[Bioperl-l] Getting subject length with BPlite

Jason Eric Stajich jason@cgt.mc.duke.edu
Wed, 10 Oct 2001 14:40:49 -0400 (EDT)

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.


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
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Jason Stajich
Duke University