RGBEPP/RGBEPP.d

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#!/usr/bin/env rdmd
import std.stdio;
import std.file;
import std.process;
import std.algorithm;
import std.conv;
import std.array;
import std.path;
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import std.parallelism;
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import std.regex;
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void show_help(string pkgver) {
writeln("\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m
\t\t\tReference Genome based Exon Phylogeny Pipeline
Version: ", pkgver, "
License: GPL-2.0-only
Author: Guoyi Zhang
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-c\t--config\tconfig file for software path (optional)
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-g\t--genes\t\tgene file path (optional, if -r is specified)
-f\t--functions\tfunctions type (optional): all clean map
\t \tpostmap varcall consen align
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-h\t--help\t\tshow this information
-l\t--list\t\tlist file path
-m\t--memory\tmemory settings (optional, default 16 GB)
-r\t--reference\treference genome path
-t\t--threads\tthreads setting (optional, default 8 threads)
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--fastp\t\tFastp path (optional)
--bowtie2\t\tBowtie2 path (optional)
--samtools\t\tSamtools path (optional)
--bcftools\t\tBcftools path (optional)
--macse\t\tMacse jarfile path (optional)
--delstop\t\tDelstop path (optional)
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--trimal\t\tTrimal path (optional)
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--spades\t\tSpades python path (optional)
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for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n");
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}
bool testJava() {
bool pass = true;
auto result = execute(["java", "-version"]);
if (result.status != 0) {
pass = false;
writeln("Error: Java is not found");
}
return pass;
}
bool testFiles(string[] filePaths) {
bool pass = true;
foreach(filePath; filePaths){
if (!exists(filePath) && filePath != "") {
writeln("Error: " ~ filePath ~ " does not exists.");
pass = false;
}
}
return pass;
}
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void createDir(string path) {
if (!exists(path)) {
mkdir(path);
}
}
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void executeCommand(string[] cmd) {
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auto process = spawnProcess(cmd);
if (wait(process) != 0) {
writeln("Error executing command: ", cmd.join(" "));
}
}
void executeCommandPipe(string[][] cmds) {
Pid[] pids;
scope(exit) {
foreach (pid; pids) {
wait(pid);
}
}
// pipe init
auto temp_pipe = pipe();
// process first
pids ~= spawnProcess(cmds[0], stdin, temp_pipe.writeEnd);
// process cmd2 ~ cmdN-1
for (int i = 1; i < cmds.length - 1; i++) {
auto new_pipe = pipe(); // create next pipe
pids ~= spawnProcess(cmds[i], temp_pipe.readEnd, new_pipe.writeEnd);
temp_pipe = new_pipe; // update the pipe
}
// process final, output to stdout
pids ~= spawnProcess(cmds[$-1], temp_pipe.readEnd, stdout);
}
string[] readArrFromFile(string filename) {
string[] arr;
try {
arr = filename.readText().splitter.array;
} catch (FileException ex) {
writeln("Error reading file: ", ex.msg);
} catch (Exception ex) {
writeln("Exception: ", ex.msg);
}
return arr;
}
string getBaseName(string ARG_R){
string ARG_R_extension = extension(ARG_R); // get extension
string baseNameRef = baseName(ARG_R, ARG_R_extension); //rm dir and extension
return baseNameRef;
}
string[] getRef(string ARG_R, string DirMap){
string baseNameRef = getBaseName(ARG_R);
string ARG_R_index = DirMap ~ "/index/" ~ baseNameRef; // bt2_index_base
string ARG_R_refer = ARG_R_index ~ ".fasta"; //reference_in fasta file
string[] Refs = [ARG_R_index, ARG_R_refer];
return Refs;
}
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string[] getARG_G(string ARG_R){
string[] ARG_G;
// if ARG_G is empty
if (ARG_G.length == 0) {
auto file = File(ARG_R, "r");
ARG_G = file.byLine
.filter!(line => line.startsWith(">")) // flitering
.map!(line => line[1..$].idup) // convert to word
.array;
}
return ARG_G;
}
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string getValueFromConfig(string file, string key) {
string content = readText(file);
string value;
auto regex = regex(key ~ r"\s*=\s*(.+)");
foreach (line; content.splitter("\n")) {
if (auto match = matchFirst(line, regex)) {
value = match.captures[1];
break;
}
}
return value;
}
void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, string PathFastp) {
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// Prepare directory
createDir(DirQcTrim);
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writeln("QcTrimming::Start");
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foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputFileR1 = DirRaw ~ "/" ~ baseName ~ "_R1.fastq.gz";
string inputFileR2 = DirRaw ~ "/" ~ baseName ~ "_R2.fastq.gz";
string outputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
string outputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
string jsonFile = DirQcTrim ~ "/" ~ baseName ~ ".json";
string htmlFile = DirQcTrim ~ "/" ~ baseName ~ ".html";
// Perform quality control and trimming using external program `fastp`
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string[] cmdQcTrim = [PathFastp, "-i", inputFileR1, "-I", inputFileR2,
