[Bioperl-l] Subject length using BPlite.pm

Jason Stajich jason at cgt.duhs.duke.edu
Thu Feb 19 10:56:11 EST 2004

BTW SearchIO is the only supported Blast parser so I will always suggest
moving to SearchIO::blast for your parsing needs....

But I don't think Ian/Peter put a method call in there so you have to use
$sbjct->{'LENGTH'} where sbjct came from the nextSbjct call like:

  use Bio::Tools::BPlite;
  my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
  while(my $sbjct = $report->nextSbjct) {


On Thu, 19 Feb 2004, Adam Witney wrote:

> Hi,
> I am using BPlite.pm to parse a BLAST output, is it possible to get the
> Subject length? (that¹s the length of the whole subject sequence, not just
> the part involved in the hsp)
> Thanks for any help
> Adam

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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