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simpiTB.pl
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#!/usr/bin/perl
use strict;
#use warnings;
#Examples of use:
#perl simpiTB.pl <options> *.fasta
#perl simpiTB.pl <options> *.fastq
#perl simpiTB.pl <options> *.fastq.gz
#perl simpiTB.pl <options> list.txt
#(please note that the txt file must finish by extension ".txt", and it must contain one accession perl line such as the following example)
#SRR13015794
#SRR13015795
#accessions could also be separated by commas as follows:
#perl simpiTB.pl SRR13015794,SRR13015795,SRR13015796
#variables
my $seqfasta = "";
my $seqfastq = "";
my $recap_total_seq = "reconciledTB_list.xls"; # global summary file
my $spollineages_entries = "spollineages.csv"; # input file for spollineages
my $phyloviz_entries = "phyloviz_profiles.tab"; # input file for phyloviz
my $grapetree_entries = "grapetree.tab"; # input file for grapetree
my $grapeMethod = "RapidNJ"; # value for -m option in grapetree
my %hSPOL = (); # hash map for all Spol sequences
my %hSPOLoctal = ();
my %hMIRU = (); # hash for 24-loci MIRU-VNTRs
my %h12miru = (); # hash for 12-loci MIRU-VNTRs
my %h15miru = (); # hash for 15-loci MIRU-VNTRs
my @tabFiles = ();
#my @tabRuns = ();
my %hResistance = ();
my %hLineageMyk = (); # lineage from mykrobe
my %galruSpol = ();
my %spollineages = ();
my $isList = 0;
my $isFasta = 0;
my $isFastq = 0;
my $tbProf = "TBProfiler_result";
my $resultTBprof = "";
my %hLineageTBP = ();
my %hDrugTBP = ();
my %hDrugListTBP = ();
my %hFLC = (); # results for fast-lineage-caller program
my %hSB =();
my $sbFile = "SBnumbers_Mbovis_240221.tab";
my $useMykrobe = 0;
my $useTBP = 0;
my $doMiru = 0;
my $useGrape = 0;
my $useRoary = 0;
my $fasttree = 0;
my $spades = 0;
my $sbPath = "";
my $fastaDir = "FASTAsimpi";
my $outdir = "simpiTBResults";
my $removeS = 0;
my $pathToBin = "."; # "./bin/" replaced by ""
my $useResFinder = 0;
my %hReads = ();
my %hRF = ();
my $genCode = 11;
my %hGrape = ();
my %cladeInfo = ();
my $cpus = 16; #CPUs to be used for programs
my $useParsnp = 0; # option to use Parsnp
my $reference = ""; # reference sequence (in FASTA format) to be used
my $version = "1.0.2";
my $start = time();
print "##################################################################\n";
print "# --> Welcome to $0 (version $version)!\n";
print "##################################################################\n";
print "\n";
#my $spadesProg = isProgInstalled("spades");
#if($spadesProg){
# print "spades is...............OK \n";
#}
#my $prodigalProg = isProgInstalled("prodigal");
#if($prodigalProg){
# print "prodigal is...............OK \n";
#}
my $tbprofilerProg = isProgInstalled("tb-profiler");
if($tbprofilerProg){
print "tb-profiler is...............OK \n";
}
#my $parsnpProg = isProgInstalled("parsnp");
#if($parsnpProg){
# print "parsnp is...............OK \n";
#}
#my $roaryProg = isProgInstalled("roary");
#if($roaryProg){
# print "roary is...............OK \n";
#}
#my $fasttreeProg = isProgInstalled("fasttree");
#if($fasttreeProg){
# print "fasttree is...............OK \n";
#}
my $miruhero = isProgInstalled("MiruHero");
if($miruhero){
print "MiruHero is...............OK \n";
}
my $grapetreeProg = isProgInstalled("grapetree");
if($grapetreeProg){
print "grapetree is...............OK \n";
}
my $flcProg = isProgInstalled("fast-lineage-caller");
if($flcProg){
print "fast-lineage-caller is...............OK \n";
}
print "\n";
if (@ARGV<1) {
help_user_simple($0);
exit 1;
}
if ($ARGV[0] eq "--help" || $ARGV[0] eq "-h") {
help_user_advance($0);
exit 0;
}
if ($ARGV[0] eq "--version" || $ARGV[0] eq "-v") {
program_version($0);
