#This script annotates  genomic positions to genes for ingenuity analyses.
#Aaron Sarver November 15, 2010
#version #1.0

$in =$ARGV[0];
$out = $ARGV[1];

@lib_list=();
%seen=();

@uniq = ();
$libstring = '';



#open SOURCE, "< Med-nr-7-0.01.txt";
open SOURCE, "< $in";
open OUT, "> CIS/input.txt";
open FIN, "> $out";
while (defined($line = <SOURCE>)) {
$count++;
chomp $line;
@field= split(/\t/, $line);
$start = $field[1]-50;
$stop = $field[1]+50;

print OUT "$field[0]\t$start\t$stop\n";
}
close OUT;

system('perl lib/feature_finder.pl -i CIS/input.txt -icol 1:2:3:6:13 -f lib/mm9.bed -o CIS/input2.txt');


open SOURCE, "< CIS/input2.txt";
while (defined($line = <SOURCE>)) {
$count++;
chomp $line;
@field= split(/\t/, $line);
#print "$field[0]\n";
@genes= split(/,\s/,$field[3]);
foreach $gene (@genes) {
#print "$gene\n";
push (@lib_list,$gene);
}
}


foreach $item (@lib_list) {
unless ($seen{$item}) {
$seen{$item}= 1;
push(@uniq,$item)
}

}

#open OUT, "> ingenuity_nr.txt";
foreach $item(@uniq) {

print FIN "$item\t10\n";

}
close FIN;