[Bioperl-l] strange behavior of Bio::Tools::Run::Alignment::StandAloneFasta

[Chris Fields]

You should file this as a bug.  My guess is something here is checking for boolean context instead of defined(), so is failing when set to 0.  

The other issue, setting of 'q', might be unimplemented.

chris

On Apr 13, 2010, at 10:02 PM, Dimitar Kenanov wrote:

> Hello guys,
> i found some strange behavior of the the module "Bio::Tools::Run::Alignment::StandAloneFasta". I am trying to run "ssearch36" or "fasta36" locally and parse the report. I want to get the hits name, e-values, and sequences out of the report and print them to another file which i can process further.
> 
> Below is the code where - $fh_dbs=file with a list of fasta libraries; $line=my current fasta library; $seq=my query.
> 
> my @arg=(
>    'E' => '0.01',
>    'd' => '0', #problem here
>    'H' => '',
>    'w' => '100',
>    'O' => "$output",
>    'program' => 'ssearch36',
>    );
> 
> my $line;
> while($line=<$fh_dbs>){
>    chomp($line);
>    print "DB:$line:\n";
> 
> 
>    my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg);
>    $factory->library($line);
>    my @fastreport=$factory->run($seq);
> 
>    foreach  (@fastreport) {
>    print "Parsed fasta report:\n";
>    my $result = $_->next_result;
> 
>        while( my $hit = $result->next_hit()) {
>            print "\thit name: ", $hit->name();
>            while( my $hsp = $hit->next_hsp()) {
>                my $e_val=$hsp->evalue;
>                my $qseq=$hsp->query_string;
>                my $hseq=$hsp->hit_string;
>                print "E:$e_val:\n",
>                print "Q-SEQ:$qseq:\n";
>                print "HIT-SEQ:$hseq:\n";
> 
> 
>            }
>        }
>    }
> }
> 
> Now the weird thing is that if i mark the line 'd' => '0' then i can get the HIT and QUERY sequences but not the E-value and if its unmarked as i want it then i can get the E-value but not the sequences.
> Its strange and i dont know how to solve that problem.
> If someone has any idea how i can go around that i would be very thankful.
> 
> 
> Thanks
> Dimitar
> 
> PS: Another problem i found is the "q" option. Even if i pass it through the @arg, its not working. I still see the output on my terminal.
> 
> -- 
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> email: dimitark at bii.a-star.edu.sg
> tel: +65 6478 8514
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l