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tef.pl
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#!/usr/bin/perl
#
# tef.pl - transposable element finder
# A program for transposable elements detection from NGS reads.
#
# Copyright (C) 2020 National Agriculture and Food Research Organization. All Rights Reserved.
#
# License: refer to https://github.com/akiomiyao/tef
#
# Author: Akio Miyao <miyao@affrc.go.jp>
#
if ($ARGV[0] eq ""){
print "
tef.pl - transposable element finder
A program for detection of active transposable elements from NGS reads.
e.g. perl tef.pl a=ttm2,b=ttm5,ref=IRGSP1.0
perl tef.pl a=ttm2,b=ttm5,ref=IRGSP1.0,tsd_size=5,th=0.7
perl tef.pl a=ttm2,b=ttm5,ref=IRGSP1.0,debug=yes,compress=yes,max_process=8,sort_tmp=/mnt/ssd/tmp
tef.pl requires a pair of NGS reads from different conditions.
For example, ttm2 and ttm5 are from regenerated rice individuals from callus.
Save fastq files into ttm2/read and ttm5/read directory.
Options shold be specified with 'name=value' separated by a comma WITHOUT space.
Default method is the junction method.
If tsd_size is specified, tef.pl will run with TSD method.
If ref is specified, gziped fasta file of reference genome should be saved
into the directory specified with ref.
At the first time of run, config file for reference will be made in the
ref directory. The config has a list of sequence name. If you do not want to
include unassaigned contig, change the name to NOP and save the contig file,
and run tef.pl again.
If ref is not specified, a or b specific transpositions without insertion
position on the genome will be detected.
This function works only by TSD method.
If tsd_size is not specified, detection will be progressed by junction method.
If th (threthold) on the TSD method is not specified, default value 0.2 will be used.
If a lot of noize are detected, try again with higher value e.g. th=0.7
Because tmp directries in targets grow huge size, tmp directories will be deleted
at the end of analysis. If debug=yes is added in options, tmp directories will not
deleted. In addition, to save disk space, the compress=yes option is used to compress
temporary files.
sort_tmp=directory_for_sort is the option for temporary directory for sort command.
If sort_tmp is specified to fast disk, e.g. SSD, sorting will be accelerated.
For Linux, max process is number of CPU core. For other OS, defalt process number is 4.
If you add max_process option, e.g. max_process=8, tef use 8 cores.
If data in split and/or count.tsd_size are truncated, remove the directory in
the target and then run again.
Author: Akio Miyao
";
exit;
}
$start_time = time;
$s = {};
@nuc = ('A', 'C', 'G', 'T');
foreach $nuc (@nuc){
my $nuca = $nuc;
foreach $nuc (@nuc){
my $nucb = $nuc;
foreach $nuc (@nuc){
my $nucc = $nuc;
my $tag = $nuca . $nucb . $nucc;
push(@tag, $tag);
}
}
}
$wd = `pwd`;
chomp($wd);
foreach (split(',', $ARGV[0])){
my ($name, $val) = split('=', $_);
$$name = $val;
}
open(IN, "/proc/cpuinfo");
while(<IN>){
$processor ++ if /processor/;
}
close(IN);
