acd files

[Peter Ernst]

On Tue, 15 Jul 2003, Peter Rice wrote:

> Derek Gatherer wrote:
> > So would that allow eg. a Perl script to be called? (I ask because I
> > have many old Perl scripts of varying degrees of usefulness, but I am
> > now required to provide tools within an EMBOSS-centric department).
>
> There was also a Perl ACD wrapper from Peter Ernst, and here at EBI we

It's the CPAN Bio::Emboss module:
http://www.perl.com/CPAN/modules/by-module/Bio/

Usage: for example, a perl version of the EMBOSS program 'seqret', using
       seqret.acd:

--- snip ---

  use Bio::Emboss qw(:all);

  embInitPerl("seqret", \@ARGV);

  $seqall = ajAcdGetSeqall("sequence");
  $seqout = ajAcdGetSeqoutall("outseq");

  while ($seqall->ajSeqallNext($seq)) {
      $seqout->ajSeqAllWrite ($seq);
  }

--- snip ---

Regards,
	Peter Ernst

-- 
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 Peter Ernst
 Department of Molecular Biophysics - B020
 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ
 Im Neuenheimer Feld 580 / Technologiepark 3
 69120 Heidelberg, Germany                     phone: +49-6221-42-2330
 http://genome.dkfz-heidelberg.de/               fax: +49-6221-42-2333
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