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neoscan.pl
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#########Song Cao###########
# last updated date: 12/21/2016 #
### updated 1/3/2018 ###
### updated 08/11/2018 ##
### use docker image for submitting jobs to research-hpc queue ##
#!/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 predict neoantigen for somatic variants in cancer sample
Pipeline version: $version
$yellow Usage: perl $0 --rdir --log --bamfq --bed --step --rna --refdir $normal
<rdir> = full path of the folder holding files for this sequence run
<log> = full path of the folder saving log files
<bamfq> = 1, input is bam; 0, input is fastq: default 1
<rna> =1, input data is rna, otherwise is dna
<bed> = bed file for annotation: ensembl: /gscmnt/gc2518/dinglab/scao/db/ensembl38.85/proteome-first.bed
refseq: /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29/proteome.bed
<refdir> = ref directory: /gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29
<step_number> run this pipeline step by step. (running the whole pipeline if step number is 0)
$red [1] Generate fasta snv and indel
[2] Generate peptide for snv and indel
$green [3] Run HLA type
$purple [4] Run netMHC
[5] parse netMHC result
$normal
OUT
my $step_number = -1;
my $help = 0;
my $run_dir="";
my $log_dir="";
my $hla = 1;
my $s_bam_fq =1;
my $s_rna=1;
my $db_ref_bed="/gscmnt/gc2518/dinglab/scao/db/ensembl38.85/proteome-first.bed";
#my $db_ref_bed="/gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29/proteome.bed";
my $h38_fa="/gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29";
my $status = &GetOptions (
"step=i" => \$step_number,
"rdir=s" => \$run_dir,
"bed=s" => \$db_ref_bed,
"refdir=s" => \$h38_fa,
"bamfq=i" => \$s_bam_fq,
"rna=i" => \$s_rna,
"log=s" => \$log_dir,
"help" => \$help
);
if ($help || $run_dir eq "" || $log_dir eq "" || $step_number<0) {
print $usage;
exit;
}
#die $usage unless @ARGV == 2;
#my ( $run_dir, $step_number ) = @ARGV;
if ($run_dir =~/(.+)\/$/) {
$run_dir = $1;
}
#die $usage unless ($step_number >=0)&&(($step_number <= 10) || ($step_number>=12));
#my $email = "scao\@wustl\.edu";
my $HOME = $ENV{HOME};
my $working_name= (split(/\//,$run_dir))[-1];
my $HOME1=$log_dir;;
#store job files here
if (! -d $HOME1."/tmpNeo") {
`mkdir $HOME1"/tmpNeo"`;
}
my $job_files_dir = $HOME1."/tmpNeo";
#store SGE output and error files here
if (! -d $HOME1."/LSF_DIR_Neo") {
`mkdir $HOME1"/LSF_DIR_Neo"`;
}
my $lsf_file_dir = $HOME1."/LSF_DIR_Neo";
## hlaminer for genotype, netMHC for neoantigen prediction ##
my $db_hla_abc_cds="/gscmnt/gc2523/dinglab/neoantigen/human_DB/HLA_ABC_CDS.fasta";
my $optitype="/gscmnt/gc2518/dinglab/scao/home/tools/anaconda2/bin/OptiTypePipeline.py";
my $f_allele="/gscmnt/gc2523/dinglab/neoantigen/netMHC-4.0/Linux_x86_64/data/allelelist";
my $netMHC="/gscmnt/gc2523/dinglab/neoantigen/netMHC-4.0/netMHC";
my $samtools="/usr/bin/samtools";
#my $db_ref_bed="/gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29/proteome.bed";
#my $h38_fa="/gscmnt/gc2518/dinglab/scao/db/refseq_hg38_june29";
my $f_opti_config = "/gscmnt/gc2737/ding/neoantigen/mmy_with_sc/rna/config/config.mmy.ini";
#my $db_cdna="/gscmnt/gc3027/dinglab/medseq/fasta/human/Homo_sapiens.GRCh37.70.cdna.all.fa";
#my $db_sanger_qs="/gscmnt/gc2523/dinglab/neoantigen/neoantigen-scan/quality_sanger.table.2col.tsv";
my $run_script_path = `dirname $0`;
chomp $run_script_path;
my $run_script_path_perl = "/usr/bin/perl ".$run_script_path."/";
my $run_script_path_python = "/usr/bin/python ".$run_script_path."/";
#my $hold_RM_job = "norm";
my $current_job_file = "";#cannot be empty
