[Bioperl-l] PrimarySeqI object Exception

[Brian Osborne]

sss lll,

What this error means is that $obj is not a valid Sequence object, this is
what's passed to the write_seq method. What identifier is
$array_gene_name[$p]?

Brian O.


On 7/6/06 2:13 PM, "sss lll" <nidage at yahoo.com> wrote:

> Hi there,
> 
> I encountered a problem while calling module
> PrimarySeqI, with the following code:
> 
> my $db=Bio::DB::Fasta->new($fafile);
> my $obj=$db->get_Seq_by_id($array_gene_name[$p]);
> $seqio->write_seq($obj);
> 
> The error message was:
> MSG: Did not provide a valid Bio::PrimarySeqI object
> STACK Bio::SeqIO::fasta::write_seq
> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/fasta.pm:178
> 
> We think it had to do with the lengh of the gene name.
> For example the following gene name was a problem:
> 
> gi|59711891|ref|YP_204667.1| NAD-specific glutamate
> dehydrogenase [Vibrio fischeri ES114]*VIB*COG2902*E
> 
> Any ideas on what happened?
> 
> Thanks
> 
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