[Bioperl-l] Bioperl module: Bio::Tools::Run::Alignment::TCoffee

ChaosMK2 ChaosMK2 at gmx.net
Mon Jun 13 16:58:31 EDT 2005

I would like to use your TCoffe module but I encountered some problems. 
First I post the code then I will write my questions.

use strict;
use warnings;
use Bio::Tools::Run::Alignment::TCoffee;

print "Enter full name of directory containing t_*fasta files:\n";
chomp(my $dir = <>);
chdir $dir;

#my @params = ("ktuple" => 2, "matrix" => "BLOSUM", "tg-mode" => 0, 
"output" => "fasta_aln", "score_html");
my @params = ("ktuple" => 2, "matrix" => "BLOSUM", "output" => 
my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
my @multizFiles = grep(!-d, glob("t_MULTIZ_BLAT_*fasta"));
for my $multizFile (@multizFiles)
  open(INPUT, "<", $multizFile);
  open(FILE, ">", "Temp");
      print FILE;
  close FILE;
  close INPUT;
  my $file = File::Spec->catfile($dir, "Temp");            
  my $aln = $factory->align($file);
  open(FILE, ">", "TCoffee_$multizFile");
  print FILE $aln;
  close FILE;
  unlink $file;

First: if I use tg-mode I get the exeption "unallowed parameter TG-MODE !"
Second: the same exeption with score_html (Considering your description 
I can have more than one output format. Or is it my fault and I have to 
write it another way?)
Third and main problem: I am working on a Windows XP system so I guess 
thats the reason but here comes what the exception tells me:
TCoffee call crashed: 256 [command -in=...]
Before that windows reports an error: Command "-in" was not found...

How to resolve that. Do I have to use Linux? I would have the possiblity 
but not the admin rights to install all the modules but thats my problem 
and would not be an obstacle. Are there any other solutions for my 
problem or is my code buggy? Thank you for any help provided.


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