[Bioperl-l] Exception MSG

[Mgavi Brathwaite]

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!