[Bioperl-l] Should coords be adjusted after removing alignment columns?
cjfields at uiuc.edu
Tue Aug 14 13:19:59 EDT 2007
On Aug 14, 2007, at 12:13 PM, Sendu Bala wrote:
> Yes. For extra clarity, my thinking is that the correct answer is:
> a/6-19 tcgatcatcatc
> b/30-42 tcgatcatcatc
> c/51-63 tcgatcatcatc
> What you say in the rest of your discussion is valid and deserves
> some thought/discussion, but for now just getting the start and end
> correct, ignoring any issues with internal residues, seems like a
> For my own purposes that is all I need; having removed gaps I only
> need the start and end so I can take that region from each sequence
> and do a new alignment (for example).
It might be worth addressing the split location issue in the bug
report before it gets lost in the ether. Or maybe start a new one as
an enhancement request.
> BTW. Either my patch isn't quite perfect or there's another related
> bug I'm still tracking down. I'll commit when I've solved that,
> unless someone points out any mistakes in my thinking.
Sounds fine by me.
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