exit 0;
}
#FASTA/Q files
if(@ARGV){
for my $arg (@ARGV){
if ($arg =~ m/.fasta/ or $arg =~ m/.fna/ ){ # or $arg =~ m/.fasta.gz/ or $arg =~ m/.fna.gz/
my $tmp_arg = "";
if($arg =~ m/.fna/){
$tmp_arg = $arg;
$tmp_arg =~ s/.fna/.fasta/g;
system ("mv -f $arg $tmp_arg");
$arg = $tmp_arg;
}
print "FASTA file: $arg\n";
#$seqfasta = $arg;
push (@tabFiles,$arg);
$isFasta = 1;
}
elsif ($arg =~ m/.fastq/ or $arg =~ m/.fq/ or $arg =~ m/.fq.gz/ or $arg =~ m/.fastq.gz/){
print "FASTQ file: $arg\n";
#$seqfastq = $arg;
my $readName = $arg;
if ($arg =~ m/_1.fastq.gz/ or $arg =~ m/_R1.fastq.gz/ or $arg =~ m/_2.fastq.gz/ or $arg =~ m/_R2.fastq.gz/ ){
#my $newstring = $oldstring;
$readName =~ s/_1.fastq.gz//g;
$readName =~ s/_R1.fastq.gz//g;
$readName =~ s/_2.fastq.gz//g;
$readName =~ s/_R2.fastq.gz//g;
#print "READ NAME is : $readName\n";
$hReads{$readName} = $readName;
@tabFiles = keys %hReads;
#push (@tabFiles,$readName);
$isFastq = 0;
$isList = 1;
}
else{
push (@tabFiles,$arg);
$isFastq = 1;
}
}
elsif ($arg =~ m/.txt/){
if (-e $arg){
open my $handle, '<', $arg;
chomp(@tabFiles = <$handle>);
close $handle;
$isList = 1;
}
}
elsif ($arg =~ m/,/){
@tabFiles = split (/,/, $arg) ;
$isList = 1;
}
}
}
##requirements
for (my $i = 0; $i <= $#ARGV; $i++) {
if ($ARGV[$i]=~/--mykrobe/i or $ARGV[$i]=~/-mk/i) {
$useMykrobe = 1;
}
elsif ($ARGV[$i]=~/--tbprofiler/i or $ARGV[$i]=~/-tp/i) {
$useTBP = 1;
}
elsif ($ARGV[$i]=~/--miru/i or $ARGV[$i]=~/-mi/i) {
$doMiru = 1;
}
elsif ($ARGV[$i]=~/--grape/i or $ARGV[$i]=~/-gr/i) {
$useGrape = 1;
}
elsif ($ARGV[$i]=~/--method/i or $ARGV[$i]=~/-me/i) {
$grapeMethod = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/--roary/i or $ARGV[$i]=~/-ro/i) {
$useRoary = 1;
}
elsif ($ARGV[$i]=~/--fasttree/i or $ARGV[$i]=~/-ft/i) {
$fasttree = 1;
}
elsif ($ARGV[$i]=~/--spades/i or $ARGV[$i]=~/-sp/i) {
$spades = 1;
}
elsif ($ARGV[$i]=~/--out/i or $ARGV[$i]=~/-o/i) {
$outdir = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/--sb_path/i or $ARGV[$i]=~/--sbpath/i or $ARGV[$i]=~/-sb/i) {
$sbPath = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/--remove/i or $ARGV[$i]=~/-rm/i) {
$removeS = 1;
}
elsif ($ARGV[$i]=~/--resfinder/i or $ARGV[$i]=~/-rf/i) {
$useResFinder = 1;
}
elsif ($ARGV[$i]=~/--reference/i or $ARGV[$i]=~/-ref/i) {
$reference = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/--cpu/i or $ARGV[$i]=~/-cpu/i) {
$cpus = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/--parsnp/i or $ARGV[$i]=~/-snp/i) {
$useParsnp = 1;
}
elsif ($ARGV[$i]=~/--pathToBin/i or $ARGV[$i]=~/--path/i or $ARGV[$i]=~/-p/i) {
$pathToBin = $ARGV[$i+1];
}
}
if(-d "GFF/") { system("rm -rf GFF/"); }
if(-d $outdir) { system("rm -rf $outdir"); }
mkdir($outdir);
if(-d $fastaDir) { system("rm -rf $fastaDir"); }
mkdir($fastaDir);
if(-e "${pathToBin}/SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py"){
print "spotyping is...............OK \n";
}
if(-e "${pathToBin}/MIRUReader/MIRUReader.py"){
print "mirureader is...............OK \n";
}
if(-e "${pathToBin}/resfinder/run_resfinder.py"){
print "resfinder is...............OK \n";
}
if(-e "${pathToBin}/SpolLineages/spollineages.jar"){
print "spollineages is...............OK \n";
}
foreach my $seq (@tabFiles){
my $seqFolder = "spades".$seq;
#$newstring = $oldstring;
if ($seqFolder =~ m/\./) {
#my @tabSeq = split (/\./, $seqFolder) ;
#$seqFolder =~ $tabSeq[0];
$seqFolder =~ s/.fastq.gz//g;
$seqFolder =~ s/.fastq//g;
#print "SEQFOLDER IS : $seqFolder \n";
}
#check paired reads and consider as list
#SpoTyping, MIRUReader, Galru, and MyKrobe and TBprofiler
my $spotypingCmd = "";
my $tbProfilerCmd = "tb-profiler profile --txt "; # DC removed $pathToBin.
