[Bioperl-l] Bio::LocatableSeq warning

Sendu Bala bix at sendu.me.uk
Wed Dec 17 18:18:15 EST 2008

Chris Fields wrote:
> It is a problem with clustalw parsing not accounting for frameshifts, 
> mapping, and other odd bits coming from this format.  That could be 
> added in; LocatableSeq now allows this by specifying position => shift 
> in frameshifts() as a hash ref.
> There are other significant problems with LocatableSeq, though.   Gaps, 
> frameshifts, and residues are set and checked via globals and aren't set 
> per instance (which is definitely not optimal).  I'll file a bug report 
> on this to track it.

In this instance though, is there anything actually wrong with the 
alignment object I get?

If not, perhaps it would be appropriate to revert to the old behaviour 
and have the message be a debug() and not a warn()? I don't know - I 
didn't consider the implications - just a suggestion.

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