[Bioperl-l] Exception MSG

[Surya Saha]

If that does not fix it, try using one of the unique identifiers as the
file name (gi??) instead of the full query name. The pipe(|) characters
might cause problems.

On Wed, Nov 30, 2011 at 1:05 AM, Jason Stajich <jason.stajich at gmail.com>wrote:

> I don't think you need to give it the '>' when you specify the filename
> for the output. That is done by the filehandle opening itsself.
>
> On Nov 29, 2011, at 9:25 PM, Mgavi Brathwaite wrote:
>
> > Hello,
> >
> > Brushing up on my BioPerl and I can't figure out this MSG:
> >
> > ------------- EXCEPTION -------------
> >
> > MSG: cannot open
> >/Users/mydata/Desktop/gi|255572219|ref|XP_002527049|.out
> >
> > STACK Bio::Tools::Run::RemoteBlast::save_output
> > /Library/Perl/5.10.0/Bio/Tools/Run/RemoteBlast.pm:678
> >
> > STACK toplevel /Users/mydata/Documents/workspace/BI7643/rb_ex.pl:40
> >
> > -------------------------------------
> > Here is the code:
> >
> > #!/usr/bin/perl -w
> >
> > use strict;
> >
> > use Bio::Tools::Run::RemoteBlast;
> >
> >
> > #=cut
> >
> > my $prog = 'blastp';
> >
> > my $db = 'swissprot';
> >
> > my $e_val = '1e-10';
> >
> >
> > my @params = ('-prog' => $prog,
> >
> > '-data' => $db,
> >
> > 'expect' => $e_val,
> >
> > 'readmethod' => 'SearchIO' );
> >
> > my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >
> >
> > #human database
> >
> > $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> > [ORGN]';
> >
> >
> > my $v =1; # this is just to turn on and off the messages
> >
> > # Construct the sequence object
> >
> > my $seq_in = Bio::SeqIO->new(-file => "/Users/mydata/Desktop/rb_ex.fa",
> -format
> > => "fasta");
> >
> >
> > while (my $input = $seq_in->next_seq()){
> >
> > my $r = $factory->submit_blast($input);
> >
> > print STDERR "waiting..." if ($v > 0);
> >
> > while (my @rids = $factory->each_rid()){
> >
> > foreach my $rid (@rids){
> >
> > my $rc = $factory->retrieve_blast($rid);
> >
> > if( !ref($rc) ) {
> >
> > if($rc < 0){
> >
> > $factory->remove_rid($rid);
> >
> > }
> >
> > print STDERR "." if ($v > 0);
> >
> > sleep 5;
> >
> > } else {
> >
> > my $result = $rc->next_result();
> >
> > #save output
> >
> > my $filename =
> ">/Users/mydata/Desktop/".$result->query_name().".out";#error
> >
> > $factory->save_output($filename);
> >
> > $factory->remove_rid($rid);
> >
> > print "\nQuery Name: ", $result->query_name(), "\n";
> >
> >          while ( my $hit = $result->next_hit ) {
> >
> >            next unless ( $v > 0);
> >
> >            print "\thit name is ", $hit->name, "\n";
> >
> >            while( my $hsp = $hit->next_hsp ) {
> >
> >              print "\t\tscore is ", $hsp->score, "\n";
> >
> > }
> >
> >          }
> >
> >        }
> >
> >      }
> >
> >    }
> >
> >  }
> >
> >
> >
> > Thanks for the help!
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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