[Bioperl-l] Bio::LocatableSeq warning

Chris Fields cjfields at illinois.edu
Thu Dec 18 12:51:55 EST 2008

On Dec 17, 2008, at 5:18 PM, Sendu Bala wrote:

> 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?

The LocatableSeq has the ending reset; if it doesn't correspond to the  
actual end then something is wrong, but that would be with the parser  
(AlignIO::clustalw) not catching this and processing the data as  
needed.  As Roy said, this is Genewise-like and indicates frameshifts,  
something that LocatableSeq can handle.

> 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.

I'll file this as a bug as the set ending doesn't correspond to true  
end passed in by the parser.  I'll take a look at the example file you  
have (if it's in svn) and see if we can add this in prior to the 1.6  


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