[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)
bix at sendu.me.uk
Wed Jun 28 11:04:29 EDT 2006
Kadirvel, Selvi wrote:
> (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, " ",
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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