[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)
cjfields at uiuc.edu
Wed Jun 28 10:55:31 EDT 2006
I hate responding to myself!! Forgot to add that there is also
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.
> 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',
> > -----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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