[Bioperl-l] alignment by TCoffee as a subroutine

sergei ryazansky dr.hogart at gmail.com
Wed Apr 30 07:24:35 EDT 2008

On Tue, 29 Apr 2008 19:57:51 +0400, sergei ryazansky <dr.hogart at gmail.com>  

> Hi all!
> I am trying to perform TCoffe aligment by  
> Bio::Tools::Run::Alignment::TCoffee wrapper as subroutine into the  
> script. This subroutine works fine, but it is not single subroutine -  
> there are a lot of other ones in the script. The problem is when  
> compilation of script finish execution (nb! successful execution) of  
> tcoffee subroutine the compiliation of the end of the script also  
> interrupted. It seems that the tcoffee program itself induce  
> interraption of perl compilation. Is it possible to pass this problem?

My subroutine is following:

sub align {
	my $file=shift @_;
	my @params = ('ktuple' => 2,'matrix' => 'BLOSUM', 'output' => 'fasta',  
'outfile' => 'temp_align.out');
	my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
	my $aln=$factory->align ($file);
	open (fy,'temp_align.out'); my @temp_file=<fy>; close fy;
	return @temp_file;

This subroutine is called by the following command:

my @align_fa = align($inputfile_align);

After successful execution of this subroutine (accompaning with the  
corresponding messages on the terminal window) the execution of remainder  
script is terminated without any error messages.


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