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chi2_Moshi_dead_vs_Terem.pl
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#!/usr/bin/perl
#######################################################################
########## ###############
########## FISHER'S EXACT TEST CALCULATOR FOR MD vs T (3 vs 3)#######
########## WITHIN vs BETWEEN ALIVE/DEAD COMPARISONS ###############
########## INPUT = All_Moshi_Igor_2L/2R etc_SUBSAMPLED.sync ########
########## OUTPUT = probabilities based on 2x2 allele count ###########
########## (biallelic - major/minor alive/dead ###############
########## four comarisons: ###############
########## A1vA2,D1vD2,A1vD1,A2vD2 ###############
########## pools assigned using random_pool_picker.pl ###########
########## MD1 = 11, 15, 16 ###############
########## A2 = 12, 13, 14 ###############
########## D1 = 17, 19, 21 ###############
########## D2 = 18, 20, 22 ###############
########## by Chris Clarkson ###############
########## [email protected] ###############
#######################################################################
use strict;
use warnings;
#use Text::NSP::Measures::2D::Fisher::twotailed;
#package Statistics::FishersExactTest;
#use Exporter 'import';
#use Math::Pari ();
#my $Tolerance = 1;
#$Tolerance /= 2 while 1 + $Tolerance/2 > 1;
#@Statistics::FET::EXPORT_OK = 'fishers_exact';
use Statistics::ChisqIndep;
use POSIX;
print "Pleez inputz the name ov output file\n\n";
chomp (my $title = <STDIN>);
my $input = $ARGV[0];
open (INPUT, $input)||die "cannot open input";
open (OUTPUT, ">$title".".txt")||die "aaaaaaaaaaaaarrrrrrrrrrgh!";
my $counter = 0;
print OUTPUT "contig\tposition\tchi2MD1vMD2\tchi2T1vT2\tchi2MD1vT1\tchi2MD2vT2\n";
while(my $line = <INPUT>){
chomp($line);
my @alleles = split(/\t/, $line);
my $contig = $alleles[0];
my $position = $alleles [1];
shift @alleles for (0..2);
my @A1 = @alleles[10,14,15];
my @A2 = @alleles[11,12,13];
my @D1 = @alleles[16,18,20];
my @D2 = @alleles[17,19,21];
my $A11; my $A12; my $A13; my $A14;
my $A21; my $A22; my $A23; my $A24;
my $D11; my $D12; my $D13; my $D14;
my $D21; my $D22; my $D23; my $D24;
foreach(@A1){
my @A1alleles = split(/:/, $_);
$A11 += $A1alleles[0];
$A12 += $A1alleles[1];
$A13 += $A1alleles[2];
$A14 += $A1alleles[3];
}
foreach(@A2){
my @A2alleles = split(/:/, $_);
$A21 += $A2alleles[0];
$A22 += $A2alleles[1];
$A23 += $A2alleles[2];
$A24 += $A2alleles[3];
}
foreach(@D1){
my @D1alleles = split(/:/, $_);
$D11 += $D1alleles[0];
$D12 += $D1alleles[1];
$D13 += $D1alleles[2];
$D14 += $D1alleles[3];
}
foreach(@D2){
my @D2alleles = split(/:/, $_);
$D21 += $D2alleles[0];
$D22 += $D2alleles[1];
$D23 += $D2alleles[2];
$D24 += $D2alleles[3];
}
my $total1 = $A11 + $A21 + $D11 + $D21;
my $total2 = $A12 + $A22 + $D12 + $D22;
my $total3 = $A13 + $A23 + $D13 + $D23;
my $total4 = $A14 + $A24 + $D14 + $D24;
#print "$total1\t$total2\t$total3\t$total4\n"; #get true ATCG counts across all pools to get rid of >biallelics
push (my @totalcount, $total1, $total2, $total3, $total4);
my @sortedtotal = sort {$a <=> $b } @totalcount;
if ($sortedtotal[1] == 0){ #only use biallelics
push( my @A1_all_count, $A11 , $A12 , $A13, $A14);
push( my @A2_all_count, $A21 , $A22 , $A23, $A24);
push( my @D1_all_count, $D11 , $D12 , $D13, $D14);
push( my @D2_all_count, $D21 , $D22 , $D23, $D24);
my @A1_non_zero;
my @A2_non_zero;
my @D1_non_zero;
my @D2_non_zero;
if ($A1_all_count[0] != 0 || $A2_all_count[0] != 0 || $D1_all_count[0] != 0 || $D2_all_count[0] != 0) {
chomp($A1_all_count[0]);
chomp($A2_all_count[0]);
chomp($D1_all_count[0]);
chomp($D2_all_count[0]);
push (@A1_non_zero, $A1_all_count[0]);
