#!/usr/bin/perl -w
#Author: Qunfeng Dong
#only extract X or Y sequence from RescueMuGSS.trim
#this is used for vmatch to filter out parentials
#usage: ./ExtractXYseq.pl RescueMuGSS.trim 
#output: GridGparental.txt, GridHparental.txt ...


use strict;

open(G, '>GridG_XYseq.fsa');
open(H, '>GridH_XYseq.fsa');
open(I, '>GridI_XYseq.fsa');
open(K, '>GridK_XYseq.fsa');
open(M, '>GridM_XYseq.fsa');
open(P, '>GridP_XYseq.fsa');

$/ = '>';
open(FILE, "$ARGV[0]") || die ("Cannot open");
while(<FILE>){
	next unless /RescueMu/;
	chomp;
	my ($sid, $pid) = /gi\S+\s+(\S+)\s+(\d+)/;
	next unless ($sid =~ /\.x/ || $sid =~ /\.y/);
	if($pid eq '1006'){
		print G ">$_\n";
	}elsif($pid eq '1007'){
                print H ">$_\n";
        }elsif($pid eq '1008'){
                print I ">$_\n";
        }elsif($pid eq '3526'){
                print K ">$_\n";
        }elsif($pid eq '3590'){
                print M ">$_\n";
        }elsif($pid eq '3591'){
                print P ">$_\n";
        }else{
		print STDERR "$pid Wrong Grid!\n";
		exit;
	}

}
close(FILE);
$/ = "\n";