#!/usr/bin/perl -w

use strict;
use warnings;
use autodie;

if (@ARGV != 1){
    print "USAGE: ./parse-counts.pl file\n";
    exit(-1);
}

my $mutfile = $ARGV[0];

my (%counts, %unique, %masks);
my ($headname, @unique) = grep !$unique{$_}++, my @headers = split ' ', <DATA>;

for my $label ( @unique )
{
    $masks{$label} = join ' ',
    map { $_ eq $label ? 'M' : '_' } @headers[1..$#headers];
}

my $line;

open(INPUTR,"<$mutfile") || die "Can't open \$mutfile for reading. \n";
while($line=<INPUTR>){
#while(<DATA>)
{
    chomp $line;
    s/\s+/ /g; # for uniform spacing
    my ($name, $letters) = split ' ', $line, 2;
    $counts{$name}{$line} += ($masks{$line} | $letters) =~ /M/ for @unique;
}

print "$headname @unique\n";
print "$line @{ $counts{$_} }{@unique}\n" for sort keys %counts;

##</code><code>##

./parse-counts.pl junk.txt
Missing right curly or square bracket at ./parse-counts.pl line 36, at end of line
syntax error at ./parse-counts.pl line 36, at EOF
Execution of ./parse-counts.pl aborted due to compilation errors.