$processor = 32 if $processor > 32;
$processor = $max_process if $max_process ne "";
$processor = 4 if $processor eq "";
$sort_tmp = "$wd/$a/tmp" if $sort_tmp eq "";
$th = 0.2 if $th eq "";
$tsd_size = 20 if $tsd_size eq "";
if ($tsd_size == 20){
$method = "Junction";
}else{
$method = "TSD";
}
if ($sub eq ""){
system("rm -rf $wd/$a/child") if -e "$wd/$a/child";
system("mkdir $wd/$a/tmp") if ! -e "$wd/$a/tmp";
system("mkdir $wd/$b/tmp") if ! -e "$wd/$b/tmp";
system("mkdir $wd/$a/child");
&log("job start");
&log("Argument : $ARGV[0]");
&log("Method : $method");
&commonMethod;
if ($tsd_size == 20){
&junctionMethod;
}else{
&tsdMethod;
}
&join;
system("rm -r $wd/$a/child $wd/$a/tmp $wd/$b/tmp") if ! $debug;
system("rm $wd/$a/junction_method.all.$a.$b") if ! $debug;
$end_time = time;
$elapsed_time = $end_time - $start_time;
$hour = int($elapsed_time / 3600);
$min = $elapsed_time % 3600;
$sec = $min % 60;
$min = int($min / 60);
if ($hour >= 24){
$day = int($hour / 24);
$hour = $hour % 24;
}
if ($day > 1){
$etime .= "$day days ";
}elsif($day == 1){
$etime .= "$day day ";
}
if ($hour > 1){
$etime .= "$hour hours ";
}elsif($hour == 1){
$etime .= "$hour hour ";
}
if ($min > 1){
$etime .= "$min minutes ";
}elsif($min == 1){
$etime .= "$min minute ";
}
if ($sec > 1){
$etime .= "$sec seconds ";
}elsif($sec == 1){
$etime .= "$sec second ";
}
&log("Job completed: a=$a, b=$b, ref=$ref, method=$method
$etime ($elapsed_time seconds) elapsed.");
}else{
my $file = "$wd/$a/child/child.$$";
system("touch $file");
&$sub;
system("rm $file");
exit;
}
sub commonMethod{
if ($ref ne ""){
&mkref;
}
my $fragment_length = 20 + $tsd_size;
if (&fragmentLength($a) != $fragment_length){
&count($a);
}
if (&fragmentLength($b) != $fragment_length){
&count($b);
}
}
sub junctionMethod{
&junctionSpecific;
&join;
&junctionFirstMap($a);
&junctionFirstMap($b);
&join;
&junctionSecondMap($a);
&junctionSecondMap($b);
&join;
&junctionSort($a);
&junctionSort($b);
&join;
&junctionCandidate;
&junctionCountCandidate;
}
sub tsdMethod{
&tsdHeadTail;
&verify;
if ($ref ne ""){
↦
}
}
sub junctionCandidate{
system("cd $wd/$a/tmp/ && rm chr* first.* map.* second.* specific.* target.* && cd $wd/$b/tmp/ && rm chr* first.* map.* second.* specific.* target.*") if ! $debug;
opendir(REF, "$wd/$ref");
foreach $file (sort readdir(REF)){
if ($file =~ /^chr/){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=junctionCandidateFunc,chr=$file,sort_tmp=$sort_tmp &";
&log($cmd);
system($cmd);
}
}
&join;
}
sub junctionCandidateFunc{
open(CHR, "$wd/$ref/$chr");
binmode(CHR);
($chrnum = $chr)=~ s/^chr//;
open(OUT, "> $wd/$a/tmp/candidate.$chr");
open(IN, "cat $wd/$a/tmp/sorted.$chr.f $wd/$a/tmp/sorted.$chr.r |");
while(<IN>){
chomp;
push(@dat, $_);
next if $i++ < 40;
$dat = shift(@dat);
@row = split('\t', $dat);
foreach (@dat){
@pos = split;
$size = $pos[0] - $row[0];
next if $size > 16;
next if $size == 0;
$size ++;
if ($row[1] eq "h"){
if ($pos[1] eq "t"){
$htsd = substr($row[2], 20 - $size, $size);
$ttsd = substr($pos[2], 20, $size);
if ($htsd eq $ttsd){
