acd files
Peter Ernst
P.Ernst at dkfz-heidelberg.de
Wed Jul 16 08:44:33 UTC 2003
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
--
=======================================================================
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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