my $hold_job_file = "";
my $bsub_com = "";
my $sample_full_path = "";
my $sample_name = "";
opendir(DH, $run_dir) or die "Cannot open dir $run_dir: $!\n";
my @sample_dir_list = readdir DH;
close DH;
if ($step_number < 8 || $step_number>=12) {
#begin to process each sample
for (my $i=0;$i<@sample_dir_list;$i++) {#use the for loop instead. the foreach loop has some problem to pass the global variable $sample_name to the sub functions
$sample_name = $sample_dir_list[$i];
if (!($sample_name =~ /\./ || $sample_name=~/worklog/)) {
$sample_full_path = $run_dir."/".$sample_name;
if (-d $sample_full_path) { # is a full path directory containing a sample
print $yellow, "\nSubmitting jobs for the sample ",$sample_name, "...",$normal, "\n";
$current_job_file="";
if($step_number == 0 || $step_number>=12)
{
if($step_number==0)
{
&bsub_fa();}
if($step_number<=12)
{
&bsub_pep(); }
if($step_number<=13)
{
&bsub_hla();}
if($step_number<=14)
{
&bsub_netmhc();}
if($step_number<=15)
{
&bsub_parsemhc();}
}
elsif ($step_number == 1) {
&bsub_fa();
}
elsif ($step_number == 2) {
&bsub_pep(1);
} elsif ($step_number == 3) {
&bsub_hla(1);
} elsif ($step_number == 4) {
&bsub_netmhc(1);
}elsif ($step_number == 5) {
&bsub_parsemhc(1);
}
}
}
}
}
#if($step_number==0 || $step_number>=6)
# {
# print "generate the final report\n";
# &bsub_final_report();
# }
#if($step_number==6)
# {
# print "generate the final report\n";
# &bsub_final_report(1);
# }
#######################################################################
# send email to notify the finish of the analysis
if (($step_number == 0) || ($step_number == 6)) {
print $yellow, "Submitting the job for sending an email when the run finishes ",$sample_name, "...",$normal, "\n";
$hold_job_file = $current_job_file;
$current_job_file = "j7_email_".$sample_name.".sh";
#my $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
my $email="scao\@wustl.edu";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(EMAIL, ">$job_files_dir/$current_job_file") or die $!;
print EMAIL "#!/bin/bash\n";
print EMAIL $run_script_path."send_email.pl ".$run_dir." ".$email."\n";
close EMAIL;
my $sh_file=$job_files_dir."/".$current_job_file;
$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)\' -o $lsf_out -e $lsf_err sh $sh_file\n";
system ( $bsub_com );
}
#######################################################################
if ($step_number == 0) {
print $green, "All jobs are submitted! You will get email notification when this run is completed.\n",$normal;
}
sub bsub_fa{
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j1_fa_".$sample_name.".sh";
#my $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(FA, ">$job_files_dir/$current_job_file") or die $!;
print FA "#!/bin/bash\n";
#print FA "#BSUB -n 1\n";
#print FA "#BSUB -R \"rusage[mem=30000]\"","\n";
#print FA "#BSUB -M 30000000\n";
# print FA "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
# print FA "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
# print FA "#BSUB -q ding-lab\n";
print FA "#BSUB -J $current_job_file\n";
# print FA "#BSUB -w \"$hold_job_file\"","\n";
print FA "f_vcf_indel=".$sample_full_path."/$sample_name.indel.vcf\n";
print FA "f_vcf_snp=".$sample_full_path."/$sample_name.snp.vcf\n";
print FA "f_fa_indel_wt=".$sample_full_path."/$sample_name.indel.vcf.fa-indel-wt.fasta\n";
print FA "f_fa_indel_mut=".$sample_full_path."/$sample_name.indel.vcf.fa-indel-mut.fasta\n";
print FA "f_fa_snv_wt=".$sample_full_path."/$sample_name.snp.vcf.fa-snv-wt.fasta\n";
print FA "f_fa_snv_mut=".$sample_full_path."/$sample_name.snp.vcf.fa-snv-mut.fasta\n";
print FA "f_fa_all=".$sample_full_path."/$sample_name.transcript.fa\n";