my $fastaTbProfilerCmd = ""; #"tb-profiler fasta_profile --txt ";
#print "TBProfiler command: $tbProfilerCmd\n";
#my $resfinderCmd = "python3 ${pathToBin}/resfinder/run_resfinder.py -o RF -s \"Mycobacterium tuberculosis\" -l 0.6 -t 0.8 --acquired --point -db_res ${pathToBin}/resfinder/db_resfinder -db_point ${pathToBin}/resfinder/db_pointfinder -ifa";
my $resfinderCmd = "python3 -m resfinder -o RF -s \"Mycobacterium tuberculosis\" -l 0.6 -t 0.8 --acquired --point -db_res resfinder_db/ -db_disinf disinfinder_db/ -db_point pointfinder_db/ -ifa";
#python -m resfinder -o resfinderOUT -s "Mycobacterium tuberculosis" -l 0.6 -t 0.8 --acquired --point -ifa GCF_000195955.fasta
#RF/pheno_table.txt
if(-e $seq and $isFasta){
system ("cp -f $seq $fastaDir"); # copy original file into FASTA folder #parsnp –p $cpus –d $fastaDir –r $reference -c
#$spotypingCmd = "python2 ".$pathToBin."SpoTyping-2.1/SpoTyping-v2.1-commandLine/SpoTyping.py --noQuery -o spotyping --seq $seq ";
$spotypingCmd = "python3 ".$pathToBin."/SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py --noQuery -o spotyping --seq $seq ";
#open GALRU, "galru $seq -t 16 |";
if ($doMiru) {
print "MIRU analysis from FASTA input files... \n";
open MIRU, "python3 ${pathToBin}/MIRUReader/MIRUReader.py -r $seq -p mirus |";
readMiru($seq);
}
else { $hMIRU{$seq} = "NA"; }
if ($useMykrobe) {
#open KROBE, 'sudo singularity exec -B $PWD docker://"quay.io/biocontainers/mykrobe:0.9.0--py37h13b99d1_2" mykrobe predict my_sample tb -f --format csv --seq '. "$seq |";
open KROBE, "mykrobe predict -s my_sample --species tb -f --format csv --seq $seq |"; #-s SAMPLE --species tb
}
else {
$hResistance{$seq} = "NA";
$hLineageMyk{$seq} = "NA";
}
if($useResFinder) {
$resfinderCmd .= " ".$seq;
system ($resfinderCmd);
resfinder_out($seq);
if(-d "RF/") {
system ("rm -rf RF/ "); #remove RF folder
}
#elsif(-d "RF/"){
# system ("mv -f RF/ $outdir/");
#}
#else{
#}
}
if($useRoary){
my $nameSeq = $seq;
$nameSeq =~ s/\//_/ig;
$nameSeq =~ s/.fasta//ig;
$nameSeq =~ s/.fna//ig;
#my $prokkaCmd = "prokka --force --outdir prokka --prefix result $seq";
my $prokkaCmd = "prodigal -i $seq -c -m -g $genCode -f gff -o my_gff ";
system($prokkaCmd);
my $gff = "my_gff";
system(" echo '##FASTA' >> $gff && cat $gff $seq > ${nameSeq}.gff ");
if(! -d "GFF/") { mkdir("GFF/"); }
if(-e "${nameSeq}.gff" and -d "GFF/") { system("mv ${nameSeq}.gff GFF/ "); }
}
$fastaTbProfilerCmd = $tbProfilerCmd." -f ".$seq." -p ".$seq." -t $cpus -d ".$tbProf; #".$seq." ".$seq;
}
elsif(-e $seq and $isFastq){
#$spotypingCmd = "python2 ".$pathToBin."SpoTyping-2.1/SpoTyping-v2.1-commandLine/SpoTyping.py $seq --noQuery -o spotyping ";
$spotypingCmd = "python3 ".$pathToBin."/SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py $seq --noQuery -o spotyping ";
#SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py
#open GALRU, "galru $seq -t 16 |";
if ($doMiru) {
if($spades) {
my $nameSeq = $seq;
#$nameSeq =~ s/\//_/ig; #commented to replace by $seqFolder
if(-d $seqFolder) { system("rm -rf spades$nameSeq"); } #spades$nameSeq replaced by $seqFolder
my $spadesCmd = "spades --careful -s $seq -o $seqFolder "; #--only-assembler replaced by --careful
my $pathContig = $seqFolder."/scaffolds.fasta";
system($spadesCmd);
if(-e $pathContig) {
open MIRU, "python3 ".$pathToBin."/MIRUReader/MIRUReader.py -r $pathContig -p mirus |";
