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Calculate.Hse.pl
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Calculate.Hse.pl
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#! perl
use warnings;
use strict;
use MCE::Loop;
use Cwd;
use File::Basename;
use List::Util qw/max min/;
print STDERR "======> script used for calculate HE\n\n####USEAG : perl $0 \$dir####
(dir created by bamdst, must contain a folder named \"region.tsv.gz.split with\" include files split region.tsv.gz by chr)\n\n";
my $thread = 5;
my $dir = shift or die "need dir \n";
my $window = shift;
$window //= 10000;
###para
my $dup_max_fold = 5; #5
my $dup_min_fold = 1.5; #1.5
my $del_max_fold = 0.6; #0.6
my $del_min_fold = 0; #0
my $min_cov = 60; #60 no_use
my $confict_rate = 0.2; #0.2
my $no_means_rate = 0.3; #0.3
my $he_window = 0.3; #0.3
###load_depth
my %d = &read_depth("$dir/chromosomes.report");
###main
my $o = "$dir/HSE.out";
mkdir $o unless -e $o;
my @fs = sort{$a cmp $b} grep {/.split.file$/} `find $dir/region.tsv.gz.split`;
print STDERR "======> calculate start\n";
MCE::Loop::init {max_workers => $thread, chunk_size => 1};
mce_loop {&run($_)} @fs;
print STDERR "======> calculate done, please check $o\n";
print STDERR "======> gather result\n";
my $o_name = basename dirname $o;
my @dupf = sort{$a cmp $b} grep{/\.dup.HSE.txt/} `find $o`;
my @delf = sort{$a cmp $b} grep{/\.del.HSE.txt/} `find $o`;
&gather_res(\@dupf,"dup",$o_name);
&gather_res(\@delf,"del",$o_name);
print STDERR "======> gather done\n";
sub gather_res{
my $ref = shift @_;
my $type = shift @_;
my $name = shift @_;
my @fs = @{$ref};
open O,'>',"1.$name.$type.hse.link.txt";
for my $f (@fs){
chomp $f;
(my $chr = basename $f) =~ s/(.*?)\..*/$1/;
open IN,'<',$f;
my %p;
my @a = ();
my $c = 0;
readline IN;
my ($s,$e,$n);
while(<IN>){
if(/^#/){
$s = min(@a);
$e = max(@a);
$n = ($e - $s)/$window;
if($c/$n > $he_window){
print O "$chr\t$n\t$c\t$s\t$e\n";
}
@a = ();
$c = 0;
}elsif(/^\d+/){
my @l = split/\t/;
push @a,($l[0],$l[1]);
$c += 1;
}elsif(/^\s+/){
next;
}
}
if(scalar @a > 0){
$s = min(@a);
$e = max(@a);
$n = ($e - $s)/$window;
if($c/$n > $he_window){
print O "$chr\t$n\t$c\t$s\t$e\n";
}
}
}
}
sub run{
my $f = shift @_;
chomp $f;
my $dir = dirname $f;
(my $name = basename $f) =~ s/(.*?)\..*/$1/;
die "$name not depth info\n" if(!exists $d{$name});
my $ave = $d{$name};
my $h_max = $ave * $dup_max_fold;
my $h_min = $ave * $dup_min_fold;
my $l_min = $ave * $del_min_fold;
my $l_max = $ave * $del_max_fold;
open IN,'<',"$f";
my $c = 1;
my %m;my %h;
while(<IN>){
chomp;
my @l = split/\s+/;
my $start = $l[1] - 1;
my $end = $l[2] + 1;
#next if $l[-1] < $min_cov;
if($l[3] <= $h_max && $l[3] >= $h_min){
$m{$c} = "dup";
}elsif ($l[3] <= $l_max && $l[3] >= $l_min) {
$m{$c} = "del";
}elsif ($l[3] > $l_max && $l[3] < $h_min){
$m{$c} = "nor";
}else{
$m{$c} = "l2h";
}
$h{$c} = [$start,$end,$l[3]];
$c += 1;
}
close IN;
my @dup = &window_link(\%m,"dup",1);
my @del = &window_link(\%m,"del",1);
my @dup_f = &window_filter(\%m,\@dup,"del");
my @del_f = &window_filter(\%m,\@del,"dup");
&window_print("$o/$name.dup.HSE.txt",\%h,\@dup_f);
&window_print("$o/$name.del.HSE.txt",\%h,\@del_f);
}
sub window_print{
my $name = shift @_;
my $ref1 = shift @_;
my $ref2 = shift @_;
my %h = %{$ref1};
open my $o,'>',$name;
for my $e(@{$ref2}){
print $o "###\n";
map{print $o join"\t",@{$h{$_}};print $o "\n"} @{$e};
print $o "\n";
}
}
sub window_filter{
my $ref1 = shift @_;
my $ref2 = shift @_;
my %m = %{$ref1};
my @a = @{$ref2};
my @res;
for my $e (@a) {
my @x = @{$e};
my $w_num = $x[-1] - $x[0] +1;
my $f_num = 0;
my $r_num = 0;
for my $v(@x){
if($m{$v} eq "$type"){
$f_num += 1;
}elsif($m{$v} eq "l2h"){
$r_num += 1;
}
}
next if ($f_num/$w_num) > $confict_rate;
next if ($r_num/$w_num) > $no_means_rate;
push @res, \@x;
}
return @res;
}
sub window_link{
my $ref1 = shift @_;
my $type = shift @_;
my $a = shift @_;
my %m = %{$ref1};
my @res;
for(my $i = $a;$i < scalar(keys %m);$i+= 1){
if(!exists $m{$i}){
print "not exists depth row : ".$i."\n";
exit;
}
if($m{$i} eq $type){
my @a = &window_extend($i,\%m,$type);
unshift @a, $i;
$i = $a[-1] + 1;
### filter window_link
next if (scalar @a < 3 || $a[-1] - $a[0] < 6);
push @res, \@a;
}
}
return @res;
}
sub window_extend{
my $i = shift @_;
my $ref = shift @_;
my $type = shift @_;
my @a;
my %m = %{$ref};
for (my $n = $i + 1; $n <= $i + 10;$n += 1){
if(!exists $m{$n}){
next;
}
if($m{$n} eq $type){
push @a , $n;
push @a , &window_extend($n,\%m,$type);
last;
}
}
return @a;
}
sub read_depth{
my $f = shift @_;
my %h;
open I,'<',"$f" or die "$!";
readline I;
while(<I>){
chomp;
s/\s+//;
my @l = split/\s+/;
$h{$l[0]} = $l[2];
}
close I;
return %h;
}