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hmp2CSS_sw_v2.pl
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#!/usr/perl
#This script takes in a hapmap file and a population label file, and calculates the genetic distance between each pair of samples for a sliding window.
#Eventually it will call an R script to run a PCoA and extract euclidean distances between pairs.
#V2: This version creates 95% confidence intervals around the parental groups and then asks if the samples are within the ellipses and if the ellipses overlap
#Make sure that a sample is not intermediate because it doesn't have any data.
use warnings;
use strict;
use File::Basename;
use Cwd 'abs_path';
use List::Util qw(shuffle);
use lib '/home/owens/bin/pop_gen/'; #For GObox server
my ( $name, $path, $suffix ) = fileparse( $0, qr{\.[^.]*$} );
#print "NAME=$name\n";
#print "PATH=$path\n";
#print "SFFX=$suffix\n";
my %t; #Convert from IUPAC to normal
$t{"N"} = "NN";
$t{"A"} = "AA";
$t{"T"} = "TT";
$t{"G"} = "GG";
$t{"C"} = "CC";
$t{"W"} = "AT";
$t{"R"} = "AG";
$t{"M"} = "AC";
$t{"S"} = "CG";
$t{"K"} = "GT";
$t{"Y"} = "CT";
my %flip; #Flip bases so they're always in alphabetical order
$flip{"TA"} = "AT";
$flip{"GA"} = "AG";
$flip{"CA"} = "AC";
$flip{"GC"} = "CG";
$flip{"TC"} = "CT";
$flip{"TG"} = "GT";
my $min_sites = 2; #Minumum number of sites with data for a pair within a window.
my $min_variable_sites = 5; #Number of sites in the dataset in a window. Skips the window if they don't have it. This is before considering missing data.
my $window_size = 1000000; #Number of bases in each sliding window
my $max_null_pairs; #max number of excluded pairs for a sliding window. Calculated as half of possible pairs.
my $permute_number = 200; #Number of permutations.
my $minimum_hybrid_comparisons = 5; #Minumum number of comparisons with each parental for hybrid calculation.
my $infile = $ARGV[0]; #A snp table in hmp format. Only include samples you're using.
my $popfile = $ARGV[1]; #A population file.
my $out = $ARGV[2]; #outfile prefix
open (FINALOUT, "> $out.final.txt") or die "Could not open a file\n"; #open outfile
open (POPFILE, "> $out.popfile.txt") or die "Could not open a file\n"; #open population file
my %pop;
my %popList;
my %samplepop;
my %samplename;
#Window variables
my $current_chrom;
my $end = $window_size;
open POP, $popfile;
while (<POP>){ #Load in population information linked with sample name
chomp;
my @a = split (/\t/,$_);
$pop{$a[0]}=$a[1];
$popList{$a[1]}++;
}
close POP;
require "countbadcolumns.pl"; #Identify the number of columns before genotype data starts
my ($iupac_coding, $badcolumns) = count_bad_columns($infile);
$. = 0;
#Distance hashes
my %nullcounter;
my %sitecount;
my %distance;
my %took_average_dist;
my $finalcolumn;
my $pop1;
my $pop2;
my $popH;
my $parenttotal;
my %parenthash;
my %hybridhash;
my @hybridarray;
my $variablesites;
open IN, $infile;
while (<IN>){
chomp;
my @a = split(/\t/,$_);
if ($. == 1){ #Load in sample names associated with column numbers, as well as population
$finalcolumn = $#a;
print POPFILE "population";
my $number_samples = (($#a - $badcolumns) + 1);
$max_null_pairs = ($number_samples * ($number_samples -1)) / 2;
foreach my $i($badcolumns..$#a){
if ($pop{$a[$i]}){
$samplepop{$i} = $pop{$a[$i]};
$samplename{$i} = $a[$i];
print POPFILE "\n$samplepop{$i}";
if ($samplepop{$i} eq "P1"){
$pop1++;
$parenthash{$i} = $samplepop{$i};
}elsif ($samplepop{$i} eq "P2"){
$pop2++;
$parenthash{$i} = $samplepop{$i};
}elsif ($samplepop{$i} eq "H"){
$popH++;
$hybridhash{$i} = $samplepop{$i};
push (@hybridarray, $i);
}
}
}
$parenttotal = $pop1 + $pop2;
print FINALOUT "chrom\tstart\tend\tn_sites\toverlap";
foreach my $hybrid_number (@hybridarray){
print FINALOUT "\t$samplename{$hybrid_number}";
}
}else{
my $loc = $a[0];
my $chrom = $a[2];
my $pos = $a[3];
unless ($current_chrom){
$current_chrom = $chrom;
}
if ($. == 2){
until($end > $pos){ #move the end point of the window until it is after the current marker.
