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misplice.pl
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######### Song Cao###########
## Pipeline for discovering mutation-induced splice creating events from RNA-Seq ##
# MiSplice.pl #
### updated date: 04/24/2017 ###
### 04/26/2017 ####
### 10/20/2017 ###
### 01/29/2018 ###
## add reference, bed as option for user to input ##
## can be used for HG38 reference as well ##
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
#use POSIX;
my $version = 1.1;
#color code
my $red = "\e[31m";
my $gray = "\e[37m";
my $yellow = "\e[33m";
my $green = "\e[32m";
my $purple = "\e[35m";
my $cyan = "\e[36m";
my $normal = "\e[0m";
#usage information
(my $usage = <<OUT) =~ s/\t+//g;
This script will detect mutation-induced splice events from cancer patients.
Pipeline version: $version
$yellow Usage: perl $0 --rdir --step --bed --ref --q $normal
<run_folder> = full path of the folder holding files for this sequence run
<step_number> run this pipeline step by step. (running steps [1-3] if step number is 11 and running steps [4-9] if step number is 12)
<bed> bed file for ensembl db
<ref> human reference file
<q> research-hpc, long, or ding-lab
$red [1] Split maf
[2] Run discovery for splice creating events
$gray [3] Generate control maf
[4] Calculate # of supporting reads for control samples
$green [5] Generate table for # of supporting reads in case and control
$purple [6] Calculate the splice score
$cyan [7] Split novel sites for bam readcounts
[8] Do bam readcounts
[9] Run rc, hla and expression filtering
$normal
OUT
#die $usage unless @ARGV == 2;
my $step_number = -1;
#my ( $run_dir, $step_number ) = @ARGV;
my $run_dir="";
my $q_name="";
my $help="";
my $f_bed="";
my $f_ref="";
my $status = &GetOptions (
"step=i" => \$step_number,
"q=s" => \$q_name,
"help" => \$help,
"rdir=s" => \$run_dir,
"bed=s" => \$f_bed,
"ref=s" => \$f_ref
);
if ($run_dir =~/(.+)\/$/) {
$run_dir = $1;
}
#die $usage unless (($step_number >=0)&&($step_number <= 9) || ($step_number==11) || ($step_number==12));
if ($help || $run_dir eq "" || $f_bed eq "" || $f_ref eq "" || $step_number<0) {
print $usage;
exit;
}
if($q_name eq "")
{
$q_name="long";
}
my $email = "scao\@wustl\.edu";
# everything else below should be automated
my $HOME = $ENV{HOME};
my $working_name= (split(/\//,$run_dir))[-2];
my $HOME1=$run_dir."/log";
if(! -d $HOME1) { `mkdir $HOME1`; }
#store job files here
if (! -d $HOME1."/tmp_misplice") {
`mkdir $HOME1"/tmp_misplice"`;
}
my $job_files_dir = $HOME1."/tmp_misplice";
#store SGE output and error files here
if (! -d $HOME1."/LSF_DIR_MISPLICE") {
`mkdir $HOME1"/LSF_DIR_MISPLICE"`;
}
my $file_number_of_spliting = 200;
my $lsf_file_dir = $HOME1."/LSF_DIR_MISPLICE";
### USER can define them ###
my $run_script_path =`echo \$PWD`;
chomp $run_script_path;
#my $run_script_path = `dirname $0`;
my $script_dir=$run_script_path;
print $script_dir,"\n";
#my $script_dir="/gscuser/scao/gc2524/dinglab/splice/git/MiSplice_MMY";
my $fmaf=$run_dir."/misplice.input.maf";
#/gscuser/rjayasin/projects/new_WG/Splice_project/dat/MAF/tcga_filtered_ucsc_rc.MAFFINAL.NEW";
my $rcbam=$run_dir."/rna_bam_path.tsv";
#my $rcbam=$script_dir."/resource/RNA_bampaths_021417_chr.txt";
#############
#my $run_script_path = `dirname $0`;
#my $run_script_path=$script_dir;
#chomp $run_script_path;
$run_script_path = "/usr/bin/perl ".$run_script_path."/";
#print $run_script_path,"\n";
my $current_job_file = "";#cannot be empty
my $hold_job_file = "";
my $bsub_com = "";