$head = substr($row[2], 20, 20);
$hflanking = substr($row[2], 0, 20);
$tail = substr($pos[2], 0, 20);
$tflanking = substr($pos[2], 20, 20);
seek(CHR, $row[0] - 21, 0);
read(CHR, $wt, 40);
next if $wt =~ /N/;
print OUT "$row[2]\t$chrnum\t$row[0]\t$pos[0]\tah\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]
$pos[2]\t$chrnum\t$row[0]\t$pos[0]\tat\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]
$wt\t$chrnum\t$row[0]\t$pos[0]\taw\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]\n";
}
}
}else{
if ($pos[1] eq "h"){
$htsd = substr($pos[2], 20 - $size, $size);
$ttsd = substr($row[2], 20, $size);
if ($htsd eq $ttsd){
$head = substr($pos[2], 20, 20);
$hflanking = substr($pos[2], 0, 20);
$tail = substr($row[2], 0, 20);
$tflanking = substr($row[2], 20, 20);
seek(CHR, $pos[0] - 21, 0);
read(CHR, $wt, 40);
next if $wt =~ /N/;
print OUT "$pos[2]\t$chrnum\t$pos[0]\t$row[0]\tah\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]
$row[2]\t$chrnum\t$pos[0]\t$row[0]\tat\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]
$wt\t$chrnum\t$pos[0]\t$row[0]\taw\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]\n";
}
}
}
}
}
close(IN);
open(IN, "cat $wd/$b/tmp/sorted.$chr.f $wd/$b/tmp/sorted.$chr.r |");
while(<IN>){
chomp;
push(@dat, $_);
next if $i++ < 40;
$dat = shift(@dat);
@row = split('\t', $dat);
foreach (@dat){
@pos = split;
$size = $pos[0] - $row[0];
next if $size > 16;
next if $size == 0;
$size ++;
if ($row[1] eq "h"){
if ($pos[1] eq "t"){
$htsd = substr($row[2], 20 - $size, $size);
$ttsd = substr($pos[2], 20, $size);
if ($htsd eq $ttsd){
$head = substr($row[2], 20, 20);
$hflanking = substr($row[2], 0, 20);
$tail = substr($pos[2], 0, 20);
$tflanking = substr($pos[2], 20, 20);
seek(CHR, $row[0] - 21, 0);
read(CHR, $wt, 40);
next if $wt =~ /N/;
print OUT "$row[2]\t$chrnum\t$row[0]\t$pos[0]\tbh\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]
$pos[2]\t$chrnum\t$row[0]\t$pos[0]\tbt\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]
$wt\t$chrnum\t$row[0]\t$pos[0]\tbw\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[5]\n";
}
}
}else{
if ($pos[1] eq "h"){
$htsd = substr($pos[2], 20 - $size, $size);
$ttsd = substr($row[2], 20, $size);
if ($htsd eq $ttsd){
$head = substr($pos[2], 20, 20);
$hflanking = substr($pos[2], 0, 20);
$tail = substr($row[2], 0, 20);
$tflanking = substr($row[2], 20, 20);
seek(CHR, $pos[0] - 21, 0);
read(CHR, $wt, 40);
next if $wt =~ /N/;
print OUT "$pos[2]\t$chrnum\t$pos[0]\t$row[0]\tbh\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]
$row[2]\t$chrnum\t$pos[0]\t$row[0]\tbt\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]
$wt\t$chrnum\t$pos[0]\t$row[0]\tbw\t$head\t$tail\t$hflanking\t$htsd\t$tflanking\t$row[8]\n";
}
}
}
}
}
close(IN);
}
sub junctionCountCandidate{
my (@chr, $chr);
opendir(DIR, "$wd/$ref");
foreach (sort readdir(DIR)){
if (/^chr/){
($chr = $_) =~ s/^chr//;
push(@chr, $chr);
}
}
&log("junctionCountCandidate: $a : sorting candidates");
foreach $tag (@tag){
open($tag, "> $wd/$a/tmp/tmpa.$tag ");
}
open(IN, "cat $wd/$a/tmp/candidate.* |");
