I have noticed that the in the nightly build, no Exception is thrown. I guess it just simply ignored the features at position 0, as David suggested.
I tend to like the idea of relax the location constraint. Another approach might be create a RelaxLocation class. Regards, Tao ----- Original Message ----- From: Matthew Pocock <[EMAIL PROTECTED]> Date: Friday, May 14, 2004 3:21 am Subject: Re: [Biojava-dev] Feature at position 0 > I think for the sake of useability, we could either relax the > location > constraint to allow point locations at 0, or in the sp parser, re- > write > these as <1 - what do people think? > > Matthew > > Tao Xu wrote: > > >Hi there, > > > >I am trying to use SeqIOTools.readSwissport() to process a > SwissProt flat file. An Exception is thrown whenever a feature at > position 0 is encountered. The user manual from UniProt/SwissProt > says that a feature at position 0 means the initiator methionine > was cleaved off. > >This happens quite often ( at least a few persent of the > SwissProt records has this line "FT INIT_MET 0 0". I > googled and found your message. Is there a solution to this > problem now? Thanks a lot for your help. > > > >Regards, > > > >Tao > > > >On Wednesday 15 Oct 2003 2:11 pm, Mark Southern wrote: > > > > > >>This is a real world example. > >> > >>Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence > with a > >>feature entry at sequence location 0: > >> > >>FT INIT_MET 0 0 BY SIMILARITY. > >> > >> > >>This raises an IllegalArgumentException when the sequence is > read in via > >>SeqIOTools.fileToBiojava (see below). > >> > >>I don't know how oftem this would come up but its definitely a > situation>>that isn't handled at the moment. Thoughts anyone? > >> > >> > >> > >Hmm, this one could be a problem - our coordinate system starts > from one. > >What do they mean by position 0? A cleaved methionine that's > gone alreadY? > > > >Maybe our code ought to have the option to skip these silently? > > > >Regards, > >David Huen > > > > > > > >------------------------------------------------------------------ > ------ > > > >_______________________________________________ > >biojava-dev mailing list > >[EMAIL PROTECTED] > >http://biojava.org/mailman/listinfo/biojava-dev > > > > > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
