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PSIsigma-filter-v.1.0.pl
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PSIsigma-filter-v.1.0.pl
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=begin
PSI-Sigma: A splicing-detection method for short-read and long-read RNA-seq data
© Kuan-Ting Lin, 2018-2024
PSI-Sigma is free for non-commercial purposes by individuals at an academic or non-profit institution.
For commercial purposes, please contact tech transfer office of CSHL via narayan@cshl.edu
=end
=cut
#!/usr/bin/perl -w
use strict;
my ($db,$mapping,$input,$fmode) = @ARGV;
print "Filtering mode = $fmode\n";
#$fmode = 1;
my $criteria = 0.75;
my %symbol;
my %strand;
print "Reading... $mapping\n";
open(FILE,"$mapping") || die "Aborting.. Can't open $mapping : $!\n";
while(my $line=<FILE>){
chomp $line;
my ($ENST,$symbol,$strand) = split(/\t/,$line);
$symbol{$ENST} = $symbol;
$strand{$ENST} = $strand;
}
close(FILE);
print "Reading... $db\n";
my %ET;
my %wing;
my %names;
open(FILE, "$db") || die "Aborting.. Can't open $db\n";
while(my $line=<FILE>){
chomp $line;
next if($line eq "");
my ($chr,$i1s,$i1e,$i2s,$i2e,$tes,$tee,$anno,$as,$ae,$name,$gn) = split(/\t/,$line);
my ($et) = "-";
my ($accession,$num) = ($1,$2) if($name=~/(.*)\_(\d+)$/);
my @array = split(/\_/,$accession);
#$accession=~s/(.*)\_//;
my $ENST = $array[4];
if($ENST eq ""){
print "WARNNING: ENST format in the .db file is not correct\n";
print "accession = $accession\n";
$ENST = $accession;
$ENST=~s/(.*)\_//;
exit;
}
$wing{$name} = "$chr,$i1s,$i1e,$i2s,$i2e";
$ENST=~s/^Ex\.//;
$ENST=~s/^TSS\.//;
if($name=~/\_W\_/){
if($i1s == $as && $i2e == $ae){
$ET{$accession} = "SES" if($num == 1);
}else{
$ET{$accession} = "MES" if($num > 1);
}
}
if($name=~/\_S\_/){
if($i1s == $i1e){
$ET{$name} = "A3SS" if($strand{$ENST} eq "+");
$ET{$name} = "A5SS" if($strand{$ENST} eq "-");
}
if($i2s == $i2e){
$ET{$name} = "A5SS" if($strand{$ENST} eq "+");
$ET{$name} = "A3SS" if($strand{$ENST} eq "-");
}
if($i1s != $i1e && $i2s != $i2e){
print "[ERROR] coordinates are not A5SS or A3SS!\n";
print "$i1s,$i1e; $i2s,$i2e; $accession:$num\n";
}
}
if($name=~/\_R\_/){
$ET{$name} = "IR";
$ET{$name} = "IR (overlapping region)" if($gn=~/\,/);
}
}
close(FILE);
my %output;
my %asae;
my %es;
my %ee;
my %exonR;
my ($maxn,$maxt) = (0,0);
open(FILE,"$input") || die "Aborting.. Can't open $input : $!\n";
while(my $line=<FILE>){
chomp $line;
next if($line=~/^Event ID/);
my ($ID,$tmpgn,$exon,$eventtype,$N,$T,$exontype,$ENST,$dPSI,$pvalue,$FDR,$nvalues,$tvalues) = split(/\t/,$line);
my @nvalue = split(/\|/,$nvalues);
my @tvalue = split(/\|/,$tvalues);
my $wing = $wing{$ID};
if(!$wing{$ID}){
print "(ERROR) $ID can't find wings in the database.\n";
print "Aborting...\n";
exit;
}
if($fmode == 0){
next if($pvalue >= 0.01 || abs($dPSI) <= 10);
}
if($fmode == 1){
next if(abs($dPSI) <= 10);
}
if($fmode == 2){
next if($pvalue >= 0.05);
}
if($fmode == 3){
my ($avgn,$avgt) = (average(\@nvalue),average(\@tvalue));
#next if(abs($dPSI) < 5);
#next if($avgn < 10 && $avgt < 10);
#next if($avgn < 5 || $avgt < 5);
if($N > 1 && $T > 1){
#next if($pvalue > 0.05);
}
#my $no = 0;
#if($avgn < 20 || $avgt < 20){
# next if($avgn < 20 && $avgt < 20);
#}else{
# $no++;
#}
#if($avgn > 80 || $avgt > 80){
# next if($avgn > 80 && $avgt > 80);
#}else{
# $no++;
#}
#if($no == 2){
# next if($pvalue >= 0.01 || abs($dPSI) <= 10);
#}else{
# next if($pvalue >= 0.5 || abs($dPSI) <= 5);
#}
}
$maxn = $N if($maxn < $N);
$maxt = $T if($maxt < $T);
$line=~s/\, /\|/g;
my ($chr,$as,$ae,$t,$tmpENST,$num) = split(/\_/,$ID);
