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

[Noah Zaitlen]

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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