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Merge_SyRI_SV_spe2.pl
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Merge_SyRI_SV_spe2.pl
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#########################################################################
# File Name: Merge_SyRI_SV_spe_with_Individual_position_info.pl
# > Author: hwlu
# > Mail: hongweilu@genetics.ac.cn
# Created Time: Mon 23 Mar 2020 07:50:33 PM CST
#########################################################################
#!/usr/bin/perl -w
use strict;
#my @bed = `ls *.syri.out.SV.bed`;
my @bed = `ls *.syri.out.SV.bed.mergeDel.CPV2InDel.50.bp`;
my $ins_distance=0;
my $overlap=0.9;
my $coverage=0.9;
my @spe;
my %hash_SV;
my %length_SV;
print "Reading SV bed files...\n";
foreach my $bed (@bed){
chomp($bed);
my $spe = $bed;
#$spe =~ s/\.syri.out.SV.bed//g;
$spe =~ s/\.syri\.out\.SV\.bed\..*//g;
print "\t".$spe."\n";
push(@spe,$spe);
open(IN,"$bed");
while(<IN>){
chomp;
my $line=$_;
my @line = split /\s+/,$line;
if($line[4]>$line[5]){
($line[4],$line[5])=($line[5],$line[4]);
}
if($line[1]>$line[2]){
($line[1],$line[2]) = ($line[2],$line[1]);
}
if($line[6] eq "Inversion"){
$hash_SV{$line[6]}{$line[0]}{$line[1]}{$line[2]}{$spe}="$spe\_$line[3]\_$line[4]\_$line[5]";
$length_SV{"$line[6]\_$line[0]\_$line[1]\_$line[2]\_$spe"}=abs($line[2]-$line[1]+1);
}elsif($line[6] eq "DEL" or $line[6] eq "Deletion"){
$hash_SV{"DEL"}{$line[0]}{$line[1]}{$line[2]}{$spe}=1;
$length_SV{"DEL\_$line[0]\_$line[1]\_$line[2]\_$spe"}=abs($line[2]-$line[1]+1);
}elsif($line[6] eq "INS" or $line[6] eq "Insertion" ){
$hash_SV{"INS"}{$line[0]}{$line[1]}{$line[2]}{$spe}="$spe\_$line[3]\_$line[4]\_$line[5]";
$length_SV{"INS\_$line[0]\_$line[1]\_$line[2]\_$spe"}=abs($line[5]-$line[4]+1);
}elsif($line[6] =~/Translocation/ or $line[6] =~ /TR/){
$hash_SV{$line[6]}{$line[0]}{$line[1]}{$line[2]}{$spe}="$spe\_$line[3]\_$line[4]\_$line[5]";
$length_SV{"$line[6]\_$line[0]\_$line[1]\_$line[2]\_$spe"}=abs($line[2]-$line[1]);
}else{
next;
}
}
close IN;
}
print "Done...\n";
print "Format data ...\n";
my %hash_SV_array;
foreach my $type (keys %hash_SV){
foreach my $chr (keys %{$hash_SV{$type}}){
foreach my $start (sort {$a <=> $b} keys %{$hash_SV{$type}{$chr}}){
foreach my $end (sort {$a <=> $b} keys %{$hash_SV{$type}{$chr}{$start}}){
foreach my $spe (keys %{$hash_SV{$type}{$chr}{$start}{$end}}){
push(@{$hash_SV_array{$type}{$chr}},"$start\t$end\t$spe");
}
}
}
}
}
print "Done...\n";
print "Merge SV ... \n";
my %hash_merged_result;
foreach my $type (keys %hash_SV_array){
print "\t$type...\n";
my $SV_ID=1;
foreach my $chr (keys %{$hash_SV_array{$type}}){
my @tmp_chr = @{$hash_SV_array{$type}{$chr}};
my $num_sv=@tmp_chr;
print "\t\t$chr contains $num_sv SVs ...\n";
for(my $i=0;$i<@tmp_chr;$i++){
my ($start_1,$end_1,$spe_1)=split /\t/,$tmp_chr[$i];
next if (exists $hash_merged_result{$type}{$chr}{$start_1}{$end_1}{$spe_1});
$SV_ID++;
$hash_merged_result{$type}{$chr}{$start_1}{$end_1}{$spe_1}=$SV_ID;
for(my $j=$i+1;$j<@tmp_chr;$j++){
my ($start_2,$end_2,$spe_2)=split /\t/,$tmp_chr[$j];
next if (exists $hash_merged_result{$type}{$chr}{$start_2}{$end_2}{$spe_2});
last if ($start_2 - $end_1 > $ins_distance);
