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codom_calling.pl
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codom_calling.pl
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##!/usr/bin/perl -w
###################################################################
#-this progrome is used to genotyping codomiant marker
###################################################################
###################################################################
my $len ;
my $pro_num=0 ;
my $PP =3.84;
my $p =0.8 ;
mkdir("genotype");
my $out ="genotype/all_codom";
my $out1 ="genotype/poly_codom";
my $out2 ="genotype/LOG";
parse_command_line();
if($a==0.05){$PP=3.84;}
else {$PP=5.9;}
opendir (DIR, "reads_mapping");
@dire = readdir DIR;
@dire = sort @dire;
print "@dire\n";
here();
SNP_genotype("P1");
SNP_genotype("P2");
print $out2 "the number of progeny from left to right\n";
for($kk=0;$kk<@dire;$kk++){
print "@dire[$kk]\n";
if(@dire[$kk] eq "P1"||@dire[$kk] eq "P2"|| @dire[$kk] eq "."|| @dire[$kk] eq ".."){;}
else{SNP_genotype(@dire[$kk]);}
}
filter();
sub filter(){
open FIG,"<$out";
open OUT,">$out1";
foreach $word(<FIG>){
chomp($word=$word);
@file=split(/\s+/,$word);
$len=@file;
$child_num=$len-6;
$female=@file[4];$male=@file[5];
$a=substr($female,0,1);$b=substr($female,1,1);
$c=substr($male,0,1) ;$d=substr($male,1,1) ;
if(($a ne $b) && ($c ne $d)&& ($female eq $male)){
$AA=0;$AT=0;$TT=0;
for($i=6;$i<$len;$i++){
if(@file[$i] eq $a."$a"){$AA++;}
elsif(@file[$i] eq $a."$b"){$AT++;}
elsif(@file[$i] eq $b."$b"){$TT++;}
}
$sum=($AA+$AT+$TT)/4;
if($sum>=$child_num*$p/4 && ($AA>2 || $AT>2||$TT>2)){print OUT "$word\n";}
}
if(($a eq $b) && ($c ne $d)&&($a eq $c || $a eq $d)){
$AA=0;$AT=0;$TT=0;
for($i=6;$i<$len;$i++){
if(@file[$i] eq $female){$AA++;}
elsif(@file[$i] eq $male) {$AT++;}
}
$sum=($AA+$AT)/2;
if($sum>$child_num*$p/2 && ($AA>2 || $AT>2)){print OUT "$word\n";}
}
if(($a ne $b) && ($c eq $d)&&($a eq $c || $b eq $c)){
$AA=0;$AT=0;$TT=0;
for($i=6;$i<$len;$i++){
if(@file[$i] eq $female){$AT++;}
elsif(@file[$i] eq $male) {$AA++;}
}
$sum=($AA+$AT)/2;
if($sum>$child_num*$p/2 && ($AA>2 || $AT>2)){print OUT "$word\n";}
}
}
}
sub here(){
open FIG,"<ref/HQ_ref_codom";
open OUT,">$out";
$cnt=0;
foreach $word(<FIG>){
chomp($word=$word);
$cnt++;
@file=split(/\s+/,$word);
$len=length @file[1];
$ref[$cnt]=@file[1];
$female{@file[2]}++;
$male{@file[3]}++;
@dep_1[$cnt]=@file[2];
@dep_2[$cnt]=@file[3];
for($i=1;$i<=$len;$i++){
$a=substr(@file[1],$i-1,1);
print OUT "@file[0] @file[1] $i $a \n";
}
}
close FIG;
}
#---------------------SNP-------------------------------------------
