#  join_map_file_converter.pl: Convert Illumina SNP genotyping array data to Joinmap format.
#  Copyright (C) 2010 James Harriman

#  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 3 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.

#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.

#!/usr/bin/perl


###Variables###
#Enter Illumina ID of parent 1 below.
$P1 = qw/
4560195059_A
/;

#Enter Illumina ID of parent 2 below.
$P2 = qw/
4560195059_A
/;
 
 #Enter Illumina IDs of offspring below, one per line.
 @O = qw/
 4560195150_A
 4560195149_A
 4560195142_A
 4560195088_A
 4560195099_A
 4560195063_A
 4560195058_C
 4560195059_C
 4560195150_C
 4560195149_C
 4560195142_C
 4560195088_C
 4560195099_C
 4560195063_C
 4560195058_E
 4560195059_E
 4560195150_E
 4560195149_E
/;

###Program Logic###

#print header line
@i =(1..$#O+1);
print"SNPparentals," . join(",",@i), "\n";
@i=();

#load .csv file

while(<>){
	$_ =~ s/\r//g;
	chomp;
	push @data, [split(',',$_)];
}

#Nested loop over SNPs (rows) and samples (columns).  Store in HoA structure.
for $snp (2..$#data){
	for $sample(1..$#{$data[$snp]}){
		if($verbose){print "$data[$sample][1]\t";}
		@snpinfo = split('\|', $data[$snp][$sample]);
		if($verbose){print "$snp,$sample = $snpinfo[0],$snpinfo[1]\t";}
		$allele{$data[$snp][0]}{$data[1][$sample]} = $snpinfo[0]; 
		if($verbose){$confidence{$data[$snp][0]}{$data[1][$sample]} = $snpinfo[1]; }
		if($verbose){print "Stored $allele{$data[$snp][0]}{$data[1][$sample]} in $data[$snp][0], $data[1][$sample]\t";}
		if($verbose){print "Stored $confidence{$data[$snp][0]}{$data[1][$sample]} in $data[$snp][0], $data[1][$sample]\t";}
	}
	if($verbose){print "\n";}
}
if($verbose){print $allele{"VV\:1\:1002317"}{"4560195049_L"};}
if($verbose){print join(",", keys %{$allele{1_10241041}});}

for $curr_snp(keys %allele){
	if($verbose){print "Moving to SNP $curr_snp.\n$allele{$curr_snp}{$P1}$allele{$curr_snp}{$P2}\n";}
	if($verbose){if($allele{$curr_snp}{$P1} =~ m/\-/ || $allele{$curr_snp}{$P2} =~ m/\-/){print "$allele{$curr_snp}{$P1}$allele{$curr_snp}{$P2}\n";next;}}
	@segregation_code =();
	@allele_parent =();
	@allele_offspring =();
	
	@allele_parent = split('', join('',($allele{$curr_snp}{$P1},$allele{$curr_snp}{$P2})));
	
	if($allele_parent[0] eq $allele_parent[1]){
		if($allele_parent[2] ne $allele_parent[3]){
				@segregation_code = ("n","n","n","p"); #2nd parent heterozygous
		}else{next;} #Both parents homozygous
	}else{
		if($allele_parent[2] ne $allele_parent[3]){
			@segregation_code = ("h","k","h","k"); 	#Both parents heterozygous
		}else{
			@segregation_code = ("l","m","l","l");	#1st parent heterozygous
		}
	}

	for $curr_offspring(0..$#O){
		@allele_offspring = split('', $allele{$curr_snp}{$O[$curr_offspring]});
		if(join('',@segregation_code) =~ m/n/){
			if($allele_offspring[0] eq $allele_offspring[1]){
				$segregation_code_offspring[$curr_offspring]="nn";
			}else{
				$segregation_code_offspring[$curr_offspring]="np";
			}
		}

		if(join('',@segregation_code) =~ m/h/){
			if($allele_offspring[0] eq $allele_offspring[1]){
				if($allele_offspring[0] eq $allele_parent[0]){
					$segregation_code_offspring[$curr_offspring]="hh";
				}else{
					$segregation_code_offspring[$curr_offspring]="kk";
				}
			}else{
				$segregation_code_offspring[$curr_offspring]="hk";
			}
		}

		if(join('',@segregation_code) =~ m/l/){
			if($allele_offspring[0] eq $allele_offspring[1]){
				$segregation_code_offspring[$curr_offspring]="ll";
			}else{
				$segregation_code_offspring[$curr_offspring]="lm";
			}
		}

	#$segregation_code_offspring[$curr_offspring] = join('', ($segregation_code_offspring[$curr_offspring], "=",$allele_offspring[0],$allele_offspring[1]));
	}
		
	print "$curr_snp,\<$segregation_code[0]$segregation_code[1]x$segregation_code[2]$segregation_code[3]\>," .
	join(",", @segregation_code_offspring) . "\n";
}