readMiru($seq);
if($useResFinder) {
$resfinderCmd .= " ".$pathContig;
system ($resfinderCmd);
resfinder_out($seq);
if(-d "RF/") {
system ("rm -rf RF/ "); #remove RF folder
}
#elsif(-d "RF/"){
# system ("mv -f RF/ $outdir/");
#}
#else{
#}
}
}
if(-d $seqFolder) {
if ($outdir =~ m/\//) { $outdir =~ s/\///i; }
system ("cp -f $pathContig $outdir/scaffolds_$seq.fasta"); #removed scaffolds_$seq.fasta?
if($removeS) {
system ("rm -rf $seqFolder");
}
else { system ("mv -f $seqFolder $outdir/"); }
}
}
else{
open MIRU, "python3 ".$pathToBin."MIRUReader/MIRUReader.py -r $seq -p mirus --nofasta |";
readMiru($seq);
}
}
else {
$hMIRU{$seq} = "NA";
$h15miru{$seq} = "NA";
$h12miru{$seq} = "NA";
}
if ($useMykrobe) {
#open KROBE, 'sudo singularity exec -B $PWD docker://"quay.io/biocontainers/mykrobe:0.9.0--py37h13b99d1_2" mykrobe predict my_sample tb --format csv --seq '. "$seq |";
open KROBE, "mykrobe predict -s my_sample --species tb -f --format csv --seq $seq |";
}
else {
$hResistance{$seq} = "NA";
$hLineageMyk{$seq} = "NA";
}
$tbProfilerCmd = $tbProfilerCmd." -1 ".$seq." -p ".$seq." -t $cpus -d ".$tbProf;
}
elsif($isList){
my $read1 = $seq."_1.fastq.gz";
my $read2 = $seq."_2.fastq.gz";
if(-e $seq."_R1.fastq.gz" and $seq."_R2.fastq.gz" ) {
$read1 = $seq."_R1.fastq.gz";
$read2 = $seq."_R2.fastq.gz";
}
if(-e $read1 and -e $read2){
#$spotypingCmd = "python2 ".$pathToBin."SpoTyping-2.1/SpoTyping-v2.1-commandLine/SpoTyping.py $read1 $read2 --noQuery -o spotyping ";
$spotypingCmd = "python3 ".$pathToBin."SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py $read1 $read2 --noQuery -o spotyping ";
#$spotypingCmd = "python3 ".$pathToBin."SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py $seq --noQuery -o spotyping ";
#open GALRU, "galru $read1 -t 16 |";
if ($doMiru) {
if($spades) {
if(-d $seqFolder) { system("rm -rf $seqFolder"); }
my $spadesCmd = "spades --careful -1 $read1 -2 $read2 -o $seqFolder "; # --disable-rr --isolate? default (last run was 2772 seconds) --only-assembler (2526 seconds) good mirus
my $pathContig = $seqFolder."/scaffolds.fasta";
system($spadesCmd);
if(-e $pathContig) {
open MIRU, "python3 ".$pathToBin."MIRUReader/MIRUReader.py -r $pathContig -p mirus |";
readMiru($seq);
if($useResFinder) {
$resfinderCmd .= " ".$pathContig;
system ($resfinderCmd);
resfinder_out($seq);
if(-d "RF/") {
system ("rm -rf RF/ "); #remove RF folder
}
#elsif(-d "RF/"){
# system ("mv -f RF/ $outdir/");
#}
#else{
#}
}
}
if(-d $seqFolder) {
if ($outdir =~ m/\//) { $outdir =~ s/\///i; }
system ("cp -f $pathContig $outdir/scaffolds_$seqFolder.fasta");
if($removeS) {
system ("rm -rf $seqFolder");
}
else { system ("mv -f $seqFolder $outdir/"); }
}
}
else {
open MIRU, "python3 ".$pathToBin."MIRUReader/MIRUReader.py -r $read1 -p mirus --nofasta |";
readMiru($seq);
}
}
else {
$hMIRU{$seq} = "NA";
$h15miru{$seq} = "NA";
$h12miru{$seq} = "NA";
}
if ($useMykrobe) {
#open KROBE, 'sudo singularity exec -B $PWD docker://"quay.io/biocontainers/mykrobe:0.9.0--py37h13b99d1_2" mykrobe predict my_sample tb --format csv --seq '. "$read1 $read2 |";
open KROBE, "mykrobe predict -s my_sample --species tb -f --format csv --seq $read1 $read2 |";
}
else {
$hResistance{$seq} = "NA";
$hLineageMyk{$seq} = "NA";
}
$tbProfilerCmd = $tbProfilerCmd." -t $cpus -d ".$tbProf." -1 ".$read1." -2 ".$read2." -p ".$seq;
