[Bioperl-l] Add a new parameters for Hmmpfam

[Kary Ann Del Carmen Soriano Ocana]

Dear Marc Logghe:

I have a script in perl for run hmmpfam (add following), I would like add other parameter in my @params, because when I run by shell with this "expert options command --forward" (Viterbi algorithm), it returns me much more hits in the result:

1.- SHELL COMMAND
my $factory = system("hmmpfam -E 0.1 --forward modelos_hmmer_alignm.hmm $seq >results/hmmer_alignm.out")

2.- PERL SCRIPT
#!/usr/bin/perl -w

$ENV{HMMPFAMDIR} = '/usr/local/bin/';
use lib "/usr/local/bioperl14";
use lib "/usr/local/bioperl-run-1.4";

use strict;
use Bio::Tools::Run::Hmmpfam;
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;
use Bio::SearchIO::Writer::TextResultWriter;
use Bio::SearchIO::Writer::HSPTableWriter;
use Bio::SearchIO::Writer::ResultTableWriter;
use Bio::SeqIO;

my @params = ('DB' => 'modelos_hmmer_tcoffee.hmm', 'E' => 0.1);
my $factory = Bio::Tools::Run::Hmmpfam->new(@params);
my $seq = $ARGV[0];
   
#any old protein fasta file
my $search = $factory->run($seq);

my $writer = Bio::SearchIO::Writer::HSPTableWriter -> new(
							-columns => [qw(
								 hit_name
								 query_name
								 score
								 expect
								 start_hit
								 end_hit
								 start_query
								 end_query
								  
								 )]
							 );

my $out = Bio::SearchIO->new( -writer => $writer,
			      -file   => ">results/searchio_tcoffee.out" );
 
while (my $result = $search->next_result()) {
	$out->write_result($result);
}


Thank you very much for help me.

Your faithfully

Kary Soriano