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

Sendu Bala bix at sendu.me.uk
Wed Jun 28 11:04:29 EDT 2006

Kadirvel, Selvi wrote:
> 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.

What do you mean by this? What is ??A? ?
Is this an option you're supplying to hmmpfam or a bioperl module?

> 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

Each hit you get back from each result of the SearchIO is a 
Bio::Search::Hit::HMMERHit and represents the results of a particular 
model (you can also say $result->next_model).

So you can say:
$hit->name, " ", $hit->description, " ", $hit->significance, " ", 

To get the information you want.
General information about the result can be had like so:
print $result->query_name, " ", $result->algorithm, " ", 
$result->hmm_name, "\n";

I have another problem (or the same one as you? I'm can't tell...) in 
that I can only get a single result, hit and hsp from my hmmpfam file!
It is doing my head in, but I might be doing something wrong so will 
look into it further before posting a bug report.

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