[Bioperl-l] Exception MSG

[Mgavi Brathwaite]

Surya,

As Jason suggested, I removed the '>' and it worked. Thanks for your
response.

Lom

On Wed, Nov 30, 2011 at 9:32 AM, Surya Saha <ss2489 at cornell.edu> wrote:

> 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!
>> > _______________________________________________
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>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
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>
>