#!/usr/bin/perl

use strict;
use warnings;
use File::Find;
use Scalar::Util qw(looks_like_number);

open IN, "/home/big/scratch/affy_map.txt" or die "Cannot open reference\n";
my %ref;
my $head = <IN>;
my $index = 0;
while(<IN>){
    chomp $_;
    my @row = split /\t/, $_;
    my $value = join "\t", $row[1],$row[2];
        if($row[1] == 2 && $row[2] <= 50000 && $row[2] <= 51113178) { $ref{$index}=$value; print $index."\t".$value."\n";}
        if($row[1] == 22 && $row[2] <= 16300001 && $row[2] <= 20500000) { $ref{$index}=$value; print $index."\t".$value."\n"; }
        $index++;
}
close(IN);

my @files;
my $masterDirect = "/nfs/archive02/big/Norm/norm_gcc/";

find(\&file_names, $masterDirect);

sub file_names {

  if( -f && $File::Find::name=~/\.nzd$/)
   {
       push @files, $File::Find::name;

     }
 }

my $count=0;
foreach(@files){
    $count++;
    if($count % 100 == 0 ){ print "\n","-" x 10, " $count ", "-" x 10,"\n";}
    undef my @probes;
    open IN, $_;

    #file name handling
    my @inDir = split "\/", $_;
    my $id = pop(@inDir);
    $id =~ s/\.gcc.nzd$//;

    #header test
    $head =<IN>;
    if(looks_like_number($head)) { push @probes, $head; }

    #open output
    open OUT, ">/home/big/scratch/phase1_affy/".$id."_select_probeset.txt";

    #load probe array
    @probes = <IN>;
    close(IN);
    foreach my $key (sort keys %ref){
       #intended function
        print OUT $ref{$key}."\t".$probes[$key];
       #testing   
       my @temp = split "\t", $ref{$key};
        foreach(@temp){if($temp[0] == 2){print $key."\t".$ref{$key}."\t".$probes[$key];}}
    }
    close(OUT);
}