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"-o", outputFileR1, "-O", outputFileR2,
"-j", jsonFile, "-h", htmlFile,
"-w", ARG_T.to!string];
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executeCommand(cmdQcTrim);
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}
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writeln("QcTrimming::End");
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}
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void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
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writeln("Mapping::Start");
// Prepare directory
createDir(DirMap);
createDir(DirMap ~ "/index");
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string PathBowtie2_build = PathBowtie2 ~ "-build";
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string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_index = Refs[0]; // bt2_index_base
string ARG_R_refer = Refs[1]; //reference_in fasta file
copy(ARG_R, ARG_R_refer);
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string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, ARG_R_refer, ARG_R_index];
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executeCommand(cmdBuildDB);
foreach (string file; ARG_L) {
string baseName = baseName(file, ".fastq.gz");
string outputBam = DirMap ~ "/" ~ baseName ~ ".bam";
string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
// Perform mapping using Bowtie2 and converted to Bam using samtools
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string[] cmdMap = [PathBowtie2, "-x", ARG_R_index, "-1", inputFileR1, "-2", inputFileR2,
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"-p", ARG_T.to!string];
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string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
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executeCommandPipe([cmdMap, cmdSam2Bam]);
}
writeln("Mapping::End");
}
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void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) {
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createDir(DirBam);
writeln("PostMapping::Start");
foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputBam = DirMap ~ "/" ~ baseName ~ ".bam";
string outputBam = DirBam ~ "/" ~ baseName ~ ".bam";
// Convert SAM to BAM, sort and remove duplicates using Samtools
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string[] cmdFixmate = [PathSamtools, "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
string[] cmdSort = [PathSamtools, "sort", "-@", ARG_T.to!string, "-"];
string[] cmdMarkdup = [PathSamtools, "markdup", "-@", ARG_T.to!string, "-", outputBam];
executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
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string [] cmdIndexBam = [PathSamtools, "index", "-@", ARG_T.to!string, outputBam];
executeCommand(cmdIndexBam);
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}
writeln("PostMapping::End");
}
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void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirBam, string DirVcf, string PathBcftools) {
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writeln("VarCalling::Start");
string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_refer = Refs[1]; //reference_in fasta file
createDir(DirVcf);
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foreach (string file; parallel(ARG_L, 1)) {
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string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
// Variant calling using bcftools
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string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
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executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}
writeln("VarCalling::End");
}
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void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
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createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
createDir(DirConTaxa);
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string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_refer = Refs[1]; //reference_in fasta file
writeln("Consensus::Start");
// Extract fasta from vcf file
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foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
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// index vcf.gz
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string[] cmdIndexVcf = [PathBcftools, "index", inputVcf];
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executeCommand(cmdIndexVcf);
// Generate consensus sequences using bcftools
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string[] cmdCon = [PathBcftools, "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
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executeCommand(cmdCon);
}
// Recombine the sequences based on genes
writeln("Consensus::End");
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}
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void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
string DirConGene = DirConsensus ~ "/" ~ "gene";
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createDir(DirConGene);
// create a dictory
string[string] geneSequences;
