[Biojava-l] Re: genbank contig stuff

[Matthew Pocock]

Sory - I fired that off without thinking much.

I just downloaded the genbank file NT_010783 from the ncbi. Our parsers 
spewed lots of errors about features not being within the range 1..0, 
and after a little poking arround in the code, I found that a zero 
length sequence was being generated. In despiration, I looked at the 
physical genbank file. Instead of sequences, it contains a CONTIG 
section with a single big join() describing how to build it from other 
entries.

Has anybody modified our genbank parser to process entries like this? To 
be honest, I'm not quite sure where to start.

Matthew