while(<IN>){
$tag = substr($_, 0, 3);
print $tag $_;
}
close(IN);
$org_processor = $processor;
$processor = 4;
foreach $tag (@tag){
close($tag);
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=junctionSortCandidateFunc,tag=$tag,sort_tmp=$sort_tmp &";
&log("$cmd");
system($cmd);
}
&join;
$processor = $org_processor;
foreach $tag (@tag){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=junctionCountCandidateFunc,tag=$tag,sort_tmp=$sort_tmp &";
&log("$cmd");
system($cmd);
}
&join;
foreach $tag (@tag){
open(IN, "$wd/$a/tmp/count.$tag");
foreach $chr (@chr){
open($chr, "> $wd/$a/tmp/count.$chr.$tag");
}
while(<IN>){
$chr = (split)[0];
print $chr $_;
}
foreach $chr (@chr){
close($chr);
}
close($tag);
system("rm $wd/$a/tmp/count.$tag") if ! $debug;
}
system("rm $wd/$a/tmp/candidate.*") if ! $debug;
&log("junctionCountCandidate : making junction_method.summary.$a.$b and junction_method.all.$a.$b");
foreach $chr (@chr){
&log("junctionCountCandidate : making junction_method.genotype.$a.$b.$chr");
open(OUT, "| sort -S 1M -T $sort_tmp > $wd/$a/tmp/junction_method.genotype.tmp.$chr");
open(IN, "cat $wd/$a/tmp/count.$chr.* | sort -S 1M -T $sort_tmp | uniq |");
while(<IN>){
chomp;
@row = split;
if ($row[3] =~ /h$/){
$ah = $row[10];
$bh = $row[11];
}elsif($row[3] =~ /t$/){
$at = $row[10];
$bt = $row[11];
}elsif($row[3] =~ /w$/){
$aw = $row[10];
$bw = $row[11];
$genotype = "";
if ($ah > 0 and $at > 0 and $bh == 0 and $bt == 0 and $bw > 0){
if ($aw == 0){
$genotype = "M";
}else{
$genotype = "H";
}
}elsif($ah == 0 and $at == 0 and $aw > 0 and $bh > 0 and $bt > 0){
if ($bw == 0){
$genotype = "M";
}else{
$genotype = "H";
}
}
if ($genotype){
if ($row[3] =~ /^a/){
$target = $a;
}else{
$target = $b;
}
$row[0] = "0000$row[0]";
$row[0] = substr($row[0], length($row[0]) - 4, 4);
$row[1] = "0000000000$row[1]";
$row[1] = substr($row[1], length($row[1]) - 10, 10);
$row[2] = "0000000000$row[2]";
$row[2] = substr($row[2], length($row[2]) - 10, 10);
print OUT "$target\t$row[0]\t$row[1]\t$row[2]\t$row[9]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]\t$ah\t$at\t$aw\t$bh\t$bt\t$bw\t$genotype\n";
}
undef $ah;
undef $at;
undef $at;
undef $aw;
undef $bh;
undef $bt;
undef $bw;
}
}
close(IN);
close(OUT);
}
system("rm $wd/$a/tmp/count.*") if ! $debug;
&log("junctionCountCandidate : making junction_method.all.$a.$b");
open(OUT, "> $wd/$a/junction_method.all.$a.$b");
open(IN, "cat $wd/$a/tmp/junction_method.genotype.tmp.* |sort -S 1M -T $sort_tmp |");
while(<IN>){
chomp;
@row = split;
$row[1] =~ s/^0*// ;
$row[2] += 0;
$row[3] += 0;
print OUT join("\t", @row) . "\n";
}
close(IN);
close(OUT);
&log("junctionCountCandidate : making telist");
open(OUT, "|sort -S 1M -T $sort_tmp |uniq > $wd/$a/tmp/telist");
open(IN, "$wd/$a/junction_method.all.$a.$b");
while(<IN>){
@row = split;
next if length($row[8]) > 10;
print OUT "$row[5]\t$row[6]\t$row[0]\t$row[8]\n";
}
close(IN);
close(OUT);
&log("junctionCountCandidate : making telist.count");
open(OUT, "|uniq -c > $wd/$a/tmp/telist.count");
open(IN, "$wd/$a/tmp/telist");
while(<IN>){
