[Bioperl-l] parsing clone/contig coordinates from genbank

[Hilmar Lapp]

Ewan Birney wrote:
> 
> On Thu, 1 Nov 2001, Chris Mungall wrote:
> 
> >
> > I'm trying to parse this:
> > ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/C_elegans/CHR_I/worm_I.gbs
> >
> > But I get this:
> > Can't call method "_generic_seqfeature" on an undefined value at
> > /users/cjm/cvs/bioperl-live/Bio/SeqIO/genbank.pm line 277
> >
> > is it pushing the genbank parser too far to get contig coordinates?
> 
> Which version? line 227 doesn't call _generic_seqfeature for me.
> 

genbank.pm seqIO format cannot handle CONTIGs. We had this
discussion some time ago, but no-one actually wrote the code yet
to recursively fetch the pieces.

CONTIG is not recognized presently; what do you suggest to do with
this section in absence of the recursively fetching code? Ignore
and return a seq object with empty seq? Or die with "not
implemented yet"?

	-hilmar
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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