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writeln("ConvertFasta::Start");
// read first
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foreach (file; parallel(ARG_L,1)) {
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string inputFile = DirConTaxa ~ "/" ~ file ~ ".fasta";
if (!exists(inputFile)) {
writeln("File not found: ", inputFile);
continue;
}
string content = cast(string) readText(inputFile);
bool inSequence = false;
string currentGene;
foreach (line; content.splitter("\n")) {
if (line.empty) continue;
if (line[0] == '>') {
string header = line[1 .. $];
if (ARG_G.canFind(header)) {
currentGene = header;
geneSequences[currentGene] ~= ">" ~ file ~ "\n";
inSequence = true;
} else {
inSequence = false;
}
} else if (inSequence) {
geneSequences[currentGene] ~= line ~ "\n";
}
}
}
// write different files
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foreach (gene; parallel(ARG_G,1)) {
string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta";
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File output = File(outputFile, "w");
if (gene in geneSequences) {
output.write(geneSequences[gene]);
}
}
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writeln("ConvertFasta::End");
}
void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){
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string DirConGene = DirConsensus ~ "/" ~ "gene";
string DirAlignAA = DirAlign ~ "/" ~ "AA";
string DirAlignNT = DirAlign ~ "/" ~ "NT";
writeln("Align::Start");
createDir(DirAlign);
createDir(DirAlignAA);
createDir(DirAlignNT);
foreach (gene; parallel(ARG_G, 1)) {
string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta";
string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta";
string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta";
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string[] cmdAlign = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
executeCommand(cmdAlign);
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}
writeln("Align::End");
}
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void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){
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writeln("Trimming::Start");
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string DirAA = DirAlign ~ "/" ~ "AA";
string DirNT = DirAlign ~ "/" ~ "NT";
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string DirAA_out = DirAlign ~ "/" ~ "AA_out";
string DirNT_out = DirAlign ~ "/" ~ "NT_out";
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createDir(DirAA_out);
createDir(DirNT_out);
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// copy file firstly
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foreach (gene; parallel(ARG_G,1)){
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string inputFastaAA = DirAA ~ "/" ~ gene ~ ".fasta";
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string outputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta";
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string inputFastaNT = DirNT ~ "/" ~ gene ~ ".fasta";
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string outputFastaNT = DirNT_out ~ "/" ~ gene ~ ".fasta";
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copy(inputFastaNT, outputFastaNT);
copy(inputFastaAA, outputFastaAA);
// del stop codon
string[] cmdDelStop = [PathDelstop, outputFastaAA, outputFastaNT, "--delete"];
executeCommand(cmdDelStop);
}
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string DirTrimNT = DirTrim ~ "/" ~ "NT";
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createDir(DirTrim);
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createDir(DirTrimNT);
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foreach (gene; parallel(ARG_G,1)){
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string inputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta";
string inputBackTransNT = DirNT_out ~ "/" ~ gene ~ ".fasta";
string outputFastaNT = DirTrimNT ~ "/" ~ gene ~ ".fasta";
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string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"];
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executeCommand(cmdTrim);
}
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writeln("Trimming::End");
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}
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void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){
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writeln("Assembly::Start");
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createDir(DirAssembly);
foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string DirAss = DirAssembly ~ "/" ~ baseName;
createDir(DirAss);
string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
string[] cmdAssembly = [PathSpades, "--pe1-1", inputFileR1, "--pe1-2", inputFileR2, "-t", ARG_T.to!string, "-m", ARG_M.to!string, "--careful", "--phred-offset", "33", "-o", DirAss];
executeCommand(cmdAssembly);
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}
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writeln("Assembly::End");
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}
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void main(string[] args) {
string pkgver = "0.0.3";
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string DirHome = std.file.getcwd();