chomp;
@row = split;
print OUT "$row[0] $row[1]\n";
}
close(IN);
close(OUT);
open(HEAD, "| sort -k 1 -k 2 -n -S 1M -T $sort_tmp > $wd/$a/tmp/telist.head");
open(TAIL, "| sort -k 1 -k 2 -n -S 1M -T $sort_tmp > $wd/$a/tmp/telist.tail");
open(IN, "$wd/$a/tmp/telist.count");
while(<IN>){
chomp;
@row = split;
next if $row[0] < 2;
$ht{"$row[1] $row[2]"} = " ";
}
close(IN);
open(IN, "$wd/$a/tmp/telist");
while(<IN>){
chomp;
@row = split;
if ($ht{"$row[0] $row[1]"} ne ""){
$ht{"$row[0] $row[1]"} .= "$row[3] ";
}
}
close(IN);
foreach (sort keys %ht){
$tsd = $ht{$_};
$tsd =~ s/^\ //;
$tsd =~ s/\ $//;
$flag = 1;
@tsd = split(' ', $tsd);
$flag = 0 if $#tsd < 1;
$size = length($tsd[0]);
for ($i = 1; $i <= $#tsd; $i++){
if (length($tsd[$i]) != $size){
$flag = 0;
}
}
if ($flag){
my ($head, $tail) = split;
$tsd_count = $#tsd + 1;
print HEAD "$head $tsd_count $tail\n";
print TAIL "$tail $tsd_count $head\n";
}
}
close(IN);
close(HEAD);
close(TAIL);
%select = ();
open(TAIL, "$wd/$a/tmp/telist.tail");
while(<TAIL>){
chomp;
@row = split;
$select{$row[0]} = $row[2];
}
close(TAIL);
%exclude = ();
open(TAIL, "$wd/$a/tmp/telist.tail");
while(<TAIL>){
chomp;
@row = split;
if ($select{$row[0]} ne $row[2]){
$exclude{$row[2]} = $row[0];
}
}
close(TAIL);
%select = ();
open(HEAD, "$wd/$a/tmp/telist.head");
while(<HEAD>){
chomp;
@row = split;
$select{$row[0]} = $row[2];
}
close(HEAD);
foreach $head (sort keys %select){
$tail = $select{$head};
if ($exclude{$head} ne $tail){
$tsd = $ht{"$head $tail"};
@tsd = split("\ ", $tsd);
@std = split('', $tsd[0]);
$similar = 0;
for($i = 1; $i <= $#tsd; $i++){
$hit = 0;
@tg = split('', $tsd[$i]);
for($j = 0; $j <= $#std; $j++){
if ($std[$j] eq $tg[$j]){
$hit++;
}
}
if ($hit / $#std > 0.6){
$similar++;
}
}
if ($similar / ($#tsd + 1) < 0.5){
$final{$head} = $tail;
}
}
}
&log("junctionCountCandidate : output junction_method.summary.$a.$b");
$acount = 0;
$bcount = 0;
$tea = "";
$teb = "";
open(OUT, "> $wd/$a/junction_method.summary.$a.$b");
open(IN, "$wd/$a/tmp/telist");
while(<IN>){
chomp;
@row = split;
if ($prev[0] ne $row[0] or $prev[1] ne $row[1]){
if ($prev[0] ne "" and $final{$prev[0]} eq $prev[1]){
$tea =~ s/\ $//;
$teb =~ s/\ $//;
print OUT "$prev[0]\t$prev[1]\t$acount\t$bcount\t$tea\t$teb\n";
print "$prev[0]\t$prev[1]\t$acount\t$bcount\t$tea\t$teb\n";
}
$acount = 0;
$bcount = 0;
$tea = "";
$teb = "";
if ($row[2] eq $a){
$acount ++;
$tea .= "$row[3] "
}else{
$bcount ++;
$teb .= "$row[3] "
}
}else{
if ($row[2] eq $a){
$acount ++;
$tea .= "$row[3] "
}else{
$bcount ++;
$teb .= "$row[3] "
}
}
@prev = @row;
}
close(IN);
if ($row[0] ne $prev[0] and $final{$row[0]} eq $row[1]){
if ($row[2] eq $a){
$acount ++;
$tea .= "$row[3] "
}else{
$bcount ++;
$teb .= "$row[3] "
}
$tea =~ s/\ $//;
$teb =~ s/\ $//;
print OUT "$row[0]\t$row[1]\t$acount\t$bcount\t$tea\t$teb\n";
print "$row[0]\t$row[1]\t$acount\t$bcount\t$tea\t$teb\n";
}
close(OUT);
&log("junctionCountCandidate: making junction_method.genotype.$a.$b");
open(OUT, "> $wd/$a/junction_method.genotype.$a.$b");
open(IN, "$wd/$a/junction_method.all.$a.$b");
