[Bioperl-l] PrimarySeqI object Exception

[CHANDAN SINGH]

Hi

By default ,  id is the first word encountered i.e, the first  string  after
">"  seperated from the rest by a space. The sample id u mentioned in ur
first mail contains spaces and as i mentioned in my previous mail, i am sure
the ids made by indexing and the ones u r using in the array are different.
U can see the ids used in indexing by using

@ids = $db->ids() ;
print join("\n", at ids) ;


Cheers
Chandan


On 7/7/06, Brian Osborne <osborne1 at optonline.net> wrote:
>
> 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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