[Bioperl-l] Help with hmmpfam

[Jason Stajich]

We would really need your hmmpfam output to diagnose the problem  
(result.hmmer)

-jason

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Mar 24, 2005, at 12:24 PM, Kary Ann Del Carmen Soriano Ocana wrote:

> 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);
> }
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>