[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)
selvik at ufl.edu
Wed Jun 28 16:11:56 EDT 2006
> 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
> 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 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,
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.
More information about the Bioperl-l