#!/usr/bin/perl
use strict;
use warnings;
use Term::ANSIColor;
my $file = $ARGV[0];
if (@ARGV < 1){
    print STDERR "Usage: $0 input_fasta_file\n";
    exit 1;
}
my ($header, $sequence);
open (A, "<", $file) or die "Check the file: $!";
while (my $line = <A>){
    chomp $line;
    if ($line =~ /^(>.*)/){
	$header = $1;
    }
    else{
	$sequence .= $line;
    }
}
close (A);

$sequence =~s/[\n\s]//;
#print "$sequence\n";

=comment
my @highlights = (
[ 88, 1, 'bold red' ],
[ 101, 1, 'bold red' ],
[ 113, 1, 'bold red' ],
[ 121, 1, 'bold red' ],
[ 124, 1, 'bold red' ],
[ 134, 1, 'bold red' ],
[ 140, 1, 'bold red' ],
[ 146, 1, 'bold red' ],
 );
=cut

my @highlights;
my $pos_file = "sorted_position_walk.txt";
open (A, "<", $pos_file) or die "Check the file: $!";
while (my $line = <A>){
    chomp $line;
    my $pos = (split /\t/,$line)[0];
#    push(@position, $pos);
    push(@highlights, "([ $pos, 1, 'bold yellow' ],)");
}

#foreach my $pp(@highlights){
#    print "[ $pp, 1, 'bold red' ],\n";
#}

#print "@highlights\n";

for my $ar (@highlights) {
    my ($start, $len, $color) = @$ar;
    $sequence = substr($sequence, 0, $start-1)                    # first part                               
              . colored(substr($sequence,$start,$len), $color)  # colored part                           
              . substr($sequence,$start+$len);                  # final part                             
}

print $sequence, "\n";