### mcscan.filter.pluse Getopt::Long;use strict;use Bio::SeqIO;use Bio::Seq;use File::Basename qw(basename dirname);use Cwd qw(abs_path);#get optsmy %opts;GetOptions(\%opts, "in=s", "out=s","id1=s","id2=s","h");if(!defined($opts{id2}) || !defined($opts{id1}) || !defined($opts{in}) || !defined($opts{out}) || defined($opts{h})){        print <<"       Usage End.";
        Usage        Forced parameter:                -gff        genoma gff file           <infile>          must be given                -fa                     genoma fasta file                 <infile>              must be given                -o                      output gff file                   <outfile>             must be given                -out            output fasta file                 <outfile>             must be given        Other parameter:                -h           Help document        Usage End.        exit;}open(IN,"$opts{id1}") || die "open $opts{id1} failed\n";my %gene1;while(<IN>){        next if(/^#/);        chomp;        my @line = split ("\t");        $gene1{$line[0]} = $line[0];}close(IN);open(IN,"$opts{id2}") || die "open $opts{id2} failed\n";my %gene2;while(<IN>){        next if(/^#/);        chomp;        my @line = split ("\t");        $gene2{$line[0]} = $line[0];}close(IN);open(IN,"$opts{in}") || die "open $opts{in} failed\n";open(OUT,">$opts{out}") || die "open $opts{out} failed\n";while(<IN>){        next if(/^#/);        chomp;        my @line = split ("\t");        if(exists $gene1{$line[0]} && exists $gene2{$line[1]}){                print OUT "#DC143C*$line[0]\t$line[0]\t$line[1]\t$line[1]\t100\t+\n";        }}close(IN);close(OUT);