[Bioperl-l] Help on retrieving NT contigs with Bio::DB::GenBank.

[Kun Zhang]

Hello!

I got a error message (attached below) when trying to retrieving some NT 
contigs from GenBank with the Bio::DB::Genbank module. It looks like the 
problem occurs only on NT sequence because the getGenBank.pl came with the 
bioperl-0.9.0 distribution works fine. And my perl script works when I 
replacing the "NT_001035" with "AF303112". Can anyone help me out? Thanks!

Kun Zhang
Human Genetics Center
University of Texas-Houston

------------------------My codes-----------------------------
my $gb = new Bio::DB::GenBank;
$gb->request_format('fasta') ;
$contigSeq = $gb->get_Seq_by_acc('NT_001035');	



==============================ERROR MESSAGE==================================
-------------------- EXCEPTION --------------------
MSG: Attempting to set the sequence to [<HTML] which does not look healthy
STACK Bio::PrimarySeq::seq 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/PrimarySeq.pm:251
STACK Bio::PrimarySeq::new 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/PrimarySeq.pm:226
STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/Seq.pm:132
STACK Bio::SeqIO::fasta::next_primary_seq 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/fasta.pm:130
STACK Bio::SeqIO::fasta::next_seq 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/fasta.pm:85
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc 
/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:159
STACK toplevel ./splitSeq.pl:26