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

[Matthew Pocock]

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
 

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