[Bioperl-l] Can't locate object method "seq_start" via package "Bio::DB::GenBank"

Eric Just e-just at northwestern.edu
Mon Apr 2 10:15:28 EDT 2007


Sorry about that.

As soon as I sent the email I found my problem ( an old NCBIHelper in my
inheritance path ).   There is no bug here.

Eric


On 4/2/07, Eric Just <e-just at northwestern.edu> wrote:
>
> Hello,
>
> I am getting this error while running a bioperl script that I had been
> using in bioperl 1.4.  On upgradeing to bioperl 1.5.2 I get the following
> fatal error
>
> Can't locate object method "seq_start" via package "Bio::DB::GenBank"
>
> My script is as follows:
>
>
> use Bio::DB::GenBank;
> use Bio::DB::Query::GenBank;
>
> my $gb = new Bio::DB::GenBank();
>
> my $query = Bio::DB::Query::GenBank->new(
>       -query   =>'txid44689[Organism:noexp]',
>       -reldate => 60,
>       -db      => 'nucleotide'
>
> );
>
> my $in = $gb->get_Stream_by_query($query);
>
> while ( my $seq = $in->next_seq()) {
>       print "do something";
>       #....
> }
>
>
>
> I noticed that seq_start is created in the begin block of
> Bio::DB::NCBIHelper (inherited by Bio::DB::GenBank), but I do not have
> expericence troubleshooting this kind of autoloaded method.  Any idea where
> to start?
>
> Thanks
>
> Eric
>


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