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final_process_MXE_output.pl
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#!/usr/bin/perl
use strict;
use warnings;
use List::Util qw( min max );
use List::Util qw(sum);
use List::MoreUtils qw(uniq);
#data_file_1=MXE_final; $data_file2=out1; $data_file_3=out2; $data_file_4=$condition_num; $data_file_5=$ctrl_num;
my $len=scalar(@ARGV);
if ($len < 1) {
die "Usage:final_process_MXE_output.pl <data_file_1> <data_file_2> <data_file_3> <data_file_4> <data_file_5> \n";
}
my ($data_file_1, $data_file_2, $data_file_3, $condition_num, $ctrl_num) = @ARGV;
open(IN1, "<$data_file_1") or die "can't open input1 file: $!";
open(OUT1, ">$data_file_2") || die "can't open OUT1 file";
open(OUT2, ">$data_file_3") || die "can't open OUT2 file";
my %hash;
my %readnum;
my %ratio;
my $as;
my $chr;
my $strand;
my $start;
my $end;
my @id=();
my @unique_id=();
my @sorted_id=();
my @pvalue=();
my @qvalue=();
my @array;
my $pmin;
my $qmin;
my $indicator=0;
my $lineid;
my $temp;
my $count;
my $i;
my $j;
my $s;
my $l;
my $m;
my $sum;
my $sum1;
my $sum2;
my $gene;
while(<IN1>) {
chomp;
if($_ !~ /raw_count/) {
if($indicator == 1) {
@array=split(/\s+/,$_);
$gene = $array[0];
$as = $array[1];
$lineid = 1;
$temp = $array[2];
$count = ($temp =~ s/_/_/g);
$i = $count/2;
$chr = $array[11];
$strand = $array[15];
@{ $hash{$lineid} } = @array;
push @id, $array[12];
push @id, $array[13];
push @pvalue, $array[6];
push @qvalue, $array[7];
$lineid=$lineid+1;
$indicator = $indicator + 1;
}
else {
@array=split(/\s+/,$_);
if ($array[1] eq $as) {
@{ $hash{$lineid} } = @array;
$lineid = $lineid + 1;
push @id, $array[12];
push @id, $array[13];
push @pvalue, $array[6];
push @qvalue, $array[7];
}
else {
%readnum = ();
%ratio = ();
for($j=1; $j<=$i; $j++) {
for($s=0; $s<=$ctrl_num+$condition_num-1; $s++) {
push @{$readnum{$j}}, ${$hash{$j}}[16+$s]+${$hash{$j+$i}}[16+$s];
}
# print "@{$readnum{$j}}\n";
}
for($s=0; $s<=$ctrl_num+$condition_num-1; $s++) {
$sum = 0;
for($j=1; $j<=$i; $j++) {
$sum = $sum + $readnum{$j}[$s];
}
for($j=1; $j<=$i; $j++) {
if($sum != 0) {
push @{$ratio{$j}}, $readnum{$j}[$s]/$sum;
}
else {
push @{$ratio{$j}}, "INF";
}
}
}
#for($j=1; $j<=$i; $j++) {
#print "@{$ratio{$j}}\n";
#}
@unique_id = uniq @id;
@sorted_id = sort { $a <=> $b } @unique_id;
#print "@sorted_id\n";
$pmin = min @pvalue;
s/NA/1/g for @qvalue;
$qmin = min @qvalue;
print OUT2 $as; print OUT2 "\t";
print OUT2 $chr; print OUT2 "_"; print OUT2 $strand; print OUT2 "_"; print OUT2 $sorted_id[0]; print OUT2 "_";
for($l=1; $l<=$#sorted_id-2; $l=$l+2) {
print OUT2 $sorted_id[$l]+1; print OUT2 "-"; print OUT2 $sorted_id[$l+1]; print OUT2 "_";
}
print OUT2 $sorted_id[-1]; print OUT2 "\n";
print OUT1 $gene; print OUT1 "\t"; print OUT1 $chr; print OUT1 "_"; print OUT1 $strand; print OUT1 "_"; print OUT1 $sorted_id[0]; print OUT1 "_";
for($l=1; $l<=$#sorted_id-2; $l=$l+2) {
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 "_";
}
print OUT1 $sorted_id[-1]; print OUT1 "\t";
print OUT1 $chr; print OUT1 "\t"; print OUT1 $strand; print OUT1 "\t"; print OUT1 $sorted_id[0]; print OUT1 "\t";
for($l=1; $l<$#sorted_id-2; $l=$l+2) {
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 ";";
}
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 "\t";
print OUT1 $sorted_id[-1]; print OUT1 "\t";
print OUT1 $pmin; print OUT1 "\t"; print OUT1 $qmin; print OUT1 "\t";
#print OUT1 join(';', @pvalue); print OUT1 "\t"; print OUT1 join(';', @qvalue); print OUT1 "\t";
for($j=1; $j<=$i-1; $j++) {
$sum1 = 0;
$sum2 = 0;
if ( grep( /^INF$/, @{$ratio{$j}} ) ) { print OUT1 "INF"; print OUT1 "\n";}
else {
for($m=0; $m<$condition_num; $m++) {
$sum1 = $sum1 + $ratio{$j}[$m];
}
for($m=0; $m<$ctrl_num; $m++) {
$sum2 = $sum2 + $ratio{$j}[$condition_num+$m];
}
print OUT1 $sum1/$condition_num - $sum2/$ctrl_num; print OUT1 ";"
