#!/usr/bin/perl

use Bio::SearchIO;

my ($blast) = @ARGV;

my $searchio = new Bio::SearchIO(-format => "blast",

                                 -file   => "test.bls");

while (my $result = $searchio->next_result) {

    while (my $hit = $result->next_hit) {

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

            my $query_name   = $result->query_name;

            my $query_length = $result->query_length;

            my $align        = $hsp->homology_string;

            $align           =~ s/ //g;

            my $hit_name     = $hit->name;

            my $identity     = sprintf "%0.2f", $hsp->frac_identical * ;

            my $mismatch     =()= $hsp->seq_inds('hit','nomatch');

            my $gaps         = $hsp->gaps;

            my $align_length = $hsp->hsp_length;

            my $query_start  = $hsp->start('query');

            my $query_end    = $hsp->end('query');

            my $hit_start    = $hsp->start('hit');

            my $hit_end      = $hsp->end('hit');

            my $evalue       = $hsp->evalue;

            my $bit_score    = $hsp->bits;

            print qq{$query_name\t$hit_name\t$identity\t$align_length\t$mismatch\t$gaps\t$query_start\t$query_end\t$hit_start\t$hit_end\t$evalue\t$bit_score\n};

        }

    }

}