[Bioperl-l] Problem w/ extracting start and stop of a blast alignment

Roger Hall Roger Hall" <roger@iosea.com
Thu, 23 Aug 2001 04:05:30 -0700

>From Blast.pm:
      ($qstart, $sstart) = $sbjct->start();
      ($qend, $send)   = $sbjct->end();

Since '$objct->thing' is not usually the same as '$objct->thing()', I would
suggest you try adding the empty method parens. In fact, I see where the
property 'start' is used internally in Blast.pm, which is a different
beastie than the method 'start()'.

If that doesn't fix it for you, I suggest you try BPLite, which I know
parses them correctly. See that module for a working example.

Good Luck!

Roger Hall

----- Original Message -----
From: "Erik Richly" <richly@mpiz-koeln.mpg.de>
Sent: Thursday, August 23, 2001 3:20 AM

> I'm experiencing a problem in extracting the start and stop position of
> a blast alignment.
>       ($qstart,$sstart)=$hit->start;
>       ($qend,$send)=$hit->end;