[Bioperl-l] retrieve ensembl sequence using bioperl

Mark Johnson johnsonm at gmail.com
Thu Jul 24 15:45:59 EDT 2008


On Thu, Jul 24, 2008 at 9:01 AM, Laurent Manchon
<lmanchon at univ-montp2.fr> wrote:

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

Ah.  Ye Olde Functional Interace.

> 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);

Can you give us an example of an accession / identifier / whatever
that does not work?  Are you sure your queries are valid EMBL
accessions?  If you go here:

http://www.ebi.ac.uk/ebisearch/

and plug in your input, do you get any sequences returned?


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