#!/usr/bin/perl

use strict;

my $build = "build34";

my $menu = {
	"AXB" => {
	regex => "^AXB",build => $build, founderA => "A/J", founderB => "C57BL/6J" },
	"BXA" => {
	regex => "^BXA",build => $build, founderA => "C57BL/6J", founderB => "A/J" },
	"BXD" => {
	regex => "^BXD",build => $build, founderA => "C57BL/6J", founderB => "DBA/2J" },
	"BXH" => {
	regex => "^BXH",build => $build, founderA => "C57BL/6J", founderB => "C3H/HeJ" },
	"AKXD" => {
	regex => "^AKXD",build => $build, founderA => "AKR/J", founderB => "DBA/2J" },
	"CXB" => {
	regex => "^CXB",build => $build, founderA => "BALB/cByJ", founderB => "C57BL/6J" },
	"LXS" => {
	regex => "^LXS",build => $build, founderA => "ISS", founderB => "ILS" },
	"SWXJ" => {
	regex => "^SWXJ",build => $build, founderA => "SWR/J", founderB => "SJL/J" },
};

foreach my $ril ( keys %$menu ) {

my $build = "build34";
my $date = "09052005";

for(my $c=1;$c<20;$c++) {
	my $chr = "chr$c";
	my $cmd = "ril.pl -png /home/rmott/public_html/MOUSE/INBREDS/RIL/BUILD34/$ril.$chr.$build.png -datafile /home/rmott/public_html/MOUSE/INBREDS/GENOTYPES/BUILD34/Contributed.$chr.$build.genotypes.$date.txt  -regex $menu->{$ril}{regex} -founderA $menu->{$ril}{founderA} -founderB $menu->{$ril}{founderB} ";
	warn "$chr\n";
	system($cmd);
}

my $chr = "chrX";
	my $cmd = "ril.pl -png /home/rmott/public_html/MOUSE/INBREDS/RIL/BUILD34/$ril.$chr.$build.png -datafile  /home/rmott/public_html/MOUSE/INBREDS/GENOTYPES/BUILD34/Contributed.$chr.$build.genotypes.$date.txt -regex $menu->{$ril}{regex} -founderA $menu->{$ril}{founderA} -founderB $menu->{$ril}{founderB} ";
warn "$chr\n";
warn $cmd;
system($cmd);
}