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

[Chris Fields]

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
> 
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