[Bioperl-l] Temporary name of hmmbuild model

[Jason Stajich]

you will want to either write out the alignment to a file first (with a  
name that makes sense) and pass that filename in when you run  
$hmmbuild->run()
or

pass in the -n option to hmmbuild to explicitly apply the name.  I  
don't know if the current version of Tools::HMMer supports -n but I've  
update the code recently in CVS in the bioperl-run package and you  
might give it a try.

-jason

On Apr 22, 2005, at 3:58 PM, Kary Ann Del Carmen Soriano Ocana wrote:

> Dear all:
> I am working with hmmbuild, it is working very well, but the problem  
> is, that it is generating the name model as a temporary name, and it  
> should generate it whit the same name of the origin file.
> This is a bit problem because after this I have worked whit hmmpfam  
> and the outfile is very confuse, for the temporary name.
> The hmmbuildpfam output listed below shows in the second column the  
> temporary/processing names, and not the real "description
> name"... those names are generated when we build the HMM models with
> hmmbuild/hmmcalibrate (maybe they are extracted from temporary files
> then stored in our database like that or In my mind it is reading the  
> clustalw alignment as temporary)... not sure how we could catch
> the real names.. any further tips would be greatly appreciated.
>
> [kary at vivax MGE-Tryp_Mobile_Genetic_Elements_14_01_05]$ more
> searchio.out
> tr|Q8GPE3       lEwFFhiGV0      -108    1.4e-05 Tnp-IS1191 -
> Streptococcus thermophilus.
> tr|Q8GPE3       Uge97N6Hov      1229    0.0e+00 Tnp-IS1191 -
> Streptococcus thermophilus.
> tr|Q8GPE3       5o31pMTfTD      358     2.9e-106        Tnp-IS1191 -
> Streptococcus thermophilus.
> tr|Q8GPE3       S9idxzhdAK      108     4.4e-31 Tnp-IS1191 -
> Streptococcus thermophilus.
>
> And this is the script of hmmbuild.
> #!/usr/bin/perl -w
> #'/usr/local/bin/hmmbuild';
> use lib "/usr/local/bioperl14";
> use lib "/usr/local/bioperl-run-1.4";
>
> #use Bio::Tools::Run::WrapperBase;
> use Bio::Tools::Run::Hmmer;
> #use Bio::Tools::Run::Alignment::Clustalw;
> use strict;
>
> my $outfile;
> open (LOG, ">>./log_file_hmmerbuild");
> my $in;
> my @tree;
> my $street;
>
> my $dirname =  
> "/home/kary/public_html/inserir_dados/ 
> trypanosoma_5B_0603_CLUSTALW_files_teste";
> open (DH, "find $dirname |") or die "Cannot open $dirname: $!";
>
> while ($in=<DH>){
> chomp ($in);
>
>     	for ($in =~ /\_(aln)/) {
> 		@tree = split(/[\/]/, $in);
> 		my $aln = pop @tree;
> 		my $street = join "/", @tree,"\n";
> 		chomp ($street);
> 		
> 	
> 	print LOG "File $street$aln launched and ";
> 	&hmm_build($in);
> 	
> 	
> 	}
> 	
> }
>
>
> ####################################################################### 
> ######################################################################
> sub hmm_build {
> 	my($aln) = @_;
> 	print "Your input file is: $aln\n";
> 	my $name_outfile = "$aln";
> 	$name_outfile =~ s/_aln//;
> 	my $outfile = "$name_outfile.hmm";
> 	print LOG "Your output file is: $outfile\n";
> 		
> 	#build a hmm using hmmbuild
> 	my $aio = Bio::AlignIO->new(-file=>"$in",-format=>'clustalw') or die  
> print "Error for open the file";
> 	$aln = $aio->next_aln;
> 	my $factory =   
> Bio::Tools::Run::Hmmer->new('program'=>'hmmbuild','hmm'=>$outfile);
> 	$factory->run($aln);
> 	&hmm_calibrate($in);
> }
> ####################################################################### 
> ######################################################################
> sub hmm_calibrate {
> 	my($aln) = @_;
> 	my $name_outfile = "$aln";
> 	$name_outfile =~ s/.aln//;
> 	my $outfile = "$name_outfile.hmm";
> 	print LOG "Your output file is: $outfile\n";
> 	#calibrate the hmm
> 	my $factory =   
> Bio::Tools::Run::Hmmer- 
> >new('program'=>'hmmcalibrate','hmm'=>$outfile);
> 	$factory->run();
> }
> ####################################################################### 
> ######################################################################
>
>
> Kindest regards,
> Kary
>
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