#!/usr/bin/perl -w

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

$mutfile = $ARGV[0];

%hash = ();

open(INPUTR,"<$mutfile") || die "Can't open \$mutfile for reading. \n";
while($line=<INPUTR>){
    chomp $line;
    @toks = split(/\t/,$line);
    if ($toks[0] =~ /^Gname/){
        $k = 0;
# loop over the header row to get the unique "Gname"s
        @header = split(/\t/,$line);
        for $j (1..@toks-2){
            $i = $j+1;
            if ($header[$i] ne $header[$j]){
                $k++;
                $name[$k] = $header[$j];
            }
        }
        for $i (0..$k){
            $hash{$toks[0]}{$name[$k]} = $name[$k];
        }
    } else {
        $k = 0;
        for $j (1..@toks-2){
            $i = $j+1;
            if ($header[$i] ne $header[$j]){
                $k++;
                $hash{$toks[0]}{$name[$k]} = 0;
                if ($toks[$j] =~ /M/){
                    $hash{$toks[0]}{$name[$k]} = 1;
                }
            }
        }
    }
}
close(INPUTR);

$outdata = $mutfile;
$outdata =~ /(.+).txt/;
$outdata = $1."-COUNTS.txt";
open(OUTD,">$outdata");
foreach $idname (sort keys %hash){
    if ($idname =~ /^Gname/){
        print OUTD $idname;
        foreach $gid (sort keys %{$hash{$idname}}){
            print OUTD "\t".$hash{$idname}{$gid};
        }
        print OUTD "\n";
    }
}
foreach $idname (sort keys %hash){
    if ($idname !~ /^Gname/){
        print OUTD $idname;
        foreach $gid (sort keys %{$hash{$idname}}){
            print OUTD "\t".$hash{$idname}{$gid};
        }
        print OUTD "\n";
    }
}
close(OUTD);
print "Printing $outdata file done.\n";