print FA 'if [ -s $f_vcf_snp ]',"\n";
print FA "then\n";
print FA " ".$run_script_path_perl."fasta_seq_for_snv_using_refseq_bed.pl $db_ref_bed $h38_fa \${f_vcf_snp}"."\n";
print FA "cat \${f_fa_snv_mut} > \${f_fa_all}","\n";
print FA "fi\n\n";
print FA 'if [ -s $f_vcf_indel ]',"\n";
print FA "then\n";
print FA " ".$run_script_path_perl."fasta_seq_for_indel_using_refseq_bed.pl $db_ref_bed $h38_fa \${f_vcf_indel}"."\n";
print FA "cat \${f_fa_indel_mut} >> \${f_fa_all}","\n";
print FA "fi\n\n";
print FA "";
close FA;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
my $sh_file=$job_files_dir."/".$current_job_file;
$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)\' -o $lsf_out -e $lsf_err sh $sh_file\n";
system ( $bsub_com );
}
##step 2: get peptide sequences for transcript with indel and snv mutations ##
sub bsub_pep{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}
else{
$hold_job_file = $current_job_file;
}
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j2_pep_".$sample_name.".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 $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
open(PEP, ">$job_files_dir/$current_job_file") or die $!;
print PEP "#!/bin/bash\n";
# print PEP "#BSUB -n 1\n";
# print PEP "#BSUB -R \"rusage[mem=30000]\"","\n";
# print PEP "#BSUB -M 30000000\n";
# print PEP "#BSUB -q ding-lab\n";
# print PEP "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
# print PEP "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
# print PEP "#BSUB -J $current_job_file\n";
# print PEP "#BSUB -w \"$hold_job_file\"","\n";
print PEP "f_vcf_indel=".$sample_full_path."/$sample_name.indel.vcf\n";
print PEP "f_vcf_snp=".$sample_full_path."/$sample_name.snp.vcf\n";
print PEP "f_pep_indel_wt=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-wt.fasta\n";
print PEP "f_pep_indel_mut=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-mut.fasta\n";
print PEP "f_pep_snv_wt=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-wt.fasta\n";
print PEP "f_pep_snv_mut=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-mut.fasta\n";
#print PEP "f_pep_all=".$sample_full_path."/$sample_name.pep.fa\n";
print PEP 'if [ -s $f_vcf_snp ]',"\n";
print PEP "then\n";
print PEP " ".$run_script_path_perl."protein_seq_for_snv_using_refseq_bed.pl $db_ref_bed $h38_fa \${f_vcf_snp}"."\n";
#print PEP "cat \${f_pep_snv_mut} > \${f_pep_all}","\n";
print PEP "fi\n\n";
print PEP 'if [ -s $f_vcf_indel ]',"\n";
print PEP "then\n";
print PEP " ".$run_script_path_perl."protein_seq_for_indel_using_refseq_bed.pl $db_ref_bed $h38_fa \${f_vcf_indel}"."\n";
# print PEP "cat \${f_pep_indel_mut} >> \${f_pep_all}","\n";
print PEP "fi\n\n";
print PEP "";
close PEP;
my $sh_file=$job_files_dir."/".$current_job_file;
# $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";
$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)\' -o $lsf_out -e $lsf_err sh $sh_file\n";
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
system ( $bsub_com );
}
##step 3: use bwa to align the hla reference to get HLA genotypet ##
sub bsub_hla{
#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;
}
$current_job_file = "j3_hla_".$sample_name.".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 $IN_bam = $sample_full_path."/".$sample_name.".bam";
my $f_fq_1=$sample_full_path."/".$sample_name.".1.fq";
my $f_fq_2=$sample_full_path."/".$sample_name.".2.fq";
# my $HLA_MT_sam=$sample_full_path."/".$sample_name.".rnaseq.mapped.sam";
my $dir_hla=$sample_full_path."/hla";
#if(-d $dir_hla) { `rm $dir_hla`; }
my $f_hla_type=`find $dir_hla -name \'*.tsv\'`;
chomp($f_hla_type);
print $f_hla_type,"\n";
