Re: Antw: Re: Exception thrown when parsing GenBank file
George Waldon <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l