}
}
$sum1 = 0;
$sum2 = 0;
if ( grep( /^INF$/, @{$ratio{$j}} ) ) { print OUT1 "INF"; print OUT1 "\n";}
else {
for($m=0; $m<$condition_num; $m++) {
$sum1 = $sum1 + $ratio{$j}[$m];
}
for($m=0; $m<$ctrl_num; $m++) {
$sum2 = $sum2 + $ratio{$j}[$condition_num+$m];
}
print OUT1 $sum1/$condition_num - $sum2/$ctrl_num; print OUT1 "\n";
}
$as = $array[1];
$gene = $array[0];
%hash = ();
$lineid = 1;
$temp = $array[2];
$count = ($temp =~ s/_/_/g);
$i = $count/2;
$chr = $array[11];
$strand = $array[15];
@{ $hash{$lineid} } = @array;
$lineid=$lineid+1;
@id = ();
@pvalue = ();
@qvalue = ();
push @id, $array[12];
push @id, $array[13];
push @pvalue, $array[6];
push @qvalue, $array[7];
}
$indicator = $indicator + 1;
}
}
else {
@array=split(/\s+/,$_);
print OUT1 "Gene"; print OUT1 "\t"; print OUT1 "AS_event_ID"; print OUT1 "\t"; print OUT1 "chromosome"; print OUT1 "\t"; print OUT1 "strand"; print OUT1 "\t"; print OUT1 "upstream_exon_end_coor"; print OUT1 "\t"; print OUT1 "MXE_exon_coordinates"; print OUT1 "\t"; print OUT1 "downstream_exon_start_coor"; print OUT1 "\t" ; print OUT1 "pvalue"; print OUT1 "\t"; print OUT1 "qvalue"; print OUT1 "\t"; print OUT1 "deltaPSI_"; print OUT1 $array[8]; print OUT1 "-"; print OUT1 $array[9]; print OUT1 "\n";
$indicator = $indicator+1;}
#print $indicator; print "\n";
}
%readnum = ();
%ratio = ();
for($j=1; $j<=$i; $j++) {
for($s=0; $s<=$ctrl_num+$condition_num-1; $s++) {
push @{$readnum{$j}}, ${$hash{$j}}[16+$s]+${$hash{$j+$i}}[16+$s];
}
#print "@{$readnum{$j}}\n";
}
for($s=0; $s<=$ctrl_num+$condition_num-1; $s++) {
$sum = 0;
for($j=1; $j<=$i; $j++) {
$sum = $sum + $readnum{$j}[$s];
}
for($j=1; $j<=$i; $j++) {
if($sum != 0) {
push @{$ratio{$j}}, $readnum{$j}[$s]/$sum;
}
else {
push @{$ratio{$j}}, "INF";
}
}
}
#for($j=1; $j<=$i; $j++) {
#print "@{$ratio{$j}}\n";
#}
@unique_id = uniq @id;
@sorted_id = sort { $a <=> $b } @unique_id;
#print "@id\n";
#print "@sorted_id\n";
$pmin = min @pvalue;
s/NA/1/g for @qvalue;
$qmin = min @qvalue;
print OUT2 $as; print OUT2 "\t";
print OUT2 $chr; print OUT2 "_"; print OUT2 $strand; print OUT2 "_"; print OUT2 $sorted_id[0]; print OUT2 "_";
for($l=1; $l<=$#sorted_id-2; $l=$l+2) {
print OUT2 $sorted_id[$l]+1; print OUT2 "-"; print OUT2 $sorted_id[$l+1]; print OUT2 "_";
}
print OUT2 $sorted_id[-1]; print OUT2 "\n";
print OUT1 $gene; print OUT1 "\t"; print OUT1 $chr; print OUT1 "_"; print OUT1 $strand; print OUT1 "_"; print OUT1 $sorted_id[0]; print OUT1 "_";
for($l=1; $l<=$#sorted_id-2; $l=$l+2) {
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 "_";
}
print OUT1 $sorted_id[-1]; print OUT1 "\t";
print OUT1 $chr; print OUT1 "\t"; print OUT1 $strand; print OUT1 "\t"; print OUT1 $sorted_id[0]; print OUT1 "\t";
for($l=1; $l<$#sorted_id-2; $l=$l+2) {
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 ";";
}
print OUT1 $sorted_id[$l]+1; print OUT1 "-"; print OUT1 $sorted_id[$l+1]; print OUT1 "\t";
print OUT1 $sorted_id[-1]; print OUT1 "\t";
print OUT1 $pmin; print OUT1 "\t"; print OUT1 $qmin; print OUT1 "\t";
#print OUT1 join(';', @pvalue); print OUT1 "\t"; print OUT1 join(';', @qvalue); print OUT1 "\t";
for($j=1; $j<=$i-1; $j++) {
$sum1 = 0;
$sum2 = 0;
if ( grep( /^INF$/, @{$ratio{$j}} ) ) { print OUT1 "INF"; print OUT1 "\n";}
else {
for($m=0; $m<$condition_num; $m++) {
$sum1 = $sum1 + $ratio{$j}[$m];
}
for($m=0; $m<$ctrl_num; $m++) {
$sum2 = $sum2 + $ratio{$j}[$condition_num+$m];
}
print OUT1 $sum1/$condition_num - $sum2/$ctrl_num; print OUT1 ";"
}
}
$sum1 = 0;
$sum2 = 0;
if ( grep( /^INF$/, @{$ratio{$j}} ) ) { print OUT1 "INF"; print OUT1 "\n";}
else {
for($m=0; $m<$condition_num; $m++) {
$sum1 = $sum1 + $ratio{$j}[$m];
}
for($m=0; $m<$ctrl_num; $m++) {
$sum2 = $sum2 + $ratio{$j}[$condition_num+$m];
}
print OUT1 $sum1/$condition_num - $sum2/$ctrl_num; print OUT1 "\n";
}