}
elsif(-e $read1 and ! -e $read2){
$spotypingCmd = "python3 ".$pathToBin."SpoTyping/SpoTyping-v3.0-commandLine/SpoTyping.py $read1 --noQuery -o spotyping ";
#open GALRU, "galru $read1 -t 16 |";
if ($doMiru) {
if($spades) {
#my $seqFolder = "spades".$seq;
#$newstring = $oldstring;
my $spadesCmd = "spades --careful -1 $read1 -o $seqFolder "; #--only-assembler replaced by --careful
my $pathContig = "${seqFolder}/scaffolds.fasta";
system($spadesCmd);
if(-e $pathContig) {
open MIRU, "python3 ".$pathToBin."MIRUReader/MIRUReader.py -r $pathContig -p mirus |";
readMiru($seq);
if($useResFinder) {
$resfinderCmd .= " ".$pathContig;
system ($resfinderCmd);
resfinder_out($seq);
if(-d "RF/") {
system ("rm -rf RF/ "); #remove RF folder
}
#elsif(-d "RF/"){
# system ("mv -f RF/ $outdir/");
#}
#else{
#}
}
}
if(-d $seqFolder) {
if ($outdir =~ m/\//) { $outdir =~ s/\///i; }
system ("cp -f $pathContig $outdir/scaffolds_$seq.fasta");
system ("mv -f spades$seq $outdir/");
}
}
else {
open MIRU, "python3 ".$pathToBin."MIRUReader/MIRUReader.py -r $read1 -p mirus --nofasta |";
readMiru($seq);
}
}
else {
$hMIRU{$seq} = "NA";
$h15miru{$seq} = "NA";
$h12miru{$seq} = "NA";
}
if ($useMykrobe) {
#open KROBE, 'sudo singularity exec -B $PWD docker://"quay.io/biocontainers/mykrobe:0.9.0--py37h13b99d1_2" mykrobe predict my_sample tb --format csv --seq '. "$read1 |";
open KROBE, "mykrobe predict -s my_sample --species tb --format csv --seq $read1 |";
}
else {
$hResistance{$seq} = "NA";
$hLineageMyk{$seq} = "NA";
}
$tbProfilerCmd = $tbProfilerCmd." -t $cpus -d ".$tbProf." -1 ".$read1." -p ".$seq;
}
}
else{
print "Input file does not exist or is not correct....please verify! \n";
exit(1);
}
system ($spotypingCmd);
#read SpoTyping/Galru results
open (SPO, "<spotyping") or die "open : $!";
while (<SPO>) {
chomp();
print "SPO file: $_\n";
my @tab = split (/\t/, $_) ;
$hSPOL{$seq} = $tab[1]."\t".$tab[2]; # $tab[0] replaced by $seq
$hSPOLoctal{$seq} = $tab[2];
#$hSPOL{$tab[0]} = $tab[1]."\t".$tab[2]; #$seq
}
close (SPO) or die "close file error : $!";
system ("rm -rf spotyping ");
system ("rm -f spotyping.log ");
system ("rm -f spotyping.SpoTyping.tmp.* ");
system ("rm -rf *.fasta.* "); # remove files generated when using MIRUReader
system ("rm -rf *.fna.* ");
#system ("rm -rf RF/ "); #remove RF folder
#while (<GALRU>) {
# chomp();
# $galruSpol{$seq} = "$_";
#}
#close (GALRU) or die "close file error : $!";
# gather SB numbers in hashTable taking into account SBnumbers_Mbovis_240221.tab
if(-e $sbPath){
open (SB, "<$sbPath") or die "open : $!";
}
elsif (-e $sbFile) {
open (SB, "<$sbFile") or die "open : $!";
}
if(-e $sbPath or -e $sbFile) {
while (<SB>) {
chomp();
if ($_ =~ m/^SB/) {
my @tabSB = split (/\t/, $_) ;
if ($tabSB[2] ne '') { $hSB{$tabSB[2]} = $tabSB[0]; } # $tabSB[2] replaced by $seq , and removed $tabSB[2] ne ''
#$hSPOL{$tab[0]} = $tab[1]."\t".$tab[2]; #$seq
}
}
close (SB) or die "close file error : $!";
}
if ($useMykrobe) {
while (<KROBE>) {
chomp();
#print "WE ARE IN KROBE RESULTS:\n";
print $_."\n";
if($_ =~ m/^\"my_sample\"/){
#print "MY MAIN LINE IS: $_\n";
my @tabK = split (/,/, $_) ;
print "drug: $tabK[1]; susceptibility: $tabK[2]; lineage: $tabK[12]; lineage_per_covg: $tabK[15]; lineage_depth: $tabK[18]. \n\n";
$tabK[2] =~ s/\"//g;
$tabK[12] =~ s/\"//g;
