[Bioperl-l] hmmer3.pm question re query and hit coordinates

[Thomas Sharpton]

Hi Scott,

Thanks for writing. I'm on the road at the moment so I have to be  
briefer and less thorough than I'd like to be.

What you are observing is not the intended behavior. Oddly, it's not  
what I recall obtaining in my tests on this software, though I was  
mostly interested in hmmsearch at the time and may have been sloppier  
than I should have been when it came to hmmscan.

What version of HMMER3 you're using? There have been some small  
formatting changes in the past that might be causing a burp in the  
parser, though I'm doubting it.

Kai Blin wrote some test scripts (found here: bioperl-live/t/SearchIO/ 
hmmer.t) that, if I recall correctly, evaluate query/hit coordinates.  
It might be worth giving this a shot if you haven't already.

Also, if you don't mind, I'm happy to run your code on your output  
file on my end. It might help me diagnose the problem.

Sorry this is being a thorn in your side! I've cc'ed the list in case  
anyone else has insight into this matter.

Best,
Thomas

On Jul 19, 2011, at 10:43 AM, Givan, Scott A. wrote:

> Hi Thomas,
>
> I'm using modules in the bipoerl-hmmer3 git repository to parse  
> hmmscan
> reports. When I parse the files and walk through the HSP's like:
>
> while (my $hit = $rslt->next_model) {
>
> 	while (my $domain = $hit->next_hsp) {
>
> And retrieve the "hit" coordinates like:
>
> 		print "hit coords: ", $domain->start('hit'), "-", $domain- 
> >end('hit'),
> "\n";
>
> The coordinates returned correspond to what I would call the "query",
> since they are for the sequence I fed to hmmscan to search the profile
> database. Likewise, when retrieving the query coordinates like
> $domain->start('query'), I get what I consider the "hit" coordinates,
> since they are for the domain profile. Is this the intended behavior?
>
> Thanks.
>
> scott
>
> -- 
> Scott A. Givan
> Associate Director
> Informatics Research Core Facility
> 240e Bond Life Sciences Center
> Research Assistant Professor
> Molecular Microbiology and Immunology
> University of Missouri, Columbia
>
> TEL 573-882-2948
> FAX 573-884-9676
> http://ircf.rnet.missouri.edu
>
>
>