push (@A2_non_zero, $A2_all_count[0]);
push (@D1_non_zero, $D1_all_count[0]);
push (@D2_non_zero, $D2_all_count[0]);
}
if ($A1_all_count[1] != 0 || $A2_all_count[1] != 0 || $D1_all_count[1] != 0 || $D2_all_count[1] != 0) {
chomp($A1_all_count[1]);
chomp($A2_all_count[1]);
chomp($D1_all_count[1]);
chomp($D2_all_count[1]);
push (@A1_non_zero, $A1_all_count[1]);
push (@A2_non_zero, $A2_all_count[1]);
push (@D1_non_zero, $D1_all_count[1]);
push (@D2_non_zero, $D2_all_count[1]);
}
if ($A1_all_count[2] != 0 || $A2_all_count[2] != 0 || $D1_all_count[2] != 0 || $D2_all_count[2] != 0) {
chomp($A1_all_count[2]);
chomp($A2_all_count[2]);
chomp($D1_all_count[2]);
chomp($D2_all_count[2]);
push (@A1_non_zero, $A1_all_count[2]);
push (@A2_non_zero, $A2_all_count[2]);
push (@D1_non_zero, $D1_all_count[2]);
push (@D2_non_zero, $D2_all_count[2]);
}
if ($A1_all_count[3] != 0 || $A2_all_count[3] != 0 || $D1_all_count[3] != 0 || $D2_all_count[3] != 0) {
chomp($A1_all_count[3]);
chomp($A2_all_count[3]);
chomp($D1_all_count[3]);
chomp($D2_all_count[3]);
push (@A1_non_zero, $A1_all_count[3]);
push (@A2_non_zero, $A2_all_count[3]);
push (@D1_non_zero, $D1_all_count[3]);
push (@D2_non_zero, $D2_all_count[3]);
}
if(@A1_non_zero < 2){
push(@A1_non_zero, 0);
}
if(@A2_non_zero < 2){
push(@A2_non_zero, 0);
}
if(@D1_non_zero < 2){
push(@D1_non_zero, 0);
}
if(@D2_non_zero < 2){
push(@D2_non_zero, 0);
}
#print "@A1_non_zero\t@A2_non_zero\t@D1_non_zero\t@D2_non_zero\n";
my @fixAA1;
my @fixAA2;
if ($A1_non_zero[0] <= $A1_non_zero[1]){
@fixAA1 = @A1_non_zero;
@fixAA2 = @A2_non_zero;
}
if ($A1_non_zero[0] > $A1_non_zero[1]){
@fixAA1 = sort {$a <=> $b} @A1_non_zero;
@fixAA2 = ($A2_non_zero[1],$A2_non_zero[0]);
}
my $inp1AA = $fixAA1[0];
my $inp2AA = $fixAA1[1];
my $inp3AA = $fixAA2[0];
my $inp4AA = $fixAA2[1];
my @finalAA = ([$inp1AA, $inp2AA], [$inp3AA, $inp4AA]);
my $AAchi = new Statistics::ChisqIndep;
$AAchi->load_data(\@finalAA);
my $fisherA1A2 = $AAchi->{p_value};
my @fixDD1;
my @fixDD2;
if ($D1_non_zero[0] <= $D1_non_zero[1]){
@fixDD1 = @D1_non_zero;
@fixDD2 = @D2_non_zero;
}
if ($D1_non_zero[0] > $D1_non_zero[1]){
@fixDD1 = sort {$a <=> $b} @D1_non_zero;
@fixDD2 = ($D2_non_zero[1],$D2_non_zero[0])
}
my $inp1DD = $fixDD1[0];
my $inp2DD = $fixDD1[1];
my $inp3DD = $fixDD2[0];
my $inp4DD = $fixDD2[1];
my @finalDD = ([$inp1DD, $inp2DD], [$inp3DD, $inp4DD]);
my $DDchi = new Statistics::ChisqIndep;
$DDchi->load_data(\@finalDD);
my $fisherD1D2 = $DDchi->{p_value};
my @fix1AD1;
my @fix1AD2;
if ($A1_non_zero[0] <= $A1_non_zero[1]){
@fix1AD1 = @A1_non_zero;
@fix1AD2 = @D1_non_zero;
}
if ($A1_non_zero[0] > $A1_non_zero[1]){
@fix1AD1 = sort {$a <=> $b} @A1_non_zero;
@fix1AD2 = ($D1_non_zero[1],$D1_non_zero[0]);
}
my $inp1AD1 = $fix1AD1[0];
my $inp2AD1 = $fix1AD1[1];
my $inp3AD1 = $fix1AD2[0];
my $inp4AD1 = $fix1AD2[1];
my @finalAD1 = ([$inp1AD1, $inp2AD1], [$inp3AD1, $inp4AD1]);
my $AD1chi = new Statistics::ChisqIndep;
$AD1chi->load_data(\@finalAD1);
my $fisherA1D1 = $AD1chi->{p_value};
my @fix2AD1;
my @fix2AD2;
if ($A2_non_zero[0] <= $A2_non_zero[1]){
@fix2AD1 = @A2_non_zero;
@fix2AD2 = @D2_non_zero;
}
if ($A2_non_zero[0] > $A2_non_zero[1]){
@fix2AD1 = sort {$a <=> $b} @A2_non_zero;
@fix2AD2 = ($D2_non_zero[1],$D2_non_zero[0]);
}
my $inp1AD2 = $fix2AD1[0];
my $inp2AD2 = $fix2AD1[1];
my $inp3AD2 = $fix2AD2[0];
my $inp4AD2 = $fix2AD2[1];
my @finalAD2 = ([$inp1AD2, $inp2AD2], [$inp3AD2, $inp4AD2]);
my $AD2chi = new Statistics::ChisqIndep;
$AD2chi->load_data(\@finalAD2);
my $fisherA2D2 = $AD2chi->{p_value};
print OUTPUT "$contig\t$position\t$fisherA1A2\t$fisherD1D2\t$fisherA1D1\t$fisherA2D2\n";
}
}