if($tabK[2] eq "R"){ $hResistance{$seq} .= "$tabK[1] ($tabK[2]) "; }
#$hResistance{$seq} =~ s/\"//g;
$hLineageMyk{$seq} = "$tabK[12] "; # replacing .= by =
#$hLineageMyk{$seq} =~ s/\"//g;
}
}
close (KROBE) or die "close file error : $!";
}
#TBprofiler results
if(($isFastq or $isList) and $useTBP){
system($tbProfilerCmd);
#read results
$resultTBprof = $tbProf."/results/".$seq.".results.txt";
open (TBP, "<$resultTBprof") or die "open : $!";
my $lineageTBP = "";
my $drugTBP = "";
my $drugListTBP ="";
my @tabTBP = ();
while (<TBP>) {
chomp();
if ($_ =~ m/^Strain/) {
$_ =~ s/Strain: //;
$lineageTBP = $_;
}
elsif ($_ =~ m/^Drug-resistance/) {
$_ =~ s/Drug-resistance: //;
$drugTBP = $_;
}
elsif ($_ =~ m/^Rifampicin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Rifampicin (R) "; }
}
elsif ($_ =~ m/^Isoniazid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Isoniazid (R) "; }
}
elsif ($_ =~ m/^Ethambutol/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Ethambutol (R) "; }
}
elsif ($_ =~ m/^Pyrazinamide/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Pyrazinamide (R) "; }
print "IN TBProlier File: $drugListTBP\n";
}
elsif ($_ =~ m/^Streptomycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Streptomycin (R) "; }
}
elsif ($_ =~ m/^Fluoroquinolones/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Fluoroquinolones (R) "; }
}
elsif ($_ =~ m/^Moxifloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Moxifloxacin (R) "; }
}
elsif ($_ =~ m/^Ofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ofloxacin (R) "; }
}
elsif ($_ =~ m/^Levofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Levofloxacin (R) "; }
}
elsif ($_ =~ m/^Ciprofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ciprofloxacin (R) "; }
}
elsif ($_ =~ m/^Aminoglycosides/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Aminoglycosides (R) "; }
}
elsif ($_ =~ m/^Amikacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Amikacin (R) "; }
}
elsif ($_ =~ m/^Capreomycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Capreomycin (R) "; }
}
elsif ($_ =~ m/^Kanamycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Kanamycin (R) "; }
}
elsif ($_ =~ m/^Cycloserine/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Cycloserine (R) "; }
}
elsif ($_ =~ m/^Ethionamide/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ethionamide (R) "; }
}
elsif ($_ =~ m/^Clofazimine/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Clofazimine (R) "; }
}
elsif ($_ =~ m/^Para-aminosalicylic acid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Para-aminosalicylic acid (R) "; }
}
elsif ($_ =~ m/^Delamanid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Delamanid (R) "; }
}
elsif ($_ =~ m/^Bedaquiline/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Bedaquiline (R) "; }
}
elsif ($_ =~ m/^Linezolid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Linezolid (R) "; }
}
#else{
# $drugListTBP = "ND";
#}
}
close (TBP) or die "close file error : $!";
$hLineageTBP{$seq} = $lineageTBP ;
$hDrugTBP{$seq} = $drugTBP;
$hDrugListTBP{$seq} = $drugListTBP;
#Fast-Lineage-Caller (please note that this program is used when TBProf is used because it needs the .vcf file generated by TBP)
# @ gzip vcf file from TBP directory (gzip -d
my $vcfTBprof = $tbProf."/vcf/".$seq.".vcf.gz"; # .targets.csq.vcf.gz
