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chi2_Teremi_vs_Merus.pl
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#!/usr/bin/perl
#######################################################################
########## #####
########## CHI SQUARE PROABILITY CALCULATOR Ter vs mer (6 vs 1) #####
########## INPUT = All_Moshi_Igor_2L/2R etc_SUBSAMPLED.sync #####
########## OUTPUT = probabilities based on 2x2 allele count #####
########## (biallelic - major/minor alive/dead #####
########## one comparison: #####
########## A1vA2 #####
########## Teremi = 17,18,19,20,21,22 #####
########## Merus = 23 #####
########## by Chris Clarkson #####
########## [email protected] #####
#######################################################################
use strict;
use warnings;
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\tchi2TeremivMerus\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[16,17,18,19,20,21];
my @A2 = @alleles[22];
my $A11; my $A12; my $A13; my $A14;
my $A21; my $A22; my $A23; my $A24;
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];
}
my $total1 = $A11 + $A21;
my $total2 = $A12 + $A22;
#print "$total1\t$total2\t$total3\t$total4\n"; #get true ATCG counts across all pools to get rid of >biallelics
push (my @totalcount, $total1, $total2);
my @sortedtotal = sort {$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, $A24);
my @A1_non_zero;
my @A2_non_zero;
if ($A1_all_count[0] != 0 || $A2_all_count[0] != 0 ) {
chomp($A1_all_count[0]);
chomp($A2_all_count[0]);
push (@A1_non_zero, $A1_all_count[0]);
push (@A2_non_zero, $A2_all_count[0]);
}
if ($A1_all_count[1] != 0 || $A2_all_count[1] != 0 ) {
chomp($A1_all_count[1]);
chomp($A2_all_count[1]);
push (@A1_non_zero, $A1_all_count[1]);
push (@A2_non_zero, $A2_all_count[1]);
}
if ($A1_all_count[2] != 0 || $A2_all_count[2] != 0 ) {
chomp($A1_all_count[2]);
chomp($A2_all_count[2]);
push (@A1_non_zero, $A1_all_count[2]);
push (@A2_non_zero, $A2_all_count[2]);
}
if ($A1_all_count[3] != 0 || $A2_all_count[3] != 0 ) {
chomp($A1_all_count[3]);
chomp($A2_all_count[3]);
push (@A1_non_zero, $A1_all_count[3]);
push (@A2_non_zero, $A2_all_count[3]);
}
if(@A1_non_zero < 2){
push(@A1_non_zero, 0);
}
if(@A2_non_zero < 2){
push(@A2_non_zero, 0);
}
#print "@A1_non_zero\t@A2_non_zero\t@D1_non_zero\t@D2_non_zero\n";
my @fixAA1;
my @fixAA2;
if ($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 = $AAchi->{p_value};
print OUTPUT "$contig\t$position\t$fisherA1A2\n";
}
}