while(<IN>){
@row = split;
if ($final{$row[5]} eq $row[6]){
print OUT;
}
}
close(IN);
close(OUT);
open(OUT, "|sort -S 1M -T $sort_tmp |uniq > $wd/$a/tmp/te.list");
open(IN, "$wd/$a/junction_method.summary.$a.$b");
while(<IN>){
@row = split;
next if $row[0] eq "Head";
print OUT "$row[0]\thead
$row[1]\ttail\n";
}
close(IN);
close(OUT);
open(IN, "$wd/$a/tmp/te.list");
while(<IN>){
$tag = substr($_, 0, 3);
if ($tag ne $prev){
open(OUT, "> $wd/$a/tmp/telist.$tag");
push(@tetag, $tag);
}
print OUT;
$prev = $tag;
}
close(IN);
close(OUT);
foreach $tag (@tetag){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=junctionTePosFunc,tag=$tag,sort_tmp=$sort_tmp &";
&log("$cmd");
system($cmd);
}
&join;
open(OUT, "|sort -S 1M -T $sort_tmp > $wd/$a/tmp/tmp.tepos");
open(IN, "cat $wd/$a/tmp/tepos.* |");
while(<IN>){
chomp;
@row = split;
$row[2] = "0000$row[2]";
$row[2] = substr($row[2], length($row[2]) - 4, 4);
$row[3] = "0000000000$row[3]";
$row[3] = substr($row[3], length($row[3]) - 10, 10);
print OUT "$row[2]\t$row[3]\t$row[0]\t$row[1]\t$row[4]\n";
}
close(IN);
close(OUT);
open(OUT, "> $wd/$a/junction_method.tepos.$a.$b");
open(IN, "$wd/$a/tmp/tmp.tepos");
while(<IN>){
chomp;
@row = split;
$row[0] =~ s/^0*//;
$row[1] =~ s/^0*//;
print OUT join("\t", @row) . "\n";
}
close(IN);
close(OUT);
}
sub junctionSortCandidateFunc{
system ("sort -S 1M -T $sort_tmp $wd/$a/tmp/tmpa.$tag > $wd/$a/tmp/tmp.$tag");
system ("rm $wd/$a/tmp/tmpa.$tag");
}
sub junctionCountCandidateFunc{
system("zcat $wd/$a/count.20/$tag.gz |join -a 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 2.2 -e 0 $wd/$a/tmp/tmp.$tag - > $wd/$a/tmp/tmpa.$tag");
system("zcat $wd/$b/count.20/$tag.gz |join -a 1 -o 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 2.2 -e 0 $wd/$a/tmp/tmpa.$tag - > $wd/$a/tmp/count.$tag");
system("rm $wd/$a/tmp/tmp.$tag $wd/$a/tmp/tmpa.$tag") if ! $debug;
}
sub junctionTePosFunc{
return if ! -e "$wd/$a/tmp/telist.$tag";
system("zcat $wd/$ref/ref20.$tag.gz | join $wd/$a/tmp/telist.$tag - > $wd/$a/tmp/tepos.$tag");
}
sub junctionSort{
my $target = shift;
my @chr;
&log("junctionSort : Sorting filtered data : $target");
opendir(REF, "$wd/$ref");
foreach $file (sort readdir(REF)){
if ($file =~ /^chr/){
push(@chr, $file);
$filename = $file . ".f";
open($filename, "> $wd/$target/tmp/$filename");
$filename = $file . ".r";
open($filename, "> $wd/$target/tmp/$filename");
}
}
open(IN, "cat $wd/$target/tmp/map.* |");
my ($head, $tail);
while(<IN>){
chomp;
@row = split;
$head = "chr$row[1]";
$tail = "chr$row[4]";
if($row[3] eq "f"){
$pos = $row[2] + 19;
}else{
$pos = $row[2] - 19;
}
$head = $head . "." . $row[3];
print $head "$pos\th\t$row[0]\t$row[1]\t$pos\t$row[3]\t$row[4]\t$row[5]\t$row[6]\n";
$tail = $tail . "." . $row[6];
print $tail "$row[5]\tt\t$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\n";
}
close(IN);
foreach $file (@chr){
close("$file.f");
close("$file.r");
}
$org_processor = $processor;
$processor = 2 if -s "$wd/$target/tmp/$chr[0]" > 10000000000;