system ("gzip -d -f $vcfTBprof");
my $newVCF = $tbProf."/vcf/".$seq.".vcf";
open FLC, "fast-lineage-caller --noheader $newVCF |";
# read FLC results
while (<FLC>) {
chomp();
my @flc = split (/\t/, $_) ;
my $first = shift(@flc);
$hFLC{$seq} = join( "\t", @flc );
#my $stringFLC = join( "\t", @flc );
}
close (FLC) or die "close file error : $!";
if($removeS){
system("rm -rf $tbProf ");
}
}
elsif($isFasta and $useTBP){ #IS FASTA
system($fastaTbProfilerCmd);
#read results
$resultTBprof = $tbProf."/results/".$seq.".results.txt";
open (TBP, "<$resultTBprof") or die "open : $!";
my $lineageTBP = "";
my $drugTBP = "";
my $drugListTBP ="";
my @tabTBP = ();
while (<TBP>) {
chomp();
if ($_ =~ m/^Strain/) {
$_ =~ s/Strain: //;
$lineageTBP = $_;
}
elsif ($_ =~ m/^Drug-resistance/) {
$_ =~ s/Drug-resistance: //;
$drugTBP = $_;
}
elsif ($_ =~ m/^Rifampicin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Rifampicin (R) "; }
}
elsif ($_ =~ m/^Isoniazid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Isoniazid (R) "; }
}
elsif ($_ =~ m/^Ethambutol/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") { $drugListTBP .= "Ethambutol (R) "; }
}
elsif ($_ =~ m/^Pyrazinamide/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Pyrazinamide (R) "; }
print "IN TBProlier File: $drugListTBP\n";
}
elsif ($_ =~ m/^Streptomycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Streptomycin (R) "; }
}
elsif ($_ =~ m/^Fluoroquinolones/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Fluoroquinolones (R) "; }
}
elsif ($_ =~ m/^Moxifloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Moxifloxacin (R) "; }
}
elsif ($_ =~ m/^Ofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ofloxacin (R) "; }
}
elsif ($_ =~ m/^Levofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Levofloxacin (R) "; }
}
elsif ($_ =~ m/^Ciprofloxacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ciprofloxacin (R) "; }
}
elsif ($_ =~ m/^Aminoglycosides/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Aminoglycosides (R) "; }
}
elsif ($_ =~ m/^Amikacin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Amikacin (R) "; }
}
elsif ($_ =~ m/^Capreomycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Capreomycin (R) "; }
}
elsif ($_ =~ m/^Kanamycin/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Kanamycin (R) "; }
}
elsif ($_ =~ m/^Cycloserine/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Cycloserine (R) "; }
}
elsif ($_ =~ m/^Ethionamide/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Ethionamide (R) "; }
}
elsif ($_ =~ m/^Clofazimine/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Clofazimine (R) "; }
}
elsif ($_ =~ m/^Para-aminosalicylic acid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Para-aminosalicylic acid (R) "; }
}
elsif ($_ =~ m/^Delamanid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Delamanid (R) "; }
}
elsif ($_ =~ m/^Bedaquiline/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Bedaquiline (R) "; }
}
elsif ($_ =~ m/^Linezolid/) {
#$_ =~ s/Drug-resistance: //;
@tabTBP = split (/\t/, $_) ;
if(defined($tabTBP[1]) and $tabTBP[1] eq "R") {$drugListTBP .= "Linezolid (R) "; }
}
#else{
# $drugListTBP = "ND";
#}
}
close (TBP) or die "close file error : $!";
$hLineageTBP{$seq} = $lineageTBP ;
$hDrugTBP{$seq} = $drugTBP;
$hDrugListTBP{$seq} = $drugListTBP;
