[Bioperl-l] Bio::LocatableSeq warning
Mark A. Jensen
maj at fortinbras.us
Wed Dec 17 19:52:30 EST 2008
----- Original Message -----
From: "Sendu Bala" <bix at sendu.me.uk>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>; "Mark A. Jensen"
<maj at fortinbras.us>
Sent: Wednesday, December 17, 2008 6:18 PM
Subject: Re: [Bioperl-l] Bio::LocatableSeq warning
> 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.
A softer warning would be convenient. I will frequently set end() just
to get the side-effect of a correct recalculation of the end coord. (This is
in itself, of course.)
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