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

Eric Just e-just at northwestern.edu
Mon Apr 2 10:12:33 EDT 2007


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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