[Biojava-l] Re: genbank contig stuff

[Schreiber, Mark]

Hi -

I did this once for an EMBL contig file. From memory I called the file EMBLAssemble :) The only problem is that you have to make available all the other Genbank or EMBL records that are referenced. I also found quite a few errors in the syntax of the join statements which indicates to me that they where not well used in those days.

- Mark



-----Original Message-----
From:	Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk]
Sent:	Fri 27/06/2003 6:57 a.m.
To:	Matthew Pocock
Cc:	biojava-l
Subject:	[Biojava-l] Re: genbank contig stuff

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

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