#! /usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Getopt::Std;

#Written by CSR on 3.7.08
#Simple blast parser

my %args;
getopts('i:n:', \%args);
my $usage = "Warning, missing information\nUsage is: scriptname.pl -i [infile] -n [number of blast hits]\n"; 
my $infile;
my $num;
my $count = 0;

#command line arguments
if ($args{i}) {
    $infile = $args{i};
} else {
    die "$usage";
}
if ($args{n}) {
    $num = $args{n};
} else {
    die "$usage";
}

#input
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => $infile);
#output
my $outfile = $infile.".parsed";
open (PARSED , "> $outfile") or die "COULD NOT WRITE TO THE OUTFILE\n";

#headerline
print PARSED "SeqID\tHit Acc#\tDescription\tEvalue\n";

#parse with bioperl
while( my $result = $in->next_result ) {
    my $qname = $result->query_name;
    $count = 0;
  while( my $hit = $result->next_hit ) {
      my $check = $result->num_hits;
      $count++;
      if ($num > $check) {
	  die "# of hits is too high...pick a smaller number.\n";
}
      if ($count <= $num) {
      my $acc = $hit->accession;
      my $desc = $hit->description;
      my $signif = $hit->significance;
      print PARSED "$qname\t$acc\t$desc\t$signif\n";
  }
  }
}

close (PARSED);