#!/usr/bin/perl

$ENV{'PATH'} = "../bin:$ENV{'PATH'}";

$filename = $ARGV[0];
$eignum = $ARGV[1];
if ($eignum == false)
{
	$eignum = 2;
}

open (PAR, ">", "par.".$filename) or die $!;
print PAR "genotypename:    ".$filename.".ped\n";
print PAR "snpname:         ".$filename.".map\n";
print PAR "indivname:       ".$filename.".ind\n";
print PAR "evecoutname:     ".$filename.".evec\n";
print PAR "evaloutname:     ".$filename.".eval\n";
print PAR "altnormstyle:    NO\n"; 
print PAR "numoutevec:      ".$eignum;

$command = "smartpca";
$command .= " -p par.".$filename." >".$filename.".log";
print("$command\n");
system("$command");

unlink("par.".$filename);
close PAR;

$command = "ploteig";
$command .= " -i ".$filename.".evec ";
$command .= " -c 1:2 ";
$command .= " -p Case:Control ";
$command .= " -x ";
$command .= " -o ".$filename.".plot.xtxt "; # must end in .xtxt
print("$command\n");
system("$command");

$command = "evec2pca.perl ".$eignum. " ".$filename.".evec ".$filename.".ind ".$filename.".pca";
print("$command\n");
system("$command");