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

[Givan, Scott A.]

I'll try the bioperl-live version. Thanks guys. 

Scott Givan
541-740-4685
Sent from an iPhone (so expect typos). 

On Jul 19, 2011, at 10:34 PM, "Chris Fields" <cjfields at illinois.edu> wrote:

> This might be a disconnect between the HMMER3 version in bioperl-live and the one in Kai's bioperl-hmmer3 repo.  I believe the one in bioperl-live is newer.  Scott, can you give that a try?
> 
> chris
> 
> On Jul 19, 2011, at 9:45 PM, Thomas Sharpton wrote:
> 
>> 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
>>> 
>>> 
>>> 
>> 
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>