[Bioperl-l] Bio::LocatableSeq warning
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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