[Bioperl-l] LocatableSeq::subseq(): bug or not?

Chris Fields cjfields at illinois.edu
Tue Nov 25 15:03:23 EST 2008

On Nov 25, 2008, at 1:00 PM, Mark A. Jensen wrote:

> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Tuesday, November 25, 2008 12:34 PM
> Subject: Re: [Bioperl-l] LocatableSeq::subseq(): bug or not?
>> Mark,
>> Your subseq() patch appears to work just fine; no apparent tests  
>> are failing, API doesn't change, so that will be added for the  
>> release. We may need to define a new subseq()-like method to work  
>> properly with  start/end coordinates that match only residues and  
>> are consistent with  different coordinate systems (i.e. mapping),  
>> or we can add that in as  a flag.
> I'm willing to try my hand at this, if desired-- can you point me to  
> the modules involved off the top of yer head?

The test suite has the beginnings for mapping() and frameshifts()  
methods; the former is a simple two element array of # residues  
mapping to # positions.  This is primarily so endpoint calculations  
are correct.  frameshifts() accepts/returns a simple hash indicating  
position of frameshifts and their shift (-+, integer).  Both are  
necessary for HSPs.

I haven't integrated checking of frameshift symbol positions yet (they  
are mainly used for sequence validation).  That will probably need to  
be done first before working this into subseq() as frameshifting will  
affect what the start/end position is in the sequence.


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