[Bioperl-l] get html-output on my prompt

Mark Aquino maquino at knome.com
Sun Jun 24 09:51:46 EDT 2012


Your use of the $x variable prevents you from
ever entering the while loop at the beginning of the program. You also use it in loops elsewhere, but nowhere in the code do you have an incrementer. 

Sent from my iPhone

On Jun 24, 2012, at 9:46 AM, "ak2083" <ankh.egypt.public at googlemail.com> wrote:

> 
> Hello,
> 
> i try to blast a protein sequence (in sequence.fasta) against the blast-db.
> If i parse this
> with the command 'perl file.pl', then the programm displayed html-code on my
> prompt and the out-file
> was not created. What could i do so that the results write into the
> out-file?
> 
> my $report = $blast_obj->submit_blast('sequence.fasta');
> my $x = 0;
> print STDERR "waiting..." if ($x > 0);
> 
> while (my @rids = $blast_obj->each_rid() && $x == 5)
> {
>    foreach my $rid (@rids)
>    {
>        my $rc = $blast_obj->retrieve_blast($rid);
>        if (!ref($rc))
>        {
>            if ($rc < 0)
>            { $blast_obj->remove_rid($rid); }
>            print STDERR "." if ($x > 0);
>            sleep 5;
>        }
>        else
>        {
>            my $result   = $rc->next_result();
>            my $filename = $result->query_name(), '\.out';
>            $blast_obj->save_output($filename);
>            $blast_obj->remove_rid($rid);
>            print "\nQuery Name: ", $result->query_name();
>            
>            while (my $hit = $result->next_hit())
>            {
>                next unless ($x > 0);
>                print "\thit name is ", $hit->name, "\n";
>        
>                while (my $hsp = $hit->next_hsp())
>                {
>                    print "\t\tscore is ", $hsp->score(), "\n";
>                }
>            }
>        }
>    }
> } 
> -- 
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> 
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