[Bioperl-l] TCoffee.pm in windows

[Jason Stajich]

On Wed, 25 Sep 2002, Fernandez-Capetillo, Oscar (NCI) wrote:

>
> 	Hi there,
>
> 	I've modified Tcoffe.pm and IO.pm so that now it works in windows
> environments in case someone wants it (it didn't before because the system
> calls assume it is a UNIX environment). Just one question,
>
we'd be happy to fold this back into the code if you provide it.

> 	Using tcoffe.pm for my scripts it does not create an .aln file so
> that I can use it in other programs like clustalx. It just creates the
> alignment object but there is no available method I can see that serves to
> generate an aln file from an align object. Any suggestions?
>
use Bio::AlignIO;
my $out = new Bio::AlignIO(-format => "clustalw", # or phylip,msf,gcg,fasta,etc
		           -file   => ">myfile.aln");
$out->write_aln($aln);

> 	Thanks,
>
> 	Oskar
>
> Oskar Fernandez-Capetillo, Ph. D.
>  NCI Build., 10 Room 4A01
> National Institute of Health
> 10 Center Drive
> Bethesda, MD
> 20892, 1360
>
> Phone: 301-594-3044
> Fax:      301-496-0887
> e-mail: fernando@mail.nih.gov
> www: http://usuarios.lycos.es/h2ax/
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu