[Bioperl-l] Bio::LocatableSeq warning
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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