[Bioperl-l] using HMMER

Chris Fields cjfields at illinois.edu
Thu Aug 12 12:14:44 EDT 2010


Fayroz,

Please keep responses on-list.

It seems you need to update your local bioperl, as 'hmmer3' is a recent addition, after 1.6.1.  It will be in 1.6.2 if I can get the time to make a release :>

chris

On Aug 12, 2010, at 10:58 AM, fayroz wrote:

> dear chris,
> from HMMER documentation i found this statement
> "The HMMER programs must either be in your path, or you must set the environment
> variable HMMERDIR to point to their location." 
> is it will solve the problem?
> how can i do it please ? i work under windows7 platform
> 
> 
> when i appled this line with hmmer3
> my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm', -_READMETHOD => 
> 'hmmer3');
> 
> this output apper: 
> 
> Bio::SearchIO: hmmer3 cannot be found
> 
> and when try with hmmer2 the same output apper: 
> 
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SearchIO::hmmer3. Can't locate 
> Bio\SearchIO\hmmer3.pm in @INC (@INC contains: D:\Perl\bin\ D:/Perl/site/lib 
> D:/Perl/lib .) at D:/Perl/site/lib/Bio/Root/Root.pm line 439, <GEN0> line 1.
> STACK Bio::Root::Root::_load_module D:/Perl/site/lib/Bio/Root/Root.pm:441
> STACK (eval) D:/Perl/site/lib/Bio/SearchIO.pm:446
> STACK Bio::SearchIO::_load_format_module D:/Perl/site/lib/Bio/SearchIO.pm:445
> STACK Bio::SearchIO::new D:/Perl/site/lib/Bio/SearchIO.pm:189
> STACK Bio::Tools::Run::Hmmer::_run D:/Perl/site/lib/Bio/Tools/Run/Hmmer.pm:431
> STACK Bio::Tools::Run::Hmmer::hmmsearch 
> D:/Perl/site/lib/Bio/Tools/Run/Hmmer.pm:353
> STACK toplevel C:\Users\Khaled\AppData\Local\Temp\dzprltmp.pl:13
> -------------------------------------
> For more information about the SearchIO system please see the SearchIO docs.
> This includes ways of checking for formats at compile time, not run time
> '--informat' is not recognized as an internal or external command,
> operable program or batch file.
> Can't call method "next_result" on an undefined value at 
> C:\Users\Khaled\AppData\Local\Temp\dzprltmp.pl line 15, <GEN0> line 1.
> 
> 
> 
> ----- Original Message ----
> From: Chris Fields <cjfields at illinois.edu>
> To: Kai Blin <kai.blin at biotech.uni-tuebingen.de>
> Cc: fayroz <fayroz_farouk at yahoo.com>; bioperl-l at bioperl.org
> Sent: Thu, August 12, 2010 6:28:50 PM
> Subject: Re: [Bioperl-l] using HMMER
> 
> On Aug 12, 2010, at 7:09 AM, Kai Blin wrote:
> 
>> On Wed, 11 Aug 2010 10:07:36 -0500
>> Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> might also want to check whether you are using hmmer2 vs hmmer3.  not sure if 
>>> the wrapper works for hmmer3.
>> 
>> It might if you initialize it using
>> my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm', -_READMETHOD => 
>> 'hmmer3');
>> 
>> at least for the programs that still exist with the same name in
>> hmmer3. It won't support hmmer3 using the default options, though.
>> 
>> If I have some spare time, I'll look into this, no promises on the
>> timeframe, though.
>> 
>> Cheers,
>> Kai
>> 
>> -- 
>> Dipl.-Inform. Kai Blin        kai.blin at biotech.uni-tuebingen.de
>> Institute for Microbiology and Infection Medicine
>> Division of Microbiology/Biotechnology
>> Eberhard-Karls-University of Tübingen
>> Auf der Morgenstelle 28                Phone : ++49 7071 29-78841
>> D-72076 Tübingen                        Fax :  ++49 7071 29-5979
>> Deutschland
>> Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
> 
> Would be nice to convert this over (at some point) to use Mark's CommandExts.  
> I'm thinking of doing this with Infernal, so if I get that running it wouldn't 
> be terribly difficult to get hmmer3 working as well.
> 
> chris
> 
> 
> 




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