[Bioperl-l] Bio::DB::GenBank get_Seq_by_acc($acc);

[Mick Watson]

Hi Liisa

The reason you get the error is that you probably have some code like this


    print $seq->desc, "\n";

However, $seq is undefined because get_Seq_by_acc is not returning a valid
$seq object.  The reason for this, I fear, is that you example accession
does not exist in either GenBank or EMBL:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=AAH06375

    (check out http://www.ebi.ac.uk/cgi-bin/emblfetch)

If you are not sure if your accessions are valid accession numbers or not,
then put in something like:

my $seq = $db->get_Seq_by_acc($acc);

if (defined $seq) {
    #some code
}
else {
    print STDERR "Not a valid accession\n";
}

Thanks

Mick

Liisa Koski wrote:

> Hi,
> I'm trying to get sequences by accession numbers using
>
> Bio::DB::GenBank
> my $seq = $db->get_Seq_by_acc($acc);
>
> This works fine for Accession numbers that begin with NP_ but when when
> I'm using an accession number like AAH06375 I get the following error:
>
> Can't call method "desc" on an undefined value at ...
>
> Any ideas?
>
> Cheers,
> Liisa
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