[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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