#Fast-Lineage-Caller (please note that this program is used when TBProf is used because it needs the .vcf file generated by TBP)
# @ gzip vcf file from TBP directory (gzip -d
my $vcfTBprof = $tbProf."/vcf/".$seq.".vcf.gz"; # .targets.csq.vcf.gz
system ("gzip -d -f $vcfTBprof");
my $newVCF = $tbProf."/vcf/".$seq.".vcf";
open FLC, "fast-lineage-caller --noheader $newVCF |";
# read FLC results
while (<FLC>) {
chomp();
my @flc = split (/\t/, $_) ;
my $first = shift(@flc);
$hFLC{$seq} = join( "\t", @flc );
#my $stringFLC = join( "\t", @flc );
}
close (FLC) or die "close file error : $!";
if($removeS){
system("rm -rf $tbProf ");
}
}
}
#########################
#Summary files
open (RECAP,'>', $recap_total_seq) or die "could not open $!"; # removed Spoligotype (Galru)\t
print RECAP "#ID\tSpoligotype (SpoTyping)\tSpoligo (octal)\t24-loci MIRU-VNTR\t15-loci MIRU-VNTR\t12-loci MIRU-VNTR\tLineage (SpolLineages)\tSpoligotype International Type (SIT)\tSBnumber (Mbovis)\tResistance (Mykrobe)\tLineage (Mykrobe)\tResistance (TBProfiler)\tLineage (TBProfiler)\tResFinder\tColl2014\tFreschi2020\tLipworth2019\tShitikov2017\tStucki2016\n";
#SpolLineages and GrapeTree files
open (LINE,'>', $spollineages_entries) or die "could not open $!";
if($useGrape){
open (PHYLO,'>', $phyloviz_entries) or die "could not open $!";
if($doMiru){
print PHYLO "#Strain\tGene_1\tGene_2\tGene_3\tGene_4\tGene_5\tGene_6\tGene_7\tGene_8\tGene_9\tGene_10\tGene_11\tGene_12\tGene_13\tGene_14\tGene_15\tGene_16\tGene_17\tGene_18\tGene_19\tGene_20\tGene_21\tGene_22\tGene_23\tGene_24\tGene_25\tGene_26\tGene_27\tGene_28\tGene_29\tGene_30\tGene_31\tGene_32\tGene_33\tGene_34\tGene_35\tGene_36\tGene_37\tGene_38\tGene_39\tGene_40\tGene_41\tGene_42\tGene_43\tGene_44\tGene_45\tGene_46\tGene_47\tGene_48\tGene_49\tGene_50\tGene_51\tGene_52\tGene_53\tGene_54\tGene_55\tGene_56\tGene_57\tGene_58\tGene_59\tGene_60\tGene_61\tGene_62\tGene_63\tGene_64\tGene_65\tGene_66\tGene_67\n";
}
else{
print PHYLO "#Strain\tGene_1\tGene_2\tGene_3\tGene_4\tGene_5\tGene_6\tGene_7\tGene_8\tGene_9\tGene_10\tGene_11\tGene_12\tGene_13\tGene_14\tGene_15\tGene_16\tGene_17\tGene_18\tGene_19\tGene_20\tGene_21\tGene_22\tGene_23\tGene_24\tGene_25\tGene_26\tGene_27\tGene_28\tGene_29\tGene_30\tGene_31\tGene_32\tGene_33\tGene_34\tGene_35\tGene_36\tGene_37\tGene_38\tGene_39\tGene_40\tGene_41\tGene_42\tGene_43\n";
}
#my $count = 0;
}
#foreach my $key (keys %hSPOL)
foreach my $key (@tabFiles)
{
my @tabSpo = split (/\t/, $hSPOL{$key}) ;
print LINE "$key;$tabSpo[1];$hMIRU{$key}\n";
if($useGrape){
my @spo43 = split (//, $tabSpo[0]) ;
my $spolString = join( "\t", @spo43 );
my @miru24 = split (//, $hMIRU{$key}) ;
my $miruString = join( "\t", @miru24 );
$miruString =~ s/A/10/ig;
$miruString =~ s/B/11/ig;
$miruString =~ s/C/12/ig;
$miruString =~ s/D/13/ig;
$miruString =~ s/E/14/ig;
$miruString =~ s/F/15/ig;
#$miruString =~ s/-/0/ig;
my @tabKey = split (/\./, $key) ;
#my $id = $count++; # $tabKey[0]
if($doMiru){
print PHYLO "$tabKey[0]\t$spolString\t$miruString\n";
my $spoligomiru = $tabSpo[0].$hMIRU{$key};
$hGrape{$spoligomiru} .= $tabKey[0]."|";
}
else{
print PHYLO "$tabKey[0]\t$spolString\n";
my $spoligo = $tabSpo[0];
$hGrape{$spoligo} .= $tabKey[0]."|";
}
}
}
if($useGrape){ close (PHYLO) or die "close file error : $!"; }
close (LINE) or die "close file error : $!";