malacology/RGBEPP
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

polish: add get path from config file

Browse source
This commit is contained in:
kuoi 2024-09-09 11:33:50 +10:00
parent 9ae0c38656
commit 391dc5c17d
1 changed files with 70 additions and 32 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

102
RGBEPP.d
View file

@ -8,6 +8,7 @@ import std.conv;
import std.array; import std.array;
import std.path; import std.path;
import std.parallelism; import std.parallelism;
import std.regex;
void show_help(string pkgver) { 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 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
@ -107,10 +108,10 @@ string[] getARG_G(string ARG_R){
return ARG_G; return ARG_G;
} }
void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) { void processQualityControl(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, string PathFastp) {
// Prepare directory // Prepare directory
createDir(DirQcTrim); createDir(DirQcTrim);
writeln("QcTrimming::Start");
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string inputFileR1 = DirRaw ~ "/" ~ baseName ~ "_R1.fastq.gz"; string inputFileR1 = DirRaw ~ "/" ~ baseName ~ "_R1.fastq.gz";
@ -121,30 +122,30 @@ void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int
string htmlFile = DirQcTrim ~ "/" ~ baseName ~ ".html"; string htmlFile = DirQcTrim ~ "/" ~ baseName ~ ".html";
// Perform quality control and trimming using external program `fastp` // Perform quality control and trimming using external program `fastp`
string[] cmd = ["fastp", "-i", inputFileR1, "-I", inputFileR2, string[] cmdQcTrim = [PathFastp, "-i", inputFileR1, "-I", inputFileR2,
"-o", outputFileR1, "-O", outputFileR2, "-o", outputFileR1, "-O", outputFileR2,
"-j", jsonFile, "-h", htmlFile, "-j", jsonFile, "-h", htmlFile,
"-w", ARG_T.to!string]; "-w", ARG_T.to!string];
executeCommand(cmd); executeCommand(cmdQcTrim);
} }
writeln("QcTrimming::End");
} }
void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) { void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
writeln("Mapping::Start"); writeln("Mapping::Start");
// Prepare directory // Prepare directory
createDir(DirMap); createDir(DirMap);
createDir(DirMap ~ "/index"); createDir(DirMap ~ "/index");
string PathBowtie2_build = PathBowtie2 ~ "-build";
string[] Refs = getRef(ARG_R, DirMap); string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_index = Refs[0]; // bt2_index_base string ARG_R_index = Refs[0]; // bt2_index_base
string ARG_R_refer = Refs[1]; //reference_in fasta file string ARG_R_refer = Refs[1]; //reference_in fasta file
copy(ARG_R, ARG_R_refer); copy(ARG_R, ARG_R_refer);
string[] cmdBuildDB = ["bowtie