foreach $file (@chr){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,target=$target,sub=junctionSortFunc,chr=$file,sort_tmp=$sort_tmp &";
&log($cmd);
system($cmd);
}
$processor = $org_processor;
}
sub junctionSortFunc{
$cmd = "sort -k 1 -n -S 1M -T $sort_tmp $wd/$target/tmp/$chr.f > $wd/$target/tmp/sorted.$chr.f";
system($cmd);
$cmd = "sort -k 1 -n -S 1M -T $sort_tmp $wd/$target/tmp/$chr.r > $wd/$target/tmp/sorted.$chr.r";
system($cmd);
}
sub junctionSecondMap{
my $target = shift;
&log("junctionSecondMap : $target");
foreach $tag (@tag){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,target=$target,sub=junctionSecondMapFunc,tag=$tag,sort_tmp=$sort_tmp &";
&log("$cmd");
system($cmd);
}
}
sub junctionSecondMapFunc{
system("rm $wd/$target/tmp/map.$tag") if -e "$wd/$target/tmp/map.$tag";
$cmd = "cat $wd/$target/tmp/first.$tag.* | sort -S 1M -T $sort_tmp > $wd/$target/tmp/second.$tag";
system($cmd);
open(OUT, "> $wd/$target/tmp/map.$tag");
open(IN, "zcat $wd/$ref/ref20.$tag.gz |join $wd/$target/tmp/second.$tag - |");
while(<IN>){
chomp;
@row = split;
if ($prev ne $row[1] and abs($row[3] - $row[6]) > 25){
print OUT "$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\n";
$prev = $row[1];
}
}
close(IN);
}
sub junctionFirstMap{
my $target = shift;
&log("junctionFirstMap : $target");
foreach $tag (@tag){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,target=$target,sub=junctionFirstMapFunc,tag=$tag,sort_tmp=$sort_tmp &";
&log($cmd);
system($cmd);
}
}
sub junctionFirstMapFunc{
open(IN, "$wd/$target/tmp/specific.$tag");
open(OUT, "| sort -S 1M -T $sort_tmp > $wd/$target/tmp/target.$tag");
while(<IN>){
$seq = substr($_, 0, 20);
next if $seq =~ /ATATATATATATATATAT/;
next if $seq =~ /ACACACACACACACACAC/;
next if $seq =~ /TGTGTGTGTGTGTGTGTG/;
next if $seq =~ /AGAGAGAGAGAGAGAGAG/;
next if $seq =~ /TCTCTCTCTCTCTCTCTC/;
print OUT "$seq $_";
}
close(IN);
close(OUT);
open(IN, "zcat $wd/$ref/ref20.$tag.gz |join $wd/$target/tmp/target.$tag - |");
open(OUT, "> $wd/$target/tmp/first.$tag");
while(<IN>){
@row = split;
$seq = substr($row[1], 20, 20);
print OUT "$seq\t$row[1]\t$row[2]\t$row[3]\t$row[4]\n" if $prev ne $seq;
$prev = $seq;
}
close(IN);
close(OUT);
foreach $subtag (@tag){
open($subtag, "> $wd/$target/tmp/first.$subtag.$tag");
}
open(IN, "$wd/$target/tmp/first.$tag");
while(<IN>){
$subtag = substr($_, 0, 3);
print $subtag $_;
}
close(IN);
foreach $subtag (@tag){
close($subtag);
}
}
sub junctionSpecific{
foreach $tag (@tag){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=junctionSpecificFunc,tsd_size=$tsd_size,tag=$tag,sort_tmp=$sort_tmp &";
&log($cmd);
system($cmd);
}
}
sub junctionSpecificFunc{
$cmd = "bash -c 'join -v 1 <(zcat $wd/$a/count.$tsd_size/$tag.gz) <(zcat $wd/$b/count.$tsd_size/$tag.gz) > $wd/$a/tmp/specific.$tag.tmp'";
system($cmd);
open(IN, "$wd/$a/tmp/specific.$tag.tmp");
open(OUT, "> $wd/$a/tmp/specific.$tag");
while(<IN>){
chomp;
@row = split;
next if $row[0] =~/AAAAAAAAAA|CCCCCCCCCC|GGGGGGGGGG|TTTTTTTTTT/;
if ($row[1] > 1){
print OUT "$row[0]\n";
}
}
close(IN);
close(OUT);
