[Bioperl-l] Help with hmmpfam

[Brian Osborne]

Kary,

It could be that there's something odd about your hmmpfam output file, for
that reason you should probably show us its contents.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Kary Ann Del
Carmen Soriano Ocana
Sent: Thursday, March 24, 2005 3:24 PM
To: bioperl-l at portal.open-bio.org
Cc: maruco at gmail.com
Subject: [Bioperl-l] Help with hmmpfam


Dear All,

I am new to bioperl and would like (if possible) to obtain some help with
the SearcIO module and hmmpfam. I am listing my code below and the output
containing the following error:

(partial) output and error:

[kary at vivax inserir_dados]$ perl bioperl_pfam_23_03_05.pl
Passou a definicao do arquivo query
passou abrir o arquivo mmm.hmm

sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `/usr/local/bin/hmmpfam  -E 0.0001      1       HMMER2.0
[2.3.2]\nNAME  76GJYz8zFm\nLENG  327\nALPH

I put some "print" commands everywhere to see where I am getting the error
and looks like it is not entering/printing the while results (eg:
next_result, next_hit). Any help would be greatly appreciated.

Thanks, Kary

************

Script:

#!/usr/bin/perl -w

use lib "/usr/local/bioperl14";
use lib "/usr/local/bioperl-run-1.4";

use Bio::Search::Result::HMMERResult;
use Bio::Tools::Run::Hmmer;
use Bio::Tools::Run::Hmmpfam;
use strict;

my $query;
my $db;
my $seq;
my $dbfile;
my @array;

$query = "sequencia_fasta_4_arg.txt";

print "Passou a definicao do arquivo query\n";

open (READ, "$query") or die "Cannot open $query: $!";
while (my $sequence = <READ>){
	 for ($sequence) {
		&hmmpfam($sequence);
	#print $seq;
	}
}
close (READ);

print "Passou leitura do arquivo query\n";
############################################################################
#################################################################
sub hmmpfam {
	my ($seq) = @_;
	$db = "mmm.hmm";
	open (DH, "$db") or die "Cannot open $db: $!";

	print "passou abrir o arquivo mmm.hmm\n\n";

	while ($dbfile = <DH>){

		#Build a Hmmpfam factory
		my @params = ('DB'=>$dbfile,'E'=>0.0001);


		my $factory = Bio::Tools::Run::Hmmpfam->new(@params);


		# Pass the factory a Bio::Seq object or a file name
		# returns a Bio::SearchIO object
		my $search = $factory->run($seq);
		print "Search: $search\n";

		print "Passou search com parametros \n";


		my @feat;

			my $searchio = new Bio::SearchIO(-format => 'hmmer',
                                 -file   => 'result.hmmer') or die print
"Error for open the file";

			while (my $result = $searchio->next_result){
				print "começa o while do NEXT RESULT\n\n";
			while(my $hit = $result->next_hit){
				print "começa o while do HIT - NEXT HIT\n\n";
			while (my $hsp = my $hit->next_hsp){
				print join("\t", ( my$r->query_name,
						$hsp->query->start,
						$hsp->query->end,
						$hit->name,
						$hsp->hit->start,
						$hsp->hit->end,
						$hsp->score,
						$hsp->evalue,
						$hsp->seq_str,
						)), "\n";
				print "terminou o while dos HSPs\n\n";

							 }
							}
									}

}


close (DH);
}

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