my $sample_full_path = "";
my $sample_name = "";
$current_job_file="";
if($step_number==11)
{
&bsub_maf_split();
&bsub_job_array_ns();
&bsub_control();
} elsif($step_number==12)
{
&bsub_array_control();
&bsub_support_reads_table();
&bsub_splice_score();
&bsub_novels_split();
&bsub_job_array_rc();
&bsub_rc_hla_filter();
} elsif ($step_number == 1)
{
&bsub_maf_split(1);
}elsif ($step_number == 2)
{
&bsub_job_array_ns(1);
}elsif ($step_number == 3)
{
&bsub_control(1);
}elsif ($step_number == 4)
{
&bsub_array_control(1);
}elsif ($step_number == 5)
{
&bsub_support_reads_table(1);
}elsif ($step_number == 6)
{
&bsub_splice_score(1);
} elsif ($step_number == 7)
{
&bsub_novels_split(1);
}elsif ($step_number == 8)
{
&bsub_job_array_rc(1);
}elsif ($step_number == 9)
{
&bsub_rc_hla_filter(1);
}
sub bsub_maf_split{
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j1_maf_split.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(NS, ">$job_files_dir/$current_job_file") or die $!;
print NS "#!/bin/bash\n";
print NS "#BSUB -n 1\n";
print NS "#BSUB -R \"rusage[mem=30000]\"","\n";
print NS "#BSUB -M 30000000\n";
print NS "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
print NS "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
print NS "#BSUB -J $current_job_file\n";
print NS "MAF=".$run_dir."/misplice.input.maf\n";
print NS "DIR_OUT=".$run_dir."/NS_CASE\n";
print NS "if [ ! -d \${DIR_OUT} ]\n";
print NS "then\n";
print NS "mkdir \${DIR_OUT}\n";
print NS "fi\n";
print NS " ".$run_script_path."split_maf.pl \${MAF} \${DIR_OUT} $file_number_of_spliting"."\n";
close NS;
#$bsub_com = "bsub < $job_files_dir/$current_job_file";
#$bsub_com = "qsub -V -hold_jid $hold_job_file -e $lsf_file_dir -o $lsf_file_dir $job_files_dir/$current_job_file\n";
#system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}
sub bsub_job_array_ns {
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j2"."_array_ns".".sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open (ANS, ">$job_files_dir/$current_job_file") or die $!;
print ANS "#!/bin/bash\n";
#print ANS "#BSUB -n 1\n";
#print RM "#BSUB -q ding-lab\n";
#print ANS "#BSUB -R \"span[hosts=1] rusage[mem=10000]\"","\n";
#print RM "#BSUB -R \"rusage[mem=40000]\"","\n";
# print ANS "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
# print ANS "#BSUB -q research-hpc\n";
#print ANS "#BSUB -M 10000000\n";
#print ANS "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print ANS "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print ANS "#BSUB -J $current_job_file\[1-$file_number_of_spliting\]\n";
#print ANS "#BSUB -w \"$hold_job_file\"","\n";
#print ANS "#BSUB -q ding-lab\n";
#####################
#print RM "#\$ -t 1-$file_number_of_RepeatMasker:1","\n";
print ANS "ANS_OUT=".$run_dir."/NS_CASE/misplice.input.maf.".'${LSB_JOBINDEX}'.".v2.filtered.5\n";
print ANS "ANS_IN=".$run_dir."/NS_CASE/misplice.input.maf.".'${LSB_JOBINDEX}'."\n";
#print ANS 'if [ ! -f $ANS_OUT]',"\n";
print ANS "if [ ! -f \${ANS_OUT} ]\n";
print ANS "then\n";
print ANS " ".$run_script_path."in_silico_ns.pl \${ANS_IN} $f_bed \${ANS_OUT}"."\n";
print ANS "fi\n";
close ANS;
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -J $current_job_file\[1-$file_number_of_spliting\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -J $current_job_file\[1-$file_number_of_spliting\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
# $bsub_com = "bsub < $job_files_dir/$current_job_file\n";
# system ($bsub_com);
}
sub bsub_control {
