[Bioperl-l] Getting subject length with BPlite

[Jason Eric Stajich]

I assume you mean you want the length of the entire subject rather than
just the length of the part that that is considered part of the HSP.

Cheating way:
while( my $sbjct = $report->nextSbjct ) {
	print "subject len is ", $sbjct->{LENGTH}, "\n";
}

This is cheating because it is BAD Object Oriented code, but it will work
for you, but no guarantees about future versions.  Instead we should
transition to having a function called length for the BPlite::Sbjct
object... but we don't (yet).

Could be done quickly though if someone in bioperl wants to jump on it.

-jason

On Wed, 10 Oct 2001, Alexandre Irrthum wrote:

> Hello,
>
> Is there a way to get the total length of a subject sequence (i.e. the
> Length = ... after every subject description in the blast report) with
> BPlite. Sorry if I missed the obvious but I couldn't figure out from the
> docs.
>
> Thanks,
>
> Alexandre Irrthum
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu