[Bioperl-l] Bio::SearchIO::hmmer hsp behaviour

Sendu Bala bix at sendu.me.uk
Fri Jun 30 12:14:05 EDT 2006

Chris Fields wrote:
> It may have been just simpler to have it be one HSP (domain) per Hit 
> (model) as that's how the reports are generated.  My reasoning was that 
> using the one domain per model made sense based on what you are actually 
> trying to do, which is annotate the sequence based on the order the 
> domain appears.  Most others may not view it that way, which is fine.  
> One can always gather the relevant HSP's, convert to seqfeatures, then 
> sort them if order is important, I suppose.
> I would say, if the overall consensus is to modify it to have multiple 
> domain hits per model (similar to BLAST) then Sendu should go ahead and 
> make those changes then announce it on the list so no one can gripe 
> about it later.  My main concern was not changing things so dramatically 
> that it'll break for someone

Going on your earlier suggestion, I was thinking about making 
SearchIO::hmmpfam instead, which would get used if you set the format to 
'hmmpfam' instead of the generic 'hmmer' when making a SearchIO. I 
suppose I would make a SearchIO::hmmsearch as well, if necessary.

> that the reported bug about missing hits (Bug 2036) is fixed as well.

However, having never made a SearchIO plugin before, it will be some 
time before I get my head around it. I'll want to make one the current 
HOWTO:SearchIO way before I can think about doing it a better way 
(hashes) as well. So I can say I'll make a move on this at some point in 
the future, but if someone wants to fix Bug 2036 in the mean time, they 
are welcome to. Again as suggested, my priority is Bio::Map right now.

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