[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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