Bioperl 解析blast的输出结果

Posted 2020-10-01 庐州月光

用bioperl 解析blast的默认输出结果， 整理成-m8格式的输出

#!/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/ /0/g;
            my $hit_name     = $hit->name;
            my $identity     = sprintf "%0.2f", $hsp->frac_identical * 100;
            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};
        }
    }
}