[Bioperl-l] alignment by TCoffee as a subroutine

Sendu Bala bix at sendu.me.uk
Wed Apr 30 10:22:01 EDT 2008

sergei ryazansky wrote:
> On Wed, 30 Apr 2008 16:47:17 +0400, Sendu Bala <bix at sendu.me.uk> wrote:
>> sergei ryazansky wrote:
>>> 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.
>> The problem lies somewhere within the rest of your script, so we have 
>> to see it if you want help.
> The rest of script,imho, is ok, because without this sub it is work 
> fine. May be problem lies into the TCoffee itself?

I've run your subroutine in a simple script of my own and it doesn't 
cause script termination. Again, the problem lies elsewhere in your 
script. Supply it or it is impossible for anyone to help you.

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