[Biojava-l] Re: [Biojava-dev] Feature at position 0

[Tao Xu]

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 <matthew_pocock at yahoo.co.uk>
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
> >biojava-dev at biojava.org
> >http://biojava.org/mailman/listinfo/biojava-dev
> >  
> >
> 
>