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sibsam_cluster_analysis.pl
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sibsam_cluster_analysis.pl
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#!/usr/bin/perl -w
use strict;
use cmdline_args;
if (!$ARGV[0] || $ARGV[0] eq "help"){
print <<EOF;
This script analyzes output from sibsam_1locus.pl
It requires the following arguments:
-f [file name stem]
-x [cluster number]
There must be a window file with the above stem followed by "_windows.txt"
There must be one or more simulation files from sibsam_cluster.pl with the file stem followed by "_clusterXsims*" (where X is the cluster number and * is any characters)
Output file will have this file stem appended by "_clusterXresults.txt"
EOF
exit 1;
}
my $FileStem = "";
my $ClusterNumber = "";
my %args;
$args{'-f'} = [ \$FileStem, 1];
$args{'-x'} = [ \$ClusterNumber, 1];
cmdline_args::get_options(\%args, \@ARGV);
my $SimFile = $FileStem . '_cluster' . $ClusterNumber . 'sims';
my $WinFile = $FileStem . '_windows.txt';
my $ClusterFile = $FileStem . '_cluster' . $ClusterNumber . '.txt';
my $OutputFile = $FileStem . '_cluster' . $ClusterNumber . 'results.txt';
my $tolerance = 0.05; #height of sim peaks must be within this range of real peak height to accept
#Get cM and depth information from window files
my $CMsX = 0;
my $CMsA = 0;
my $depth = 0;
my @line = ();
my @DepthsXHigh = ();
my @DepthsAHigh = ();
my @DepthsXLow = ();
my @DepthsALow = ();
my @CMStopsX = ();
my @CMStopsA = ();
my @AutoCMBreaks = ();
my @WinChrs = ();
my @AncDiffs = ();
open W, "<$WinFile" or die;
scalar (<W>);
while (<W>){
chomp;
last if m/^$/;
@line = split;
if ($line[0] =~ m/X/){
push @CMStopsX, $line[3];
$depth = int($line[4]);
push @DepthsXHigh, $depth;
$depth = int($line[5]);
push @DepthsXLow, $depth;
}
else{
push @CMStopsA, $line[3];
$depth = int($line[4]);
push @DepthsAHigh, $depth;
$depth = int($line[5]);
push @DepthsALow, $depth;
}
push @WinChrs, $line[0];
push @AncDiffs, $line[-1];
$WinChrs[-1] =~ s/L//;
$WinChrs[-1] =~ s/R//;
}
close W;
$CMsX = $CMStopsX[-1];
my $TotalWindows = @CMStopsA + @CMStopsX;
my $AWindows = @CMStopsA;
my $XWindows = @CMStopsX;
#Get real peak data
my $i = 0;
my @RealPeakWindows = ();
my @RealPeakHeights = ();
my @RealPeakValleys = ();
open C, "<$ClusterFile" or die;
scalar (<C>);
while (<C>){
chomp;
last if m/^$/;
@line = split;
push @RealPeakValleys, $line[0];
push @RealPeakWindows, $line[1];
push @RealPeakHeights, $line[2];
}
close C;
$i = @RealPeakHeights;
print "Found data for $i peaks\n";
#get simulation results
my $j = 0;
my @SimPropVars = ();
my @SimPropVarAoA = ();
my @SimPeakHeightAoA = ();
my @SimPeakWindowAoA = ();
my @SimPeakHeights = ();
my @SimPeakWindows = ();
my @AllFiles = ();
my @SimPeakFiles = ();
opendir DIR, "." or die "couldn't open directory\n";
@AllFiles = readdir(DIR);
closedir DIR;
for ($i = 0; $i < @AllFiles; $i++){
if (($AllFiles[$i] =~ m/$SimFile/) && ($AllFiles[$i] =~ m/txt/)){
unless ($AllFiles[$i] =~ m/zip/){
push @SimPeakFiles, $AllFiles[$i];
}
}
}
for ($i = 0; $i < @SimPeakFiles; $i++){
open S, "<$SimPeakFiles[$i]" or die;
scalar (<S>);
while (<S>){
chomp;
last if m/^$/;
@line = split;
@SimPropVars = ();
@SimPeakHeights = ();
@SimPeakWindows = ();