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j3_control.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(CONTR, ">$job_files_dir/$current_job_file") or die $!;
print CONTR "#!/bin/bash\n";
#print CONTR "#BSUB -n 1\n";
#print CONTR "#BSUB -R \"rusage[mem=30000]\"","\n";
#print CONTR "#BSUB -M 30000000\n";
#print CONTR "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print CONTR "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print CONTR "#BSUB -J $current_job_file\n";
#print CONTR "#BSUB -w \"$hold_job_file\"","\n";
#print CONTR "#BSUB -q ding-lab\n";
#print CONTR "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print CONTR "#BSUB -q research-hpc\n";
print CONTR "DCONTR=".$run_dir."/Controls\n";
print CONTR "FS=".$run_dir."/Samples\n";
print CONTR "FJ=".$run_dir."/novel.junctions.filtered\n";
print CONTR "FOUT=".$run_dir."/Controls/novel.junctions.filtered.controls\n";
print CONTR "if [ ! -d \${DCONTR} ]\n";
print CONTR "then\n";
print CONTR "mkdir \${DCONTR}\n";
print CONTR "fi\n";
print CONTR "cat $run_dir/NS_CASE/*.filtered.5 > \${FJ}\n";
print CONTR " ".$run_script_path."controls.pl $fmaf \${FJ} \${FOUT} \${FS}\n";
close CONTR;
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ($bsub_com);
}
sub bsub_array_control {
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j4_array_control.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
my $f_contr=$run_dir."/Controls/novel.junctions.filtered.controls";
my $cout=`wc -l $f_contr`;
my @temp=split(" ",$cout);
my $NUM_CONTR=$temp[0];
open(IN,"<$f_contr");
my $cc=1;
while(<IN>)
{
my $line=$_;
chomp($line);
my $f_out=$f_contr.".$cc";
open(OUT,">$f_out");
print OUT $line,"\n";
close OUT;
$cc++;
}
close IN;
open(CONTRS, ">$job_files_dir/$current_job_file") or die $!;
print CONTRS "#!/bin/bash\n";
#print CONTRS "#BSUB -n 1\n";
#print CONTRS "#BSUB -R \"rusage[mem=30000]\"","\n";
#print CONTRS "#BSUB -M 30000000\n";
#print CONTRS "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print CONTRS "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print CONTRS "#BSUB -J $current_job_file\[1-$NUM_CONTR\]\n";
#print CONTRS "#BSUB -w \"$hold_job_file\"","\n";
#print CONTRS "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print CONTRS "#BSUB -q research-hpc\n";
#print CONTRS "#BSUB -q ding-lab\n";
print CONTRS "CONT_OUT=".$run_dir."/Controls/novel.junctions.filtered.controls.".'${LSB_JOBINDEX}'.".v2.filtered.5\n";
print CONTRS "CONT_IN=".$run_dir."/Controls/novel.junctions.filtered.controls.".'${LSB_JOBINDEX}'."\n";
print CONTRS " ".$run_script_path."in_silico_ns.control.pl \${CONT_IN} $f_bed \${CONT_OUT}\n";
close CONTRS;
# $bsub_com = "bsub < $job_files_dir/$current_job_file\n";
# system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -J $current_job_file\[1-$NUM_CONTR\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -J $current_job_file\[1-$NUM_CONTR\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}
sub bsub_support_reads_table{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j5_support_reads_table.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
my $f_contr=$run_dir."/Controls/novel.junctions.filtered.controls";
my $cout=`wc -l $f_contr`;
my @temp=split(" ",$cout);
my $NUM_CONTR=$temp[0];
open(EXPF, ">$job_files_dir/$current_job_file") or die $!;
print EXPF "#!/bin/bash\n";
#print EXPF "#BSUB -n 1\n";
#print EXPF "#BSUB -R \"rusage[mem=30000]\"","\n";
#print EXPF "#BSUB -M 30000000\n";
#print EXPF "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print EXPF "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print EXPF "#BSUB -J $current_job_file\n";