# if(-e $f_hla_type) { print "existing \n"; }
if ((! -e $IN_bam) && ((!-e $f_fq_1) || (! -e $f_fq_2)) && (!-e $f_hla_type)) {#make sure there is a input fasta file
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
print "Warning: Died because there is no input bam or fq file for bwa:\n";
print "File $IN_bam does not exist!\n";
die "Please check command line argument!", $normal, "\n\n";
}
#if (! -s $IN_bam) {#make sure input fasta file is not empty
# print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
# die "Warning: Died because $IN_bam is empty!", $normal, "\n\n";
#}
open(HLA, ">$job_files_dir/$current_job_file") or die $!;
# my $f_fq_1=$sample_full_path."/".$sample_name.".1.fq";
# my $f_fq_2=$sample_full_path."/".$sample_name.".2.fq";
print HLA "#!/bin/bash\n";
#print HLA "#BSUB -n 1\n";
#print HLA "#BSUB -R \"rusage[mem=30000]\"","\n";
#print HLA "#BSUB -M 30000000\n";
#print HLA "#BSUB -q ding-lab\n";
#print HLA "#BSUB -w \"$hold_job_file\"","\n";
#print HLA "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print HLA "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print HLA "#BSUB -J $current_job_file\n";
print HLA "HLA_IN=".$sample_full_path."/".$sample_name.".bam\n";
print HLA "HLA_sorted=".$sample_full_path."/".$sample_name.".sorted\n";
print HLA "HLA_sorted_bam=".$sample_full_path."/".$sample_name.".sorted.bam\n";
print HLA "HLA_tsv=".$sample_full_path."/HLA_alleles.tsv\n";
print HLA "f_optitype_hla=".$sample_full_path."/hla/notexisting.tsv\n";
# print HLA "dir_hla=".$sample_full_path."/hla\n";
print HLA "if [ $s_bam_fq -eq 1 ]\n";
print HLA "then\n";
print HLA 'if [ -f $IN_bam ]',"\n"; # input file exist
print HLA "then\n";
print HLA "$samtools sort -n \${HLA_IN} \${HLA_sorted}","\n";
print HLA "$samtools view \${HLA_sorted_bam} | perl -ne \'\$l=\$_; \$f_q1=\"$f_fq_1\"; \$f_q2=\"$f_fq_2\"; if(\$first==0) { open(OUT1,\">\$f_q1\"); open(OUT2,\">\$f_q2\"); \$first=1;} \@ss=split(\"\\t\",\$l); \$flag=\$ss[1]; \$cigar=\$ss[5]; if((\$flag & 0x100) || (\$flag & 0x800) || (\$cigar=~/H/)) { next; } \$id=\$ss[0]; \$seq=\$ss[9]; \$q=\$ss[10]; if(\$id=~/\\/1\$/ || (\$flag & 0x40) ) { \$r1=\$id; \$r1=~s/\\/1\$//g; \$seq1=\$seq; \$q1=\$q; } if(\$id=~/\\/2\$/ || (\$flag & 0x80)) { \$r2=\$id; \$r2=~s/\\/2\$//g; \$seq2=\$seq; \$q2=\$q; } if((\$r1 eq \$r2)) { print OUT1 \"\@\",\$r1,\"/1\",\"\\n\"; print OUT1 \$seq1,\"\\n\"; print OUT1 \"+\",\"\\n\"; print OUT1 \$q1,\"\\n\"; print OUT2 \"\@\",\$r1,\"/2\",\"\\n\"; print OUT2 \$seq2,\"\\n\"; print OUT2 \"+\",\"\\n\"; print OUT2 \$q2,\"\\n\";}\'","\n";
print HLA " fi\n";
print HLA "fi\n";
print HLA "if [ -f $f_fq_1 ] && [ -f $f_fq_2 ]","\n"; # input file exist
print HLA "then\n";
print HLA "if [ $s_rna -eq 1 ]\n";
print HLA "then\n";
print HLA "if [ -d $dir_hla ]","\n";
print HLA "then\n";
print HLA "f_optitype_hla=`find $dir_hla -name '*tsv'`","\n";
print HLA "fi\n";
print HLA "if [ -z \${f_optitype_hla} ] || [ ! -f \${f_optitype_hla} ]\n";
print HLA "then\n";
print HLA "if [ -d $dir_hla ]","\n";
print HLA "then\n";
print HLA "rm -rf $dir_hla\n";
print HLA "fi\n";
print HLA "$optitype -i $f_fq_1 $f_fq_2 -r -c $f_opti_config -v -o $dir_hla"."\n";
# print HLA "done\n";
print HLA "fi\n";
print HLA "else\n";
# print HLA "while [ ! -f \${f_optitype_hla} ]\n";
# print HLA "do\n";
print HLA "if [ ! -f \${f_optitype_hla} ]\n";
print HLA "then\n";
print HLA "if [ -d $dir_hla ]","\n";
print HLA "then\n";
print HLA "rm -rf $dir_hla\n";
print HLA "fi\n";
print HLA "$optitype -i $f_fq_1 $f_fq_2 -d -c $f_opti_config -v -o $dir_hla"."\n";
# print HLA "done\n";
print HLA " fi\n";
print HLA " fi\n";
