[Biojava-l] Antw: Re: Exception thrown when parsing GenBank file

[Andreas Prlic]

Hi Dietmar,

The genbank parser is on top of the feature request list for biojava
3: http://biojava.org/wiki/BioJava3_Feature_Requests

Anybody who wants to take an initiative here and claim ownership of
this topic is welcome...

Andreas


On Wed, Nov 23, 2011 at 7:18 AM, Dietmar Birzer
<Dietmar.Birzer at biologie.uni-regensburg.de> wrote:
>  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 <p.j.a.cock at googlemail.com> 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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