string DirRaw = DirHome ~ "/00_raw";
string DirQcTrim = DirHome ~ "/01_fastp";
string DirMap = DirHome ~ "/02_bowtie2";
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string DirAssembly = DirHome ~ "/02_spades";
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string DirBam = DirHome ~ "/03_bam";
string DirVcf = DirHome ~ "/04_vcf";
string DirConsensus = DirHome ~ "/05_consen";
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string DirAlign = DirHome ~ "/06_macse";
string DirTrim = DirHome ~ "/07_trimal";
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string PathFastp = "/usr/bin/fastp";
string PathBowtie2 = "/usr/bin/bowtie2";
string PathSamtools = "/usr/bin/samtools";
string PathBcftools = "/usr/bin/bcftools";
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string PathMacse = "/usr/share/java/macse.jar";
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string PathDelstop = "/usr/bin/delstop";
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string PathTrimal = "/usr/bin/trimal";
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string PathSpades = "/usr/bin/spades.py";
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int ARG_T = 8;
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int ARG_M = 16;
string[] ARG_G;
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string[] ARG_L;
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string ARG_C;
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string ARG_F;
string ARG_R;
if (args.length > 1){
foreach (int i; 0 .. cast(int)args.length) {
switch (args[i]) {
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case "-c", "--config":
i++;
ARG_C = args[i];
break;
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case "-f", "--functions":
i++;
ARG_F = args[i];
break;
case "-g", "--gene":
i++;
ARG_G ~= readArrFromFile(args[i]);
break;
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case "-h", "--help":
show_help(pkgver);
return;
case "-l", "--list":
i++;
ARG_L ~= readArrFromFile(args[i]);
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break;
case "-r", "--reference":
i++;
ARG_R = args[i];
break;
case "-t", "--threads":
i++;
ARG_T = args[i].to!int;
break;
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case "--fastp":
i++;
PathFastp = args[i];
break;
case "--bowtie2":
i++;
PathBowtie2 = args[i];
break;
case "--samtools":
i++;
PathSamtools = args[i];
break;
case "--bcftools":
i++;
PathBcftools = args[i];
break;
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case "--macse":
i++;
PathMacse = args[i];
break;
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case "--trimal":
i++;
PathTrimal = args[i];
break;
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case "--delstop":
i++;
PathDelstop = args[i];
break;
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case "--spades":
i++;
PathSpades = args[i];
break;
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default:
break;
}
}
} else {
show_help(pkgver);
return;
}
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// get gene from ARG_R reference fasta
if (ARG_R.length != 0 ){
ARG_G = getARG_G(ARG_R);
}
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// get pathXXX form config file
if (ARG_C != ""){
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PathFastp = getValueFromConfig(ARG_C, "fastp");
PathBowtie2 = getValueFromConfig(ARG_C, "bowtie2");
PathSamtools = getValueFromConfig(ARG_C, "samtools");
PathBcftools = getValueFromConfig(ARG_C, "bcftools");
PathMacse = getValueFromConfig(ARG_C, "macse");
PathDelstop = getValueFromConfig(ARG_C, "delstop");
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PathTrimal = getValueFromConfig(ARG_C, "trimal");
}
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writeln("RGBEPP::Start");
// Perform steps based on provided function argument
if (ARG_F == "all" || ARG_F == "clean") {
if(testFiles([PathFastp])){
processQcTrim(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
}
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}
if (ARG_F == "assembly") {
if(testFiles([PathSpades])){
processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades);
}
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}
if (ARG_F == "all" || ARG_F == "map") {
if(testFiles([PathBowtie2, PathSamtools])){
processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
}
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}
if (ARG_F == "all" || ARG_F == "postmap") {
if(testFiles([PathSamtools])){
processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
}
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}
if (ARG_F == "all" || ARG_F == "varcall") {
if(testFiles([PathBcftools])){
processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
}
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}
if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){
processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus);
}
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}
if (ARG_F == "all" || ARG_F == "align") {
if(testFiles([PathMacse]) && testJava){
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
}
}
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if (ARG_F == "all" || ARG_F == "trim") {
if(testFiles([PathTrimal])){
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal);
}
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}
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writeln("RGBEPP::End");
}