[Bioperl-l] need subject length

Ann Loraine loraine@loraine.net
Sat, 7 Apr 2001 21:23:51 -0700 (PDT)


I'm using BPlite to read blast reports.  So far it's working well for me,
except for one critical feature:

I need to know what the full length of each "subject" sequence is.
For instance, if an HSP only covers part of a hit subject sequence, I need
to know how much of the subject was left out.

The old Blast object lets me get this info like so:

	my $slen = $hsp->subject->length()

The equivalent call using BPLite only returns the length of the
aligned portion of the subject.  What method should I call instead
to get this information using BPlite?



Ann E. Loraine