$end += $window_size;
}
}
if (($current_chrom ne $chrom) or ($end < $pos)){ #If it's starting a new window, do all the calculations
my $start = $end - $window_size;
if ($variablesites < $min_variable_sites){
print FINALOUT "\n$current_chrom\t$start\t$end\tNA\tNA";
foreach my $hybrid_number (@hybridarray){
print FINALOUT "\tNA";
}
goto RESET;
}
print "Calculating distances for $current_chrom, $start to $end\n";
open (OUTFILE, "> $out.$current_chrom.$end.txt") or die "Could not open a file\n"; #open outfile
my $paircount = 0;
my $nullpairs = 0;
my $totaldist = 0;
foreach my $i ($badcolumns..($finalcolumn-1)){ #This is to create the average distance between objects for missing data
foreach my $j (($i+1)..$finalcolumn){
unless ($sitecount{$i}{$j}){
$sitecount{$i}{$j} = 0;
}
if ($sitecount{$i}{$j} <= $min_sites){
$distance{$i}{$j} = "NA"; #Delete pairs without sufficient data within the window.
$nullpairs++;
#print "Too many null on $i $j\n";
}
else{
unless($distance{$i}{$j}){
$distance{$i}{$j} = 0;
}
}
if ($distance{$i}{$j} ne "NA"){
#print "For $i $j nullcounts=$nullcounter{$i}{$j}\n";
#print "For $i $j distance=$distance{$i}{$j}, sitcount=$sitecount{$i}{$j}\n";
$distance{$i}{$j} = ($distance{$i}{$j} / $sitecount{$i}{$j});
if ($i ne $j){
$paircount++;
$totaldist += $distance{$i}{$j} #Add up all distances, not including self distances
}
}
}
}
#calculate average distance for window
my $average_dist = ($totaldist / $paircount);
#print "$average_dist\t$nullpairs\t$max_null_pairs\n";
if ($nullpairs < $max_null_pairs){
foreach my $i ($badcolumns..$finalcolumn){
foreach my $j ($badcolumns..$finalcolumn){
if ($i eq $j){
$distance{$i}{$j} = 0;
}
unless (defined $distance{$i}{$j}){
$distance{$i}{$j} = $distance{$j}{$i};
}if ($distance{$i}{$j} eq "NA"){
$distance{$i}{$j} = $average_dist;
$took_average_dist{$i}{$j}++;
}if ($j eq $badcolumns){
print OUTFILE "$distance{$i}{$j}";
}else{
print OUTFILE "\t$distance{$i}{$j}";
}
}
print OUTFILE "\n";
}
}else{
print OUTFILE "Too much missing data\n";
close OUTFILE;
my $start = $end - $window_size;
print FINALOUT "\n$current_chrom\t$start\t$end\tNA\tNA";
foreach my $hybrid_number (@hybridarray){
print FINALOUT "\tNA";
}
goto RESET;
}
close OUTFILE;
#Use cmdscale in R to compress to 2 dimensions, then calculate the euclidean distance between each sample.
