[Bioperl-l] problem with needle

madhurima bhattacharjee madhurima_b at persistent.co.in
Fri Apr 14 08:41:46 EDT 2006


Hello,
I am new ti BioPerl.I am using the pise module to perform needle allignment.
I am using the following code:

use Bio::Tools::Run::AnalysisFactory::Pise;
my $factory = new Bio::Tools::Run::AnalysisFactory::Pise();
my $needle = $factory->program('needle');
my $job = $needle->run(-sequencea => $ARGV[0],
                       -seqall => $ARGV[1],
                       -gapopen => 5,
                       -gapextend => 1);
if ($job->error) {
    print ".............error: ",$job->error_message,".............\n";
    exit;
}
print STDERR "jobid: ", $job->jobid, "\n";
print $job->content('needletest.needle');

But it gives me the following error:
.............error: Bio::Tools::Run::PiseJob _submit: Can't connect to 
bioweb.pasteur.fr:80 (connect: timeout).............

Can anyone please point me to the problem in code.I am really stuck in this.

Thanks and Regards,
Madhurima.




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