[Bioperl-l] Problems getting NTs

[Stefan Kirov]

                  $seq = new Bio::DB::RefSeq(-retrievaltype =>
'tempfile', -format => 'fasta');
                  $tmp = $seq->get_Seq_by_acc('NT_005612');
or
        $refseq=new Bio::DB::RefSeq;
        $geneloc = $refseq->get_Seq_by_acc('NT_005612');
I tried both RefSeq and GenBank to get NT contigs, both FASTA and GB
format and I keep getting this error:
MSG: NT_ contigs are whole chromosome files which are not part of
regulardatabase distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.
Different methods (get_seq_by_acc, get_seq_by_gi,version, bacth) give
sometimes different error messages, but they all have one thing in
common- they fail.
Am I missing something fundamental or NCBI are in a middle of a big
shift and if you want to work on the NTs you should do this locally? I
think there was a small discussion on this previously, so if anyone has
had any success with using bioperl to directly work on the NTs, please
share your experience.
Thanks!!!


--
Stefan A. Kirov, Ph.D.
Dept Biochemistry and Cellular and Molecular Biology
F233 Walters Life Sciences Building
1414 Cumberland Avenue
University of Tennessee
Knoxville, TN  37996-0840
Tel: 865-974-6710