last if ($start_2>$end_1 and ($type ne "INS" and $type ne "Insertion"));
if($type eq "INS" or $type eq "Insertion"){ #ref overlap and query RO >0.5
my $ins_1=$hash_SV{$type}{$chr}{$start_1}{$end_1}{$spe_1};
my $ins_2=$hash_SV{$type}{$chr}{$start_2}{$end_2}{$spe_2};
my @ins_1=split /_/,$ins_1;
my @ins_2=split /_/,$ins_2;
my $length1=$ins_1[3]-$ins_1[2]+1;
my $length2=$ins_2[3]-$ins_2[2]+1;
if($length1>$length2){
($length1,$length2)=($length2,$length1);
}
next if($length1/$length2<$coverage);
}elsif($type eq "DEL" or $type eq "INV" or $type eq "TRANS" or $type eq "INVTR" or $type eq "Inversion" or $type eq "Translocation"){ #ref RO >0.5
my $RO=0;
if($end_2 > $end_1) {
$RO=($end_1-$start_2+1)/($end_2-$start_1+1);
}else{
$RO=($end_2-$start_2+1)/($end_1-$start_1+1);
}
next if ($RO<$overlap);
}else{ #HDR,CPG,CPL,TDM : ref RO >0.5 and query RO > 0.5
my $RO=0;
if($end_2>$end_1){
$RO=($end_1-$start_2+1)/($end_2-$start_1+1);
}else{
$RO=($end_2-$start_2+1)/($end_1-$start_1+1);
}
next if ($RO<$overlap);
my $ins_1=$hash_SV{$type}{$chr}{$start_1}{$end_1}{$spe_1};
my $ins_2=$hash_SV{$type}{$chr}{$start_2}{$end_2}{$spe_2};
my @ins_1=split /_/,$ins_1;
my @ins_2=split /_/,$ins_2;
my $length1=$ins_1[3]-$ins_1[2]+1;
my $length2=$ins_2[3]-$ins_2[2]+1;
if($length1>$length2){
($length1,$length2)=($length2,$length1);
}
next if($length1/$length2<$coverage);
}
$hash_merged_result{$type}{$chr}{$start_2}{$end_2}{$spe_2}=$SV_ID;
}
}
print "\t\t\tNow $type\tSV_ID is :\t$SV_ID\n";
}
}
print "Done...\n";
my %result;
foreach my $type (keys %hash_merged_result){
foreach my $chr (sort keys %{$hash_merged_result{$type}}){
foreach my $start (sort {$a <=> $b} keys %{$hash_merged_result{$type}{$chr}}){
foreach my $end (sort {$b <=> $a} keys %{$hash_merged_result{$type}{$chr}{$start}}){
foreach my $spe (keys %{$hash_merged_result{$type}{$chr}{$start}{$end}}){
my $SV_ID=$hash_merged_result{$type}{$chr}{$start}{$end}{$spe};
push(@{$result{$type}{$SV_ID}},"$type\_$chr\_$start\_$end\_$spe");
}
}
}
}
}
print "OUTPUT...\n";
open(OUT,">Merge_Syri_bed.result.$overlap.$coverage.v2");
foreach my $type (keys %result){
foreach my $ID (sort {$a <=> $b} keys %{$result{$type}}){
my $present_sv;
foreach my $sv (sort {$length_SV{$b} <=> $length_SV{$a}} @{$result{$type}{$ID}}){
$present_sv=$sv;
last;
}
foreach my $sv (sort {$length_SV{$b} <=> $length_SV{$a}} @{$result{$type}{$ID}}){
next if ($sv !~ /R527/);
$present_sv=$sv;
last;
}
my @present_sv=split /_/,$present_sv;
if($type eq "DEL"){
print OUT "$type\t$ID\t$present_sv[1]\t$present_sv[2]\t$present_sv[3]\t$present_sv[4]\t-\t-\t-\t$length_SV{$present_sv}\t";
my @spe=();
foreach my $sv (@{$result{$type}{$ID}}){
my @tmp = split /_/,$sv;
push(@spe,$sv);
#push(@spe,$tmp[-1]);
}
my $spe_out= join "|",@spe;
print OUT "$spe_out\n";
}else{
my $target=$hash_SV{$type}{$present_sv[1]}{$present_sv[2]}{$present_sv[3]}{$present_sv[4]};
my @target=split /\_/,$target;
my @spe=();
foreach my $sv (@{$result{$type}{$ID}}){
my @tmp = split /_/,$sv;
#push(@spe,$tmp[-1]);
push(@spe,$sv);
}
my $spe_out=join "|",@spe;
print OUT "$type\t$ID\t$present_sv[1]\t$present_sv[2]\t$present_sv[3]\t$present_sv[4]\t$target[1]\t$target[2]\t$target[3]\t$length_SV{$present_sv}\t$spe_out\n";
}
}
}
close OUT;