blast format：  5 = BLAST XML,  格式 相比于  6 格式 包含更多的信息内容，包括比对的序列信息，长度信息等等；接下来我们可以用bioperl包来解析，获取自己想要的信息；

#!/usr/bin/perl
use strict;
use Bio::SearchIO;
use Data::Dumper;
my $fi     = $ARGV[0];
my $out = $ARGV[1];
my $format;

$format||="blastxml";
my $searchio     = new Bio::SearchIO(
    -format => "$format",
    -file   => "$fi"
);
open OUT,">$out" or die "$!";
######################################
print OUT "query_name\thit_name\tquery_length\thit_length\tidentity\talign_length\tmismatch\tgaps\tquery_start\tquery_end\thit_start\thit_end\tevalue\tbit_score\tquery_string\thit_string\tqfame\thfame\thit_description\n";
while(my $result = $searchio->next_result){
my  $algorithm_type =  $result->algorithm;
my $algorithm_version = $result ->algorithm_version;
	
while( my $hit = $result->next_hit ) {
# process the Bio::Search::Hit::HitI object
        while (my $hsp = $hit->next_hsp) {
        #print Dumper($hsp);
        # process the Bio::Search::HSP::HSPI object
            my $query_name   = $result->query_name;
            my $query_length = $result->query_length;
            my $query_description = $result->query_description;
            
            my $query_string   = $hsp->query_string;
            my $hit_string    = $hsp->hit_string;
            my $align        = $hsp->homology_string;
            $align           =~ s/ //g;
            my $qfame         = $hsp->query->frame;
            my $hfame           =$hsp->hit->frame;
            
            my $hit_name     = $hit->name;
            my $hit_description     = $hit->description;
            my $hit_length     = $hit->length;
            
            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    = $hsp->bits;
            print OUT qq{$query_description\t$hit_name\t$query_length\t$hit_length\t$identity\t$align_length\t$mismatch\t$gaps\t$query_start\t$query_end\t$hit_start\t$hit_end\t$evalue\t$bit_score\t$query_string\t$hit_string\t$qfame\t$hfame\t$hit_description\n};
        }
		
		
}
}
close(OUT);
$searchio->close();

$result 对象 信息：  

Table of Methods

Table 2.1: The data returned by the Result object methods when the report shown above is used as input.

$hit 对象包含的信息：

Note that many of the methods shown can be used to either get or set values, but we’re just showing what they get.

Table 2.2. The data returned by Hit object methods when the report shown above is used as input.

$hsp 包含的信息：

Many of the methods shown can be used to either get or set values, but we’re just showing what they get.

Table 2.3. The data returned by HSP object methods when the report shown above is used as input.

更多说明见：https://bioperl.org/howtos/SearchIO_HOWTO.html