[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)

Chris Fields cjfields at uiuc.edu
Wed Jun 28 10:55:31 EDT 2006


I hate responding to myself!!  Forgot to add that there is also
Bio::Tools::Hmmpfam :

http://www.bioperl.org/wiki/Module:Bio::Tools::Hmmpfam

I'll check if Bio::SearchIO catches this data and let you know what I find
out.  It should at least some according to the mapping.

Chris

> Selvi,
> 
> Can you send me the report you are trying to parse as an attachment?  I'll
> give it a look.
> 
> Judging by the pdoc this is mapped for the event handler so it should be
> there.  From the %MAPPING hash:
> 
>                  'HMMER_program'   => 'RESULT-algorithm_name',
>                  'HMMER_version'   => 'RESULT-algorithm_version',
>                  'HMMER_query-def' => 'RESULT-query_name',
>                  'HMMER_query-len' => 'RESULT-query_length',
>                  'HMMER_query-acc' => 'RESULT-query_accession',
>                  'HMMER_querydesc' => 'RESULT-query_description',
>                  'HMMER_hmm'       => 'RESULT-hmm_name',
>                  'HMMER_seqfile'   => 'RESULT-sequence_file',
> 	           'HMMER_db'        => 'RESULT-database_name',
> 
> Chris
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Kadirvel, Selvi
> > Sent: Tuesday, June 27, 2006 7:55 AM
> > To: bioperl-l at lists.open-bio.org
> > Cc: selvik at ufl.edu
> > Subject: [Bioperl-l] Bio::SearchIO - Accessing Model parameters (score,
> > evalue, description)
> >
> > All,
> >
> > (I am new to Bioinformatics and Bioperl, so please apologize if I
> > get my terminology wrong)
> >
> > I am currently using Bio::SearchIO to parse HMMPFAM reports. This
> > report consists of three sections namely;
> >
> > 1. A ranked list of the best scoring HMMs
> > 2. A list of the best scoring domains in order of their occurrence
> > in the sequence
> > 3. Alignments for all the best scoring domains.
> >
> > Section 3 can be truncated to a specific number using the ??A?
> > option when building the report.
> >
> > Though the Bio::SearchIO::hmmer module parses through the entire
> > HMMER report (Section 1, 2 and 3), the set of values made
> > available through Bio::Search::Result::ResultI seem to be using
> > Section 3 alone. So when we use the ?A option to truncate, we lose
> > otherwise useful information in Section 1. This information is
> > lost (only) for those models that do not have any of their domains
> > in the top ?A number of? best scoring domains. The fields that are
> > not available are:
> >
> > 1.	Description of a model
> > 2.	Score of a model
> > 3.	Evalue of a model
> >
> > If I use the older Bio::Tools::HMMER:Results module, NEITHER
> > Bio::Tools::HMMER::Domain or Bio::Tools::HMMER::Set allow me to
> > retrieve the above listed values. Scores and Evalues are available
> > for each domain but not for the model it belongs to.
> >
> > I was wondering if there is any other method to access these
> > values or do I have to write my own module to do this?
> >
> > Any ideas/suggestions would be greatly appreciated.
> >
> > Thank you!
> >
> >
> >
> >
> > Selvi Kadirvel
> >
> > Graduate Research Assistant
> > High Performance Computing Center
> > University of Florida
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
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