[Bioperl-l] retrieve ensembl sequence using bioperl

Laurent Manchon lmanchon at univ-montp2.fr
Thu Jul 24 10:01:32 EDT 2008


Hi,

I try to download sequence from ensembl database submiting the ID via
the perl code below.
For swiss or genbank ID submission it works fine but for ensembl it fails and
i don't know why.
Tell me if you have an idea .

thank you.


#!/usr/bin/perl -w
use Bio::Perl;

if ($#ARGV < 0) {
print "Usage: $0 databaseID\n";
exit;
}
#database availables 'swiss','genbank','genpept','embl','refseq'
$seq_object = get_sequence('embl',$ARGV[0]);
write_sequence(">${ARGV[0]}.fasta",'fasta',$seq_object);


+---------------------------------------------+
  Laurent Manchon
  Email: lmanchon at univ-montp2.fr
+---------------------------------------------+


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