Hi Dietmar,
The GenbankLocationParser from biojava-1.8.1 is working perfectly as
long as you feed him with DNA locations that use the syntax described
in the DDBJ/EMBL/GenBank feature table definition. What you've got
(join(bond(9),bond(125))...) is a pseudo GenBank format that
apparently describes protein structure and uses a slightly different
syntax to indicate heteroatom locations. That is why you get all these
exceptions thrown.
George
Quoting Dietmar Birzer <[email protected]>:
Hi all,
as the GenbankLocationParser from biojava-1.8.1 is not working
properly anymore, I was wondering if there is an equivalent way to
do this ( GenpeptRichSequenceDB().getRichSequence("14719485") )
using BioJava 3.
Unfortunately I could not find any GenBank/GenPept parser so far. Is
that because it does not exist (yet), or just because I have not
looked properly?
Best wishes
Dietmar
Peter Cock <[email protected]> 11/14/2011 6:29 PM >>>
On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
Hi all,
I am currently trying to debug a little software application which
uses BioJava's core-1.8.1.jar library because it has started to
throw exceptions a while ago.
I guess the problem is, that the GenbankLocationParser is not
able to handle "Het" entries in the features section of the
GenBank/GenPept format, e.g.
Het join(bond(9),bond(125))
/heterogen="( NA, 5 )"
for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
Interesting - note the bond locations are not in the official
DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
that seems to be intended only for nucleotides and not proteins as here.
It might be worth contacting the NCBI to find out if there is an official
specification covering these location strings?
Peter
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