print "Calculating euclidean distances for $current_chrom, $start to $end\n";
my $cmd = "Rscript $path/MDS_ellipse.R $out.$current_chrom.$end.txt $out.popfile.txt $out.$current_chrom.$end.P1hyb.txt $out.$current_chrom.$end.P2hyb.txt $out.$current_chrom.$end.overlap.txt";
system($cmd);
my @conf_levels = ("0.75", "0.80", "0.85", "0.90", "0.95", "0.99");
open P1HYB, "$out.$current_chrom.$end.P1hyb.txt"; #Load in distance scores from R
my $hybcounter = 0;
my %hyb_conf;
while (<P1HYB>){
chomp;
my @a = split(/\t/, $_);
$hybcounter++;
$hyb_conf{"P1"}{$hybcounter} = "No";
foreach my $i (4){
if ($a[$i] > 0){
$hyb_conf{"P1"}{$hybcounter} = "Yes";
last;
}
}
}
close P1HYB;
my $hybnumber = $hybcounter;
open P2HYB, "$out.$current_chrom.$end.P2hyb.txt"; #Load in distance scores from R
$hybcounter = 0;
while (<P2HYB>){
chomp;
my @a = split(/\t/, $_);
$hybcounter++;
$hyb_conf{"P2"}{$hybcounter} = "No";
foreach my $i (4){
if ($a[$i] > 0){
$hyb_conf{"P2"}{$hybcounter} = "Yes";
last;
}
}
}
close P2HYB;
open OVERLAP, "$out.$current_chrom.$end.overlap.txt"; #Load in distance scores from R
my $overlap = "No";
while (<OVERLAP>){
chomp;
my @a = split(/\t/, $_);
foreach my $i (4){
if ($a[$i] eq "TRUE"){
$overlap = "Yes";
last;
}
}
}
close OVERLAP;
print FINALOUT "\n$current_chrom\t$start\t$end\t$variablesites\t$overlap";
foreach my $i (1..$hybnumber){
if (($hyb_conf{'P1'}{$i} eq "No") and ($hyb_conf{'P2'}{$i} eq "No")){
print FINALOUT "\tNeither";
}elsif (($hyb_conf{'P1'}{$i} eq "No") and ($hyb_conf{'P2'}{$i} eq "Yes")){
print FINALOUT "\tP2";
}elsif (($hyb_conf{'P1'}{$i} eq "Yes") and ($hyb_conf{'P2'}{$i} eq "No")){
print FINALOUT "\tP1";
}elsif (($hyb_conf{'P1'}{$i} eq "Yes") and ($hyb_conf{'P2'}{$i} eq "Yes")){
print FINALOUT "\tBoth";
}
}
#Reset the variables
RESET:
my $cleaner = "rm $out.$current_chrom.$end*";
system($cleaner);
undef %distance;
undef %sitecount;
undef $variablesites;
undef %took_average_dist;
if ($current_chrom ne $chrom){ #If on the next chromosome, reset the end point for the window
$current_chrom = $chrom;
$end = $window_size;
}
until($end > $pos){ #move the end point of the window until it is after the current marker.
$end += $window_size;
}
}
$variablesites++;
foreach my $i($badcolumns..$#a){ #If IUPAC coding used, convert to paired nucleotide.
if ($iupac_coding eq "TRUE"){
$a[$i] = $t{$a[$i]};
}
else{
if ($flip{$a[$i]}){
$a[$i] = $flip{$a[$i]};
}
}
}
foreach my $i($badcolumns..$#a){
foreach my $j ($i..$#a){
if (($a[$i] eq "NN") or ($a[$j] eq "NN")){ #If either is missing, count as missing for that pair.
#nothing happens
}else{
my @tmp1 = split('',$a[$i]);
my @tmp2 = split('',$a[$j]);
if ($a[$i] eq $a[$j]){ #If they're identical, don't add to the distance but do add to the site count.
$distance{$i}{$j} += 0;
$sitecount{$i}{$j}++;
}elsif (($tmp1[0] eq $tmp2[0]) or ($tmp1[0] eq $tmp2[1]) or ($tmp1[1] eq $tmp2[0]) or ($tmp1[1] eq $tmp2[1])){ #If any have any matches, they are 0.5 distance away.
$sitecount{$i}{$j}++;
$distance{$i}{$j} += 0.5;
}else{
$sitecount{$i}{$j}++;
$distance{$i}{$j}++;
}
}
}
}
}
}
close IN;