for ($j = 0; $j < @line; $j = $j + 3){
push @SimPropVars, $line[$j];
push @SimPeakHeights, $line[$j+1];
push @SimPeakWindows, $line[$j+2];
}
push @SimPeakHeightAoA, [ @SimPeakHeights ];
push @SimPeakWindowAoA, [ @SimPeakWindows ];
push @SimPropVarAoA, [ @SimPropVars ];
}
close S;
}
$i = @SimPeakHeightAoA;
print "Found data for $i simulated replicates\n";
die if ($i < 100);
if (@RealPeakHeights != @{$SimPeakHeightAoA[0]}){
$j = @{$SimPeakHeightAoA[0]};
print "$i != $j\n";
die;
}
#Retain sim peak data only in cases where all cluster peaks are within tolerance of real peak heights
my @GoodPropVars = ();
my @GoodPeakWindows = ();
my @GoodSecDevs = ();
my @TotalSimsFit = ();
my @PropVar5 = ();
my @PropVar95 = ();
my @SecDev95 = ();
my @PropVar50 = ();
my @AdjustedSecValleyHeights = ();
my @AdjustedSecValleyWindows = ();
my @SecPeakPValues = ();
my @SecPeakDeviations = ();
my @LeftBounds = ();
my @RightBounds = ();
my $k = 0;
my $l = 0;
my $ClusterStart = 0;
my $ClusterStop = 0;
my $SecDev = 0;
my $AdjustedValleyHeight = 0;
my $AdjustedValleyWindow = 0;
my $LowestValleyAwayHeight = 0;
my $LowestValleyAwayWindow = 0;
my $HighThreshRank = 0;
my $LowThreshRank = 0;
my $PValue = 0;
my $half = 0;
my $MedianValue = 0;
for ($i = 0; $i < @SimPeakHeightAoA; $i++){
for ($j = 0; $j < @RealPeakHeights; $j++){
if ((abs($RealPeakHeights[$j] - $SimPeakHeightAoA[$i][$j])) > $tolerance){
splice @SimPeakHeightAoA, $i, 1;
splice @SimPeakWindowAoA, $i, 1;
splice @SimPropVarAoA, $i, 1;
$i--;
last;
}
}
}
$i = @SimPeakHeightAoA;
print "Kept data for $i simulated replicates\n";
for ($i = 0; $i < @RealPeakHeights; $i++){
@GoodPropVars = ();
@GoodPeakWindows = ();
for ($j = 0; $j < @SimPeakHeightAoA; $j++){
push @GoodPropVars, $SimPropVarAoA[$j][$i];
push @GoodPeakWindows, $SimPeakWindowAoA[$j][$i];
}
$j = @GoodPropVars;
push @TotalSimsFit, $j;
#Obtain desired critical values for each peak
@GoodPropVars = sort {$a <=> $b} @GoodPropVars;
@GoodPeakWindows = sort {$a <=> $b} @GoodPeakWindows;
$HighThreshRank = int(@GoodPropVars * 0.95) + 1;
$LowThreshRank = int(@GoodPropVars * 0.05);
push @PropVar5, $GoodPropVars[$LowThreshRank];
push @PropVar95, $GoodPropVars[$HighThreshRank];
push @LeftBounds, $GoodPeakWindows[$LowThreshRank];
push @RightBounds, $GoodPeakWindows[$HighThreshRank];
if ((@GoodPropVars % 2) == 0){
$half = @GoodPropVars / 2;
$MedianValue = ($GoodPropVars[$half] + $GoodPropVars[$half-1]) / 2;
push @PropVar50, $MedianValue;
}
else{
$half = int(@GoodPropVars / 2);
$MedianValue = $GoodPropVars[$half];
push @PropVar50, $MedianValue;
}
print "Evaluated thresholds for peak $i\n";
}
#zip up the sim files to get them out of the way
my $cmd = 'zip ' . $SimFile . '.zip';
for ($i = 0; $i < @SimPeakFiles; $i++){
$cmd = $cmd . ' ' . $SimPeakFiles[$i];
}
system($cmd);
for ($i = 0; $i < @SimPeakFiles; $i++){
$cmd = 'rm ' . $SimPeakFiles[$i];
system($cmd);
}
#Output
open O, ">$OutputFile";
print O "RealPeakWindow\tRealPeakHeight\tMatchingSims\tPropVar50th\tPropVar5th\tPropVar95th\tLeftWinBound\tRightWinBound\n";
for ($i = 0; $i < @RealPeakHeights; $i++){
print O "$RealPeakWindows[$i]\t$RealPeakHeights[$i]\t$TotalSimsFit[$i]\t$PropVar50[$i]\t$PropVar5[$i]\t$PropVar95[$i]\t$LeftBounds[$i]\t$RightBounds[$i]\n";
}
close O;