[Bioperl-l] Bug? Features with similar ranges, different IDs are considered overlapping

Scott Cain scott at scottcain.net
Tue Aug 17 08:45:27 EDT 2010


Hi Dave and Chris,

It seems to me that the genomic comparison is the thing people would do more often, so if you're going to create a flag, the default should be for the genomic comparison and if somebody is doing the protein space comparison and not getting the the expected results, they'll probably read the docs to find out why. 

Scott

--
Scott Cain, Ph. D.
scott at scottcain dot net
Ontario Institute for Cancer Research
http://gmod.org/
216 392 3087 

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On Aug 17, 2010, at 5:06 AM, Dave Messina <David.Messina at sbc.su.se> wrote:

>> Good point; it's probably the context the methods are used that matters.  So, maybe just a document clarification?
> 
> That's always good, but it really doesn't solve the issue you're describing.
> 
> I mean, who would expect to get overlaps for features on different chromosomes?
> 
> To me, that's a clear violation of reasonable user expectations. You shouldn't have to read the docs about something like that.
> 
> So what's the solution for these duelling use cases? I haven't thought about it much, but a first approximation might be to add a -genomic boolean flag that, when true, would do the right thing and check the ID when doing overlaps or other positional comparisons.
> 
> (Maybe -genomic is too obscure. Maybe it should be -same_id_for_overlaps or something like that.)
> 
> And maybe having to know to set a flag is effectively the same thing as having to read the docs to understand SeqFeature's overlap behavior.
> 
> What do the rest of you out there think?
> 
> 
> Dave
> 
> 
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