use warnings;
use strict;

my $maf = "input.maf";

open (IN1, "input.maf") or die;
open (OUT1, ">m2.maf") or die;
open (OUT2, ">m2_most-cons.gff") or die;

while (my $line1 = <IN1>) {
	chomp $line1;
	if ($line1 =~ /^s\sficAlb2/) {
		my @columns = split(/\t/, $line1);
		my $start = $columns[2] + 1;
		my $end = $columns[2] + $columns[3];
		my $chrom = $columns[1];
		my $mafBlock = qx(maf_parse --start $start --end $end $maf);
		print OUT1 "$mafBlock1\n";
		my $phastCons = qx(phastCons --target-coverage 0.3 --expected-length 45 --rho 0.31 --most-conserved m2.gff --seqname $chrom --msa-format MAF m2.maf nonconserved-all-4d.mod);
		print "$phastCons\n"
		open (IN2, "m2.gff") or die;
		while (my $line2 = <IN2>) {
			if ($line2 =~ /^fic/) {
				print OUT2 "$line2\n";
			}
		}
	}
	open (OUT1, ">m2.maf") or die;
	close IN2;
}

close IN1;
close OUT1;
close OUT2;

exit;