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

Selvi Kadirvel selvik at ufl.edu
Wed Jun 28 16:11:56 EDT 2006


Sendu,

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

I was referring to the '-A' option when running hmmpfam. So if I were  
to use  '-A 5', Section 3 will have only the top scoring (first) five  
HSPs.

>
> So you can say:
> $hit->name, " ", $hit->description, " ", $hit->significance, " ",
> $hit->score;
>
> 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 do use the same methods that you have suggested. Let me try to  
explain my problem in detail. Lets say I have a report that was  
generated using this "-A 5" option. I want to get the description,  
score, evalue of a model that *does not* have a domain in the top 5  
high scoring HSPs. This information *exists* in the report in Section  
1 but neither $result->next_hit or $hit->next_hsp can see it.

Details of ALL domains  are available through:

     foreach $domain ($result->each_Domain)
     {
            $domain-> [ hmmname, hmmacc, start, end, hstart, hend,  
evalue ]
     }

where $result is a Bio::Tools::HMMER::Results object. But this again  
represents information in Section 2. It gives us domain scores and  
evalues (and not model scores and evalues.)

I am working around this by finding the sum of scores (evalues) of  
all domains in a model. But there seems to be no work-around to  
retrieve the description. $domain->hmmacc contains only the first  
string of the description.

-Selvi



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