[BioPython] bioperl idl

[Bradley Marshall]

--- Jeffrey Chang <jchang@SMI.Stanford.EDU> wrote:
> [Andrew]
> > You didn't specific if the zero of the coordinate
> system is
> > 0 (the way Knuth intended ) or 1 (the way Watson
> intended).
> 
> My preference is to use a 1- based system.  It's
> more natural for
> biologists and seems to be more popular when
> numbering residues.  PDB ATOM
> records typically start at 1 and BLAST results are
> reported with the first
> residue as 1.
> 
> However, it's less clear how the end index should
> behave.  I personally
> prefer that the end is exclusive.
> 
> >  "ANDREW"  and start = 1 and end = 3, do you get: 
> >  AN <-- OMG's way?
> 
> I seem to fall in OMG's camp. 

Speaking from a biologists perspective, if I ask for
1-3 of the sequence 'atgtg' and get anything but 'atg'
I'm gonna be pissed. (But not in the British sense.)

As a person, I'll go either way as long as we just
pick one and go with it.
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