#!/usr/bin/perl

# Copyright 2013 O. Sotolongo <osotolongo@fundacioace.com>

# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
use strict; use warnings;
use File::Slurp qw(read_file);
use Data::Dump qw(dump);

my $flip = 0;

while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-flip/) { $flip = 1;}    
}
my $db;
my $odb;
unless ($flip) {
	$db = shift;
	die "Must supply database\n" unless $db;
	$odb = $db;
	$odb =~ s/(.*)\.(.*)/$1_bcomp_flipped\.$2/;
}else{
	$odb = 'just_flip_these.txt';
}
my $assoc_previous = shift;
my $assoc_last = shift;

print "I will try to write results to $odb\n";

my %genmap_previous;
my %genmap_last;
my %genmap;
my %data_line;
#first I store the files
unless($flip){
	%data_line = reverse map {/^(.*\s+(rs\d+)\s+.*)$/} grep {/^(.*\s+(rs\d+)\s+.*)$/} read_file $db;
	foreach my $marker (sort keys %data_line){
		(@{$genmap{$marker}} {qw/chr gposition fposition allele1 allele2/}) = $data_line{$marker} =~ /^(\d+)\s+rs\d+\s+(.*)\s+(\d+)\s+([A,T,C,G])\s+([A,T,C,G])\s*$/;
	}
}

#now I will read target markers from the assoc files 
print "OK, let see what markers I have to change, reading $assoc_previous and $assoc_last ...\n";
%data_line = reverse map {/^(.*\s+(rs\d+)\s+.*)$/} grep {/^(.*\s+(rs\d+)\s+.*)$/} read_file $assoc_previous;
foreach my $marker (sort keys %data_line){
	(@{$genmap_previous{$marker}} {qw/chr position allele1 freq1 freq2 allele2 chi2 pvalue oddratio/}) = $data_line{$marker} =~ /^\s*(\d+)\s+rs\d+\s+(\d+)\s+([A,T,C,G]+)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*)\s+([A,T,C,G]+)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*|NA)\s*$/;
}

%data_line = reverse map {/^(.*\s+(rs\d+)\s+.*)$/} grep {/^(.*\s+(rs\d+)\s+.*)$/} read_file $assoc_last;
foreach my $marker (sort keys %data_line){
	(@{$genmap_last{$marker}} {qw/chr position allele1 freq1 freq2 allele2 chi2 pvalue oddratio/}) = $data_line{$marker} =~ /^\s*(\d+)\s+rs\d+\s+(\d+)\s+([A,T,C,G]+)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*)\s+([A,T,C,G]+)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*)\s+(\d+\.*\d*e*-*\d*|NA)\s*$/;
}

#dump %genmap_last; exit;
my @outmarkers;
# and then flip the allele information of targets in db info
if($flip){
	foreach my $marker (keys %genmap_previous){
		if(exists($genmap_previous{$marker}) && exists($genmap_last{$marker})){
			if($genmap_previous{$marker}{chi2} < $genmap_last{$marker}{chi2}){
				push @outmarkers, $marker;
			}
		}
	}
}else{
	print "I'm going to flips those markers now\n";
	foreach my $marker (keys %genmap_previous){
		if(exists($genmap_previous{$marker}) && exists($genmap_last{$marker})){
			if($genmap_previous{$marker}{chi2} < $genmap_last{$marker}{chi2}){
				my $tallele = $genmap{$marker}{allele1};
				$genmap{$marker}{allele1} = $genmap{$marker}{allele2};
				$genmap{$marker}{allele2} = $tallele;
			}
		}
	}
}

# go and write .bim or markers list now
print "Writing to $odb\n";
open ODF, ">$odb" || die "Could not open output file";

if($flip){
	foreach my $marker (@outmarkers){
		print ODF "$marker\n";
	}
}else{
	foreach my $marker (sort {($genmap{$a}->{chr} <=> $genmap{$b}->{chr}) or ($genmap{$a}->{fposition} <=> $genmap{$b}->{fposition})} keys %genmap){
		print ODF "$genmap{$marker}{chr}\t$marker\t$genmap{$marker}{gposition}\t$genmap{$marker}{fposition}\t$genmap{$marker}{allele1}\t$genmap{$marker}{allele2}\n";
	}
}
close ODF;