[Bioperl-l] problem with needle

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Fri Apr 14 11:10:47 EDT 2006


The error means that the bioweb.pasteur.fr server was probably down in 
that moment or it couldn't be looked up. Try again later :)

Regards,
Mauricio.

madhurima bhattacharjee wrote:
> 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.
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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