$cmd = "bash -c 'join -v 2 <(zcat $wd/$a/count.$tsd_size/$tag.gz) <(zcat $wd/$b/count.$tsd_size/$tag.gz) > $wd/$b/tmp/specific.$tag.tmp'";
system($cmd);
open(IN, "$wd/$b/tmp/specific.$tag.tmp");
open(OUT, "> $wd/$b/tmp/specific.$tag");
while(<IN>){
chomp;
@row = split;
next if $row[0] =~/AAAAAAAAAA|CCCCCCCCCC|GGGGGGGGGG|TTTTTTTTTT/;
if ($row[1] > 1){
print OUT "$row[0]\n";
}
}
close(IN);
close(OUT);
system("rm $wd/$a/tmp/specific.$tag.tmp $wd/$b/tmp/specific.$tag.tmp");
}
sub map{
system("rm $wd/$a/tmp/map.*") if -e "$wd/$a/tmp/map.AAA";
foreach $tag (@tag){
open($tag, "|sort -S 1M -T $sort_tmp |uniq > $wd/$a/tmp/mapquery.$tag")
}
if ($method eq "TSD"){
open(IN, "$wd/$a/tsd_method.verify.$a.$b.$tsd_size");
}else{
open(IN, "$wd/$a/junction_method.verify.$a.$b");
}
while(<IN>){
@row = split;
$tag = substr($row[0], 0, 3);
print $tag "$row[0]\n";
$te{$row[0]} = "head";
$tag = substr($row[1], 0, 3);
print $tag "$row[1]\n";
$te{$row[1]} = "tail";
$tag = substr($row[2], 0, 3);
print $tag "$row[2]\n";
$tag = substr($row[4], 0, 3);
print $tag "$row[4]\n";
}
close(IN);
foreach $tag (@tag){
close($tag)
}
foreach $tag (@tag){
if (-s "$wd/$a/tmp/mapquery.$tag" > 0){
&monitorWait;
$cmd = "perl $0 a=$a,b=$b,ref=$ref,sub=mapQuery,tag=$tag,sort_tmp=$sort_tmp &";
&log($cmd);
system($cmd);
}
}
&join;
open(IN, "cat $wd/$a/tmp/map.* |");
while(<IN>){
next if /TATATATATATATATATA/;
chomp;
@row = split;
$s->{map}{$row[0]}{$row[1]}{$row[2]} = $row[3];
}
close(IN);
if ($method eq "TSD"){
open(IN, "$wd/$a/tsd_method.verify.$a.$b.$tsd_size");
}else{
open(IN, "$wd/$a/junction_method.verify.$a.$b");
}
open(OUT, "| sort -S 1M -T $sort_tmp > $wd/$a/tmp/mapped.tmp");
while(<IN>){
chomp;
@row = split('\t', $_);
for ($i = 5; $i <= 10; $i++){
$row[$i] += 0;
}
$tmp = join("\t", @row);
foreach $uchr (sort keys %{$s->{map}{$row[2]}}){
foreach $upos (sort keys %{$s->{map}{$row[2]}{$uchr}}){
foreach $dchr (sort keys %{$s->{map}{$row[4]}}){
foreach $dpos (sort keys %{$s->{map}{$row[4]}{$dchr}}){
if ($uchr eq $dchr and abs($upos - $dpos) < 37 and $s->{map}{$row[2]}{$uchr}{$upos} eq $s->{map}{$row[4]}{$dchr}{$dpos}){
$direction = $s->{map}{$row[2]}{$uchr}{$upos};
if ($direction eq "f"){
$upos += 19;
}else{
$upos -= 19;
}
if ($row[5] > 3 and $row[6] > 3){
if ($row[7] <= 2){
$genotype = "M";
}else{
$genotype = "H";
}
$uchr = "000" . $uchr if $uchr !~ /^0/;
$uchr = substr($uchr, length($uchr) - 3, 3);
$upos = "00000000000" . $upos if $upos !~ /^0/;
$upos = substr($upos, length($upos) - 11, 11);
print OUT "$a\t$uchr\t$upos\t$dpos\t$direction\t$tmp\t$genotype\n";
}
if ($row[8] > 3 and $row[9] > 3){
if ($row[10] <= 2){
$genotype = "M";
}else{
$genotype = "H";
}
$uchr = "000" . $uchr if $uchr !~ /^0/;
$uchr = substr($uchr, length($uchr) - 3, 3);
$upos = "00000000000" . $upos if $upos !~ /^0/;
$upos = substr($upos, length($upos) - 11, 11);
print OUT "$b\t$uchr\t$upos\t$dpos\t$direction\t$tmp\t$genotype\n";
}
}
}
}
}
}
}
close(IN);
close(OUT);
if ($method eq "TSD"){
open(OUT, "> $wd/$a/tsd_method.genotype.$a.$b.$tsd_size");
}else{
open(OUT, "> $wd/$a/junction_method.genotype.$a.$b");
}