#print HLA " ".$run_script_path_perl."parseHLAresult.pl \${f_optitype_hla} \${HLA_tsv}"."\n";
print HLA "if [ -d $dir_hla ]","\n";
print HLA "then\n";
print HLA "f_optitype_hla=`find $dir_hla -name '*tsv'`","\n";
print HLA "fi\n";
### finish hla type, then delete ##
print HLA "if [ ! -z \${f_optitype_hla} ] && [ -f \${f_optitype_hla} ]\n";
print HLA "then\n";
print HLA "rm \${HLA_sorted_bam}","\n";
print HLA "rm $f_fq_1","\n";
print HLA "rm $f_fq_2","\n";
print HLA " fi\n";
print HLA " fi\n";
print HLA "if [ -d $dir_hla ]","\n";
print HLA "then\n";
print HLA "f_optitype_hla=`find $dir_hla -name '*tsv'`","\n";
print HLA "fi\n";
print HLA "if [ ! -z \${f_optitype_hla} ] && [ -f \${f_optitype_hla} ]\n";
print HLA "then\n";
print HLA " ".$run_script_path_perl."parseHLAresult.pl \${f_optitype_hla} \${HLA_tsv}"."\n";
print HLA "fi\n";
close HLA;
my $sh_file=$job_files_dir."/".$current_job_file;
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>100000] rusage[mem=100000]\" -M 100000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n";
system ( $bsub_com );
}
sub bsub_netmhc{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j4_bind_".$sample_name.".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 $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
open(MHC, ">$job_files_dir/$current_job_file") or die $!;
print MHC "#!/bin/bash\n";
#print MHC "#BSUB -n 1\n";
#print MHC "#BSUB -R \"rusage[mem=30000]\"","\n";
#print MHC "#BSUB -M 30000000\n";
#print MHC "#BSUB -q ding-lab\n";
# print MHC "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
# print MHC "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
# print MHC "#BSUB -J $current_job_file\n";
# print MHC "#BSUB -w \"$hold_job_file\"","\n";
print MHC "f_pep_indel_wt=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-wt.fasta\n";
print MHC "f_pep_indel_mut=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-mut.fasta\n";
print MHC "f_pep_snv_wt=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-wt.fasta\n";
print MHC "f_pep_snv_mut=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-mut.fasta\n";
print MHC "f_pep_snv_mut_v1=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-mut.v1.fasta\n";
print MHC "f_pep_snv_mut_v2=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-mut.v2.fasta\n";
# print MHC "f_pep=".$sample_full_path."/$sample_name.pep.fa\n";
print MHC "HLA_tsv=".$sample_full_path."/HLA_alleles.tsv\n";
print MHC "f_netMHC_result=".$sample_full_path."/netMHC4.0.out.append.txt\n";
print MHC "f_netMHC_result_snv=".$sample_full_path."/netMHC4.0.out.append.snv.txt\n";
print MHC "f_netMHC_result_indel=".$sample_full_path."/netMHC4.0.out.append.indel.txt\n";
print MHC "f_out=".$sample_full_path."/result_neoantigen\n";
print MHC " ".$run_script_path_perl."generate_mut_peptide_snv.pl $db_ref_bed \${f_pep_snv_wt} \${f_pep_snv_mut} \${f_pep_snv_mut_v1}\n";
print MHC " ".$run_script_path_perl."remove_duplicate_mut_peptide_snv.pl \${f_pep_snv_mut_v1} \${f_pep_snv_mut_v2}\n";
print MHC " ".$run_script_path_python."runNetMHC4.py -a \${HLA_tsv} -f \${f_pep_snv_mut_v2} -p 8,9,10,11 -o $sample_full_path -n $netMHC -v $f_allele"."\n";
print MHC "mv \${f_netMHC_result} \${f_netMHC_result_snv}\n";
print MHC " ".$run_script_path_python."runNetMHC4.py -a \${HLA_tsv} -f \${f_pep_indel_mut} -p 8,9,10,11 -o $sample_full_path -n $netMHC -v $f_allele"."\n";
print MHC "mv \${f_netMHC_result} \${f_netMHC_result_indel}\n";
close MHC;
my $sh_file=$job_files_dir."/".$current_job_file;
# $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)\' -o $lsf_out -e $lsf_err sh $sh_file\n";
$bsub_com = "LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err sh $sh_file\n";
