[Bioperl-l] Parse BLAST report using BPlite

[Simon Chan]

Hi All,

Yeah, it's me again :)

Right now, I'm looking at exercise 2.6 of the Pasteur Tutorial.  Using the BPlite parser, I am trying
to parse the BLAST report I generated with blastall() to return the 2 best.  By default, BLAST lists the
highest scoring hits first, however, the 2 best hits may not be the first 2 returned.  How do I do this (return the
best 2 hits)?  
Here's what I've got:


while (my $hit = $report->nextSbjct()) { 
   print "Name: ", $hit->name, "\n";

   while (my $hsp = $hit->nextHSP()) {

   print "Score ". $hsp->bits . "  Start " . $hsp->subject->start . "  End " .  $hsp->subject->end .   "\n";

     
   }
   
Finally, I appreicate all the help everyone out there has given me, but are there other bio-perl docs out
there that step-by-step explain the lines of code?  I'm not new to Perl, however I am new to object-oriented
programming.  But I know the basics of oo, and shouldn't that be enough to make sense of the code in the Pasteur
tutorial?!  Going a little crazy here. ;-(


Once again, many thanks, All.