#print EXPF "#BSUB -w \"$hold_job_file\"","\n";
#print EXPF "#BSUB -q ding-lab\n";
#print EXPF "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print EXPF "#BSUB -q research-hpc\n";
print EXPF "FS=".$run_dir."/Samples\n";
print EXPF "OUTF=".$run_dir."/case.control.distributionmethod\n";
print EXPF "OUTF_K=".$run_dir."/case.control.distributionmethod.withkey\n";
print EXPF "SUFFIX="."v2.filtered.5\n";
print EXPF " ".$run_script_path."case_control_rc_5.pl \${FS} $f_contr \${SUFFIX} $NUM_CONTR > \${OUTF}\n";
print EXPF "cat \${OUTF} | awk \'{print substr(\$3,1,12)\"_\"\$5\"\t\"\$0}\' > \${OUTF_K}\n";
close EXPF;
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
# $bsub_com = "bsub < $job_files_dir/$current_job_file\n";
# system ($bsub_com);
}
sub bsub_splice_score {
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j6_splice_score.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(SSCORE, ">$job_files_dir/$current_job_file") or die $!;
print SSCORE "#!/bin/bash\n";
#print SSCORE "#BSUB -n 1\n";
#print SSCORE "#BSUB -R \"rusage[mem=30000]\"","\n";
#print SSCORE "#BSUB -M 30000000\n";
#print SSCORE "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print SSCORE "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print SSCORE "#BSUB -J $current_job_file\n";
#print SSCORE "#BSUB -w \"$hold_job_file\"","\n";
#print SSCORE "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print SSCORE "#BSUB -q research-hpc\n";
#print SSCORE "#BSUB -q ding-lab\n";
#print SSCORE "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
# print SSCORE "#BSUB -q research-hpc\n";
print SSCORE "DIRC=".$run_dir."/NS_CASE\n";
print SSCORE "INFO1=*.v2.filtered.5.detailed.alignment.5\n";
print SSCORE "INFO2=misplice.input.maf.*.v2.filtered.5\n";
print SSCORE " ".$run_script_path."prefilter.pl \${DIRC} \${INFO1}\n";
print SSCORE " ".$run_script_path."splice_score_novel.pl $script_dir \${DIRC} \${INFO2} $f_ref $f_bed\n";
print SSCORE "mv \${DIRC}/novel.splice.scores $run_dir/novel.splice.scores\n";
close SSCORE;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}
sub bsub_novels_split{
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j7_novels_split.sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(NS2, ">$job_files_dir/$current_job_file") or die $!;
print NS2 "#!/bin/bash\n";
#print NS2 "#BSUB -n 1\n";
#print NS2 "#BSUB -R \"rusage[mem=30000]\"","\n";
#print NS2 "#BSUB -M 30000000\n";
#print NS2 "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print NS2 "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print NS2 "#BSUB -J $current_job_file\n";
#print NS2 "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print NS2 "#BSUB -q research-hpc\n";
#print NS2 "#BSUB -q ding-lab\n";
print NS2 "MAF=".$run_dir."/novel.splice.scores\n";
print NS2 "DIR_OUT=".$run_dir."/RC\n";
print NS2 "if [ ! -d \${DIR_OUT} ]\n";
print NS2 "then\n";
print NS2 "mkdir \${DIR_OUT}\n";
print NS2 "fi\n";
print NS2 " ".$run_script_path."split_novels.pl \${MAF} \${DIR_OUT} $file_number_of_spliting"."\n";
close NS2;
# $bsub_com = "bsub < $job_files_dir/$current_job_file";
#$bsub_com = "qsub -V -hold_jid $hold_job_file -e $lsf_file_dir -o $lsf_file_dir $job_files_dir/$current_job_file\n";
# system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}
sub bsub_job_array_rc {
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j8"."_array_rc".".sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open (RC, ">$job_files_dir/$current_job_file") or die $!;