sub SNP_genotype(@_){
my $name=@_[0]; my %depth={}; my %SNP={}; my $tol=0;$go=0;
open FIG,"<reads_mapping/$name";
for(my $i=1;$i<=$len;$i++){
$dir[$i]->{A}=0;
$dir[$i]->{T}=0;
$dir[$i]->{G}=0;
$dir[$i]->{C}=0;
$dir[$i]->{N}=0;
}
foreach $word(<FIG>){
chomp($word=$word);
@file=split(/\s+/,$word);
if($word=~/ref/){
for($i=1;$i<=$len;$i++){
$A=$dir[$i]->{A};
$T=$dir[$i]->{T};
$G=$dir[$i]->{G};
$C=$dir[$i]->{C};
$n=$A+$T+$G+$C;
%hello=(A=>$A,T=>$T,G=>$G,C=>$C);
$tag=0;$genotype="--";$cnt=0;
foreach $key (sort hashValueDescendingNum (keys(%hello))) { @s[$cnt]=$key;$cnt++;}
$n1=$hello{@s[0]};$n2=$hello{@s[1]};$n3=$hello{@s[2]};$n4=$hello{@s[3]};
$genotype="--";
$t1=500;
if(($n1+$n2>=4 && $n1+$n2<$t1)){
$e=0.01;
$LRT1=(1-$e*3/4)**$n1*($e/4)**$n2/((0.5-$e/4)**($n1+$n2));
$LRT1=2*log(abs($LRT1)+0.000001);
if($LRT1<0 && -$LRT1>$PP){
if(@s[0] le @s[1]){$genotype="@s[0]@s[1]";}
else{$genotype="@s[1]@s[0]";}
$tol++;
}
elsif($LRT1>$PP){$genotype="@s[0]@s[0]";}
}
$SNP{@file[0]}->[$i]=$genotype;
}
for($i=1;$i<=$len;$i++){
$dir[$i]->{A}=0;
$dir[$i]->{T}=0;
$dir[$i]->{G}=0;
$dir[$i]->{C}=0;
$dir[$i]->{N}=0;
}
}
else{
for($i=1;$i<=$len;$i++){$dir[$i]->{substr(@file[0],$i-1,1)}++;}
}
}
my $cnt=0;
open FIG,"<ref/HQ_ref_codom";
foreach $word(<FIG>){
chomp($word=$word);
$cnt++;
@file=split(/\s+/,$word);
$ref[$cnt]=@file[1];
}
close FIG;
open FIG,"<$out";
open OUT,">genotype/TEMP";
$cnt=0;$new=0;$het=0;
foreach $word(<FIG>){
chomp($word=$word);
$a=int($cnt/$len);
$str=$ref[$a+1];
if(exists $SNP{$str}){
$SS=$SNP{$str}->[$cnt-$len*$a+1];
print OUT"$word $SS\n";
if($SS ne "--"){$new++;}
if(substr($SS,0,1) ne substr($SS,1,1)){$het++;}
}
else{ print OUT "$word --\n";}
$cnt++;
}
close FIG;
close OUT;
open FIG,"<genotype/TEMP";
open OUT,">$out";
foreach $word(<FIG>){
chomp($word=$word);
print OUT "$word\n";
}
close FIG;
close OUT;
}
sub hashValueDescendingNum {$hello{$b} <=> $hello{$a};}
sub parse_command_line {
while (@ARGV) {
$_ = shift @ARGV;
if ($_ =~ /^-a$/) { $a = shift @ARGV; }
elsif ($_ =~ /^-p$/) { $p = shift @ARGV; }
elsif ($_ =~ /^-o1$/) { $out = shift @ARGV; }
elsif ($_ =~ /^-o2$/) { $out1 = shift @ARGV; }
else {
print STDERR "Unknown command line option: '$_'\n";
usage();
}
}
}
sub usage {
print STDERR <<EOQ;
perl codom_calling.pl -a -p -o1 -o2[-h]
a :significance level of LRT test [0.05]
p :least percentage of genotyped progenies [0.8]
o1 :output file of all codominant genotypes [genotype/all_codom]
o2 :output file of polymorphic codominant markers[genotype/poly_codom]
h :display the help information.
EOQ
exit(0);
}