Perl--寻找两个基因组中的unique序列

原始数据：

基因组的fasta文件，两个基因组之间blast的比对坐标

scaffold1 2723   9022   contig00005    238996   1

解决方法一：

#!/usr/bin/perl -w 

use strict;
use warnings;
no strict "refs";

my $usage = " perl $0 mutation-vs-wild.m8 mutation.fa wild.fa \n";

unless(@ARGV == 3){
          die $usage;
     }


my $aln  = shift ;
my $mut  = shift;
my $wild = shift;

open ALN,"<",$aln or die "can't open $aln\n";
#open MUT,"<",$mut or die "can't open $mut\n";
#open WILD,"<",$wild or die "can't open $wild\n";

my %mut = build_fa($mut);
my %wild = build_fa($wild);

coden(\%mut);
coden(\%wild);

while(<ALN>){
       chomp;
       my ($scf,$st1,$ed1,$ctg,$st2,$ed2) = split"\t",$_;