[Bioperl-l] Re: getting non-seq data from NT_ files

[Jason Stajich]

Since NT are refseqs not normal genbank entries try using the new
Bio::DB::RefSeq handle.  I *think* it might provide what you need, but I
don't use it very often.  Documentation should be fixed in the DB::GenBank
to reflect the new option.

Otherwise I'd suggest looking at the Bio::DB::NCBIHelper/DB::GenBank code
and seeing if you can write some better dispatch methods to handle the
case where you just want the annotation.  Something like a '-noseq'
option.

-jason

On Tue, 12 Feb 2002, Noah Zaitlen wrote:

> I followed this note for GenBank.pm
>
> Note that when querying for GenBank accessions starting with 'NT_' you
> will need to call $gb-E<gt>request_format('fasta') beforehand, because in
> GenBank format (the default) the sequence part will be left out (the
> reason is that NT contigs are rather annotation with references to
> clones).
>
> However, this only gives the data from a fasta file.  I would like the other
> data from the included in the genbank file.  I.E. I would like the genbank
> file listed at
>
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=&txt=&save=0&cfm=on&query_key=2&db=nucleotide&view=gb
>
> I don't mind if the sequence is missing b/c that data is available using the
> Note above.
>
> I tried
> $seq = $gb->get_Seq_by_gi('15294447');
>
> and I get the following error message
> -------------------- WARNING ---------------------
> MSG: CONTIG found. GenBank get_Stream_by_batch about to run.
> ---------------------------------------------------
> Use of uninitialized value in string ne at
> /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm line 288.
> Use of uninitialized value in string ne at
> /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm line 288.
> Can't call method "subseq" on an undefined value at
> /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm line 301.
>
> Does anyone know a way around this?
>
> Thanks,
>    Noah Z.
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu