[Bioperl-l] Extracting domain# from hmmpfam output

[Jason Stajich]

Not really -
You can compute it though, they are numbered by their order on the
protein.

my @domains = $hit->domains;
my $domainnum = 1;
my $total = scalar @domains;
foreach my $domain ( sort { $a->start <=> $b->start } $hit->domains ) {
 print "domain $domainnum of $total,\n";
 $domainnum++;
}

Uh oh - I just spotted a bug in the SearchIO::hmmer parsing with multiple
domains - where you only got one HSP for a multi-hit domain.  No idea how
that one got through before...  Fixed on trunk and branch in CVS.

-jason

On Mon, 17 Mar 2003, Diane Benz (CCGB) wrote:

> Hello,
> Is there a method in GenericHSP or HMMERHSP to retrieve the domain
> number from hmmpfam output. I haven't been able to locate a method, but
> I would like to extract the number after the word "domain" (in this case
> "2") in the following output:
>
> SH2_5: domain 2 of 2, from 349 to 432: score 104.4, E = 1.9e-26
> Thanks, Diane Benz
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu