->next_primer)
{
    my $left_primer=$primer->get_primer('l')->seq;
    $left_primer->display_id($gene_info{seq}->primary_id()."_F");
    my $blat_handle=Bio::Tools::Run::Alignment::Blat->new;
    my @blat_result_f=$blat_handle->run($left_primer,
'~/Genomes/Rat/Genomic/All_chrs');
}

Whereas All_chrs is a text file containing paths for all chromosome 2bit
files for each line, per Blat requirment.

But the output just gave me the Blat help screen plus:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Blat call (/home/johnma/blatSuite.34/blat -out=psl  /tmp/G7dJhcOGZ4
/tmp/lDn680q46z) crashed: 65280

STACK: Error::throw
STACK: Bio::Root::Root::throw /home/johnma/bioperl-live/Bio/Root/Root.pm:357
STACK: Bio::Tools::Run::Alignment::Blat::_run
/home/johnma/bioperl-run/Bio/Tools/Run/Alignment/Blat.pm:250
STACK: Bio::Tools::Run::Alignment::Blat::run
/home/johnma/bioperl-run/Bio/Tools/Run/Alignment/Blat.pm:167
STACK: /home/johnma/workspace/NCBI-test/Blat-test.pl:20
-----------------------------------------------------------

I don't know what should I deal with this...

Cheers,

John


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