#!/Users/andreafossati/perl5/perlbrew/perls/perl-5.24.0/bin/perl 
use warnings;
use strict;
use Data::Dumper;


my $info = "\.\/INFO\/order.txt";

open my $fh, "<", $info or die "can not open 'info' txt, run order pl first\n$!\n";

my (@bb, %kk, $us, @sam);

my $sw = 0;
while (<$fh>)  {

  if (!/^[1-9]{1}/ && $sw == 0 ) 
      { @sam = split /\t/, $_;
        $sw = 1; 
        next;
        }
    
    if (/^[1-9]{1}/ && ( @sam ) ) {
        @bb = split /\t/, $_;
        @kk{@sam} = @bb;
        next;
        }
   my $st = $_;
   my @ff = split /\t/, $st;
   @ff    = uniq(@ff);
   $us    = $ff[0];
}
close $fh or die "can not close 'info' fh\n$!";

my @m      = reverse sort {$a <=> $b} values %kk;
my $gr     = $m[0];
(@m, @bb)  = ();

print "\n$gr groups found, column used for quantification: $us\n";


print "\ninsert filename to be processed\nneeds to be a tab delimited file in IN folder\n";
chomp (my $filename = <STDIN>) ;

my $in = "\.\/IN\/$filename.txt";

print "\ninsert prot identifier name\n";
chomp (my $w = <STDIN>);

 
open my $fh_2, "<", $in or die "can not open $filename,\n$!\n";

my (@h, @d, @id, %gg ) = ();

while (<$fh_2>) {
chomp;
my  %t = ();
if (/.*$w.*/) {@h = split /\t/, $_; next;}

if ( @h ) { 
    @d     = split /\t/, $_; 
    @t{@h} = @d;
    my $ll = $t{$w};
    push @id, $ll;   
    my @k;
    for (keys %kk)
    {
      my @cm = grep { /^$us.*/ } keys(%t); 
      push @k, @cm;
    }
    @k = uniq(@k);

    for (@k) { 
       my $key  = $_;
       (my $k   = $key ) =~ s/^$us.//;
       push @{$gg{$k}}, $t{$key};  
    }
  } else {next;}
}

close $fh_2 or die "can not close 'filename' fh\n$!";



sub uniq {
    my %seen;
    grep !$seen{$_}++, @_;
}