system ( $bsub_com );
}
sub bsub_parsemhc{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j5_parsebind_".$sample_name.".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 $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
open(PMHC, ">$job_files_dir/$current_job_file") or die $!;
print PMHC "#!/bin/bash\n";
# print PMHC "#BSUB -n 1\n";
# print PMHC "#BSUB -R \"rusage[mem=30000]\"","\n";
# print PMHC "#BSUB -M 30000000\n";
# print PMHC "#BSUB -q ding-lab\n";
# print PMHC "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
# print PMHC "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
# print PMHC "#BSUB -J $current_job_file\n";
# print PMHC "#BSUB -w \"$hold_job_file\"","\n";
print PMHC "f_indel=".$sample_full_path."/$sample_name.indel.vcf\n";
print PMHC "f_snv=".$sample_full_path."/$sample_name.snp.vcf\n";
print PMHC "f_indel_wt_fa=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-wt.fasta\n";
print PMHC "f_snv_wt_fa=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-wt.fasta\n";
print PMHC "f_indel_mut_fa=".$sample_full_path."/$sample_name.indel.vcf.proteome-indel-mut.fasta\n";
print PMHC "f_snv_mut_fa=".$sample_full_path."/$sample_name.snp.vcf.proteome-snv-mut.fasta\n";
print PMHC "f_netMHC_result_snv=".$sample_full_path."/netMHC4.0.out.append.snv.txt\n";
print PMHC "f_netMHC_result_indel=".$sample_full_path."/netMHC4.0.out.append.indel.txt\n";
print PMHC "f_snv_out=".$sample_full_path."/$sample_name.neoantigen.snv.tsv\n";
print PMHC "f_indel_out=".$sample_full_path."/$sample_name.neoantigen.indel.tsv\n";
print PMHC "f_snv_sum=".$sample_full_path."/$sample_name.neo.snv.summary\n";
print PMHC "f_indel_sum=".$sample_full_path."/$sample_name.neo.indel.summary\n";
# print PMHC "f_min=".$sample_full_path."/$sample_name.neo.summary.min\n";
print PMHC " ".$run_script_path_perl."parseNetMHC4result.pl \${f_netMHC_result_snv} \${f_indel_wt_fa} \${f_snv_wt_fa} \${f_snv_out}"."\n";
print PMHC " ".$run_script_path_perl."reportSummary.pl \${f_snv_out} \${f_indel} \${f_snv} \${f_indel_mut_fa} \${f_snv_mut_fa} \${f_snv_sum}"."\n";
print PMHC " ".$run_script_path_perl."parseNetMHC4result.pl \${f_netMHC_result_indel} \${f_indel_wt_fa} \${f_snv_wt_fa} \${f_indel_out}"."\n";
print PMHC " ".$run_script_path_perl."reportSummary.pl \${f_indel_out} \${f_indel} \${f_snv} \${f_indel_mut_fa} \${f_snv_mut_fa} \${f_indel_sum}"."\n";
close PMHC;
my $sh_file=$job_files_dir."/".$current_job_file;
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n";
system ( $bsub_com );
}
sub bsub_final_report()
{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j6_final_report_".$working_name.".sh";
#my $IN_sam = $sample_full_path."/".$sample_name.".exome.sam";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(REP, ">$job_files_dir/$current_job_file") or die $!;
print REP "#!/bin/bash\n";
#print REP "#BSUB -n 1\n";
#print REP "#BSUB -R \"rusage[mem=30000]\"","\n";
#print REP "#BSUB -M 30000000\n";
#print REP "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print REP "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print REP "#BSUB -q ding-lab\n";
#print REP "#BSUB -J $current_job_file\n";
#print REP "#BSUB -w \"$hold_job_file\"","\n";
print REP " ".$run_script_path_perl."generate_report_summary.pl $run_dir $version"."\n";
close REP;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ( $bsub_com );
my $sh_file=$job_files_dir."/".$current_job_file;
# $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";
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err sh $sh_file\n";
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
system ( $bsub_com );
}