use warnings;
use strict;

chdir "\.\/IN";

my @files = glob "*txt";

foreach (@files) {
    my $infile = "$_";
    print "$infile opened\n";
    open my $fh, "<", $infile or die "can not open '$infile' $infile\n$!\n";

    my @hh;
    while (<$fh>) {
        chomp;
        @hh = split /\t/, $_;
        last;
    }

    close $fh or die "can not close filehandle\n";
    print "$infile closed\n";

    chdir "\.\.";

    print
      "insert column name used for calculation\ni.e MaxQuant LFQ intensity\n";
    chomp( my $w = <STDIN> );

    my @lfq = grep { /^$w/ } @hh;
    @lfq = map { ( my $foo = $_ ) =~ s/^$w //; $foo } @lfq;

    print "insert name of control without replicate number\n";
    chomp( my $c = <STDIN> );

    my @crl = grep { /^$c*/ } @lfq;
    my @res = grep { !/^$c*/ } @lfq;
    push @crl, @res;

    print "insert number of groups\n";
    chomp( my $g = <STDIN> );

    print "insert number of replicates\n";
    chomp( my $l = <STDIN> );

    my $length = scalar @lfq;
    if ( $length == $g * $l ) {
        my @out;
        my $nn = join "\t", @crl;
        my @ll = ( 1 .. $g );
        my @dd = ( 1 .. $l );
        my @gg;
        for ( 1 .. $g ) {
            until ( scalar @gg == $_ * $l ) {
                push @gg, $_;
            }
        }
        my @cc;
        for ( 1 .. $length ) { push @cc, $w }

        my $hj = join "\t", @cc;
        my $jj = join "\t", @gg;
        push @out, "$hj\n";
        push @out, "$jj\n";
        unshift @out, "$nn\n";

        my $outfile = "\.\/INFO\/order.txt";
        open my $out, ">", $outfile or die "$!";
        print $out @out;
        print "results printed in $outfile\n";
        close $out or die "can not close filehandle for printing\n$!\n";
    }
    else {
        print
"wrong number of groups or replicates\ncheck column names for typos\n";
    }

}