#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;

my $filename = 'MET30-vs-swissprot.1.FASTA';
my $input = Bio::SearchIO->new(-format => 'fasta',
			       -file   => $filename);
#GOAL:
# Print out the query, hit names and percent identity, percent query aligned
while( my $r = $input->next_result ) {
  my $qname = $r->query_name;
  my $qlen  = $r->query_length;
  while( my $hit = $r->next_hit ) {
    my $hname = $hit->name; 
    while( my $hsp = $hit->next_hsp ) {
      my $percent_id = $hsp->frac_identical * 100; 
      my $query_aln_len = $hsp->length('query');
      # another way to do this
      # my $query_aln_len = $hsp->query->length;
      print join("\t", $qname, $hname, $hsp->evalue,
		      sprintf("%.1f",$percent_id),
	              sprintf("%.2f",100 * ( $query_aln_len / $qlen))), "\n"; 
    }
  }
}