print RC "#!/bin/bash\n";
#print RC "#BSUB -n 1\n";
#print RC "#BSUB -q ding-lab\n";
#print RC "#BSUB -R \"span[hosts=1] rusage[mem=10000]\"","\n";
#print RM "#BSUB -R \"rusage[mem=40000]\"","\n";
#print RC "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
# print RC "#BSUB -q research-hpc\n";
#print RC "#BSUB -M 10000000\n";
#print RC "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print RC "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print RC "#BSUB -J $current_job_file\[1-$file_number_of_spliting\]\n";
#print RC "#BSUB -w \"$hold_job_file\"","\n";
#print RC "#BSUB -q ding-lab\n";
#####################
print RC "RC_OUT=".$run_dir."/RC/novel.splice.scores.".'${LSB_JOBINDEX}'.".rc\n";
print RC "RC_IN=".$run_dir."/RC/novel.splice.scores.".'${LSB_JOBINDEX}'."\n";
print RC " ".$run_script_path."bamreadcount_RNA_expfile_samtools.pl \${RC_IN} $rcbam > \${RC_OUT}"."\n";
#print ANS "fi\n";
close RC;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -J $current_job_file\[1-$file_number_of_spliting\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -J $current_job_file\[1-$file_number_of_spliting\] -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}
sub bsub_rc_hla_filter{
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
$current_job_file = "j9_rc_hla_filter.sh";
open(RCHLA, ">$job_files_dir/$current_job_file") or die $!;
print RCHLA "#!/bin/bash\n";
#print RCHLA "#BSUB -n 1\n";
#print RCHLA "#BSUB -R \"rusage[mem=30000]\"","\n";
#print RCHLA "#BSUB -M 30000000\n";
#print RCHLA "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print RCHLA "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print RCHLA "#BSUB -J $current_job_file\n";
#print RCHLA "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print RCHLA "#BSUB -q research-hpc\n";
#print RCHLA "#BSUB -q ding-lab\n";
print RCHLA "RCT=".$run_dir."/novel.splice.scores.rc\n";
print RCHLA "RCTK=".$run_dir."/novel.splice.scores.rc.key\n";
print RCHLA "RCTC=".$run_dir."/novel.splice.scores.rc.key.combined\n";
print RCHLA "HLA=".$run_dir."/novel.splice.scores.rc.key.combined.noHLA\n";
print RCHLA "HLAVAF=".$run_dir."/novel.splice.scores.rc.key.combined.noHLA.vaf\n";
print RCHLA "HLAVAFH=".$run_dir."/novel.splice.scores.rc.key.combined.noHLA.vaf.highexp\n";
print RCHLA "EXPK=".$run_dir."/case.control.distributionmethod.withkey\n";
print RCHLA "MAFK=".$run_dir."/maf.key\n";
print RCHLA "FINAL=".$run_dir."/novel.splice.scores.rc.key.combined.vaf.noHLA.highexp.maf\n";
print RCHLA "cat $run_dir/RC/novel.splice.scores.*.rc > \${RCT}\n";
print RCHLA "awk \'{print \$1\"_\"\$2\"_\"\$3\"_\"\$4\"_\"\$5\"\\t\"\$0}\' \${RCT} > \${RCTK}\n";
print RCHLA " ".$run_script_path."combine.pl \${RCTK} \${EXPK} 0 0 > \${RCTC}\n";
print RCHLA "grep -v \'HLA-\' \${RCTC} > \${HLA}\n";
print RCHLA "awk -F\' \' \'{ tmp=(\$20/(\$13))*100; print \$1\"\\t\"tmp\"\\t\"\$0}\' \${HLA}|awk \'\$2>5\' > \${HLAVAF}\n";
print RCHLA "grep high_expression \${HLAVAF} > \${HLAVAFH}\n";
print RCHLA "cat $run_dir/NS_CASE/misplice.input.maf.*.filtered.5 |awk -F\'\\t\' \'{ print \$16\"_\"\$5\"_\"\$6\"_\"\$11\"_\"\$13\"\\t\"\$0}' > \${MAFK}\n";
# print RCHLA "cat $run_dir/NS_CASE/misplice.input.maf.*.filtered.5 |awk -F\'\\t\' \'{print substr(\$16,1,12)\"_\"\$5\"_\"\$6\"_\"\$11\"_\"\$13\"\\t\"\$0}' > \${MAFK}\n";
print RCHLA " ".$run_script_path."combine.pl \${MAFK} \${HLAVAFH} 0 0 > \${FINAL}\n";
close RCHLA;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n"; }
print $bsub_com;
system ($bsub_com);
}