[Biojava-l] Re: [Biojava-dev] Feature at position 0
taoxu at bioinformatics.ubc.ca
Fri May 14 13:33:07 EDT 2004
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
I tend to like the idea of relax the location constraint. Another
approach might be create a RelaxLocation class.
----- 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
> constraint to allow point locations at 0, or in the sp parser, re-
> these as <1 - what do people think?
> 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.
> >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?
> >David Huen
> >biojava-dev mailing list
> >biojava-dev at biojava.org
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