[Bioperl-l] (no subject)

[Xiaowu Gai]

Hi All:

I am using BioPerl in my project and I found something that was really 
puzzling, I am not very sure it is a bug though:

When I tried to use the get_Seq_by_acc method, it failed with the error 
message "Can not call method "_generic_seqfeature" on an undefined value at 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm line 272". 
However, it only gave me such error when I tried to get the sequence with 
the accession number of NT_006204 which is a big big sequence, and it 
worked just fine if I use another accession number such as AI770588 which 
is a short EST sequence. Can someone help me here? Thank you so much.

Here is the codes that I used to test it:

use Bio::DB::GenBank;
use Bio::Seq;

my $gb = new Bio::DB::GenBank();
my $seq = $gb->get_Seq_by_acc("NT_006204");    # does not work
         or
my $seq = $gb->get_Seq_by_acc("AI770588");      # does work
print $seq->desc();

Have a nice day.

Xiaowu


Xiaowu Gai, PhD
Associate Scientist
L. H. Baker Center for Bioinformatics and Biostatistics
Iowa State University
Ames, IA 50011
Phone: (515) 294-7624
Email: xgai@iastate.edu