$chr=~s/chr//;
my ($exonchr,$exonss,$exonee) = split(/[\:\-]/,$exon);
if($eventtype eq "R"){
$exon = "$chr:$as-$ae";
}
if(!$output{"$exon\t$wing\t$eventtype"}){
$output{"$exon\t$wing\t$eventtype"} = $line;
}else{
my @tmparray = split(/\t/,$output{"$exon\t$wing\t$eventtype"});
my $tmpp = $tmparray[9];
next if($tmpp <= $pvalue);
$output{"$exon\t$wing\t$eventtype"} = $line;
}
if($eventtype eq "W"){
$es{$exonss}++;
$ee{$exonee}++;
$asae{"$chr\t$as\t$ae"}{"$exonss\t$exonee"}++;
}
if($eventtype eq "R"){
$exonR{$exon}++;
}
}
close(FILE);
$input=~s/\.txt$//;
my $outfn = $input . ".sorted.txt";
my $tmpfn = $input . ".filtered.txt";
#$tmpfn = $input . ".0to1.filtered.txt" if($fmode == 2);
#$outfn = $input . ".0to1.sorted.txt" if($fmode == 2);
open(OUT,">" . $tmpfn) || die "Aborting.. Can't open " . $tmpfn . " : $!\n";
print OUT "Event Region Gene Symbol Target Exon Event Type N T Exon Type Reference Transcript ΔPSI (%) T-test p-value FDR (BH) N Values T Values Database ID\n";
foreach my $exoninfo(keys %output){
my ($ID,$tmpgn,$exon,$eventtype,$N,$T,$exontype,$ENST,$dPSI,$pvalue,$FDR,$nvalues,$tvalues) = split(/\t/,$output{$exoninfo});
if($eventtype eq "R"){
if(!$exonR{$exon}){
}else{
#next if($exonR{$exon} > 1);
}
}
my ($chr,$as,$ae,$tmp,$tmpENST,$tmpnum) = split(/\_/,$ID);
#$chr=~s/chr//;
my ($accession,$num) = ($1,$2) if($ID=~/(.*)\_(\d+)$/);
#$accession=~s/(.*)\_//;
=begin
if($ID=~/\_R1\./ || $ID=~/\_R2\./){
$ENST=~s/\./\_/g;
$ID=~s/\./\_/g;
($accession,$num) = ($1,$2) if($ID=~/(\w+)\_(\d+)$/);
#$accession=~s/\_/\./g;
$ENST=~s/\_/\./g;
#$accession=~s/(.*)\_R1/R1/;
#$accession=~s/(.*)\_R2/R2/;
#$accession=~s/\_/\./g;
#print "Name = $name\n";
#print "accession = $accession\n";
#print "num = $num\n";
#exit;
}
=end
=cut
if($fmode == 0){
next if($N < ($maxn*$criteria) || $T < ($maxt*$criteria));
}
my $symbol = "-";
$tmpENST=~s/^Ex\.//;
$tmpENST=~s/^TSS\.//;
if(!$symbol{$tmpENST}){
$symbol="N/A";
print "$tmpENST has no symbol!\n";
}else{
$symbol = $symbol{$tmpENST};
}
my $ETID = $ID;
$ETID = $accession if($ID=~/\_W\_/);
if(!$ET{$ETID}){
print "Can't find $accession\n";
print "ID = $ID\n";
print "ENST = $ENST\n";
print "symbol = $symbol\n";
exit;
}else{
$eventtype = $ET{$ETID};
}
if($eventtype eq "SES"){
my $mxs = 0;
my ($exonchr,$exonss,$exonee) = split(/[\:\-]/,$exon);
foreach my $loc(keys %{ $asae{"$chr\t$as\t$ae"} }){
my ($es,$ee) = split(/\t/,$loc);
next if($exonss <= $es && $exonee >= $es);
next if($exonss <= $ee && $exonee >= $ee);
next if($es < $exonss && $ee > $exonee);
$mxs = 1;
last;
}
$eventtype = "MXS" if($mxs == 1);
}
if($eventtype eq "A5SS" || $eventtype eq "A3SS"){
#my ($exonchr,$exonss,$exonee) = split(/[\:\-]/,$exon);
#if(!$es{$exonss} && !$ee{$exonee}){
#}else{
# next if($fmode != 0);
#}
}
my $eventregion = "$chr:$as-$ae";
my ($exonchr,$exonss,$exonee) = split(/[\:\-]/,$exon);
if($eventtype=~/IR/){
$eventregion = $exon;
$exon = "$chr:$as-$ae";
}
if($ENST=~/^TSS/){
$eventtype = "TSS" . "|" . $eventtype;
}
#print OUT "$eventregion\t$symbol\t$exon\t$eventtype\t$N\t$T\t$exontype\t$ENST\t$dPSI\t$pvalue\t$FDR\t$nvalues\t$tvalues\n";
print OUT "$eventregion\t$symbol\t$exon\t$eventtype\t$N\t$T\t$exontype\t$ENST\t$dPSI\t$pvalue\t$FDR\t$nvalues\t$tvalues\t$ID\n";
}
close(OUT);
my $sortcommand = "\(head \-n 1 " . $tmpfn . " \&\& tail \-n \+2 " . $tmpfn . " \| sort \-gr \-t '\t' \-k 9\) \> " . $outfn . "\n";
system($sortcommand);
system("rm " . $tmpfn);
sub average{
my($data) = @_;
if (not @$data) {
die("Empty array\n");
}
my $total = 0;
foreach (@$data) {
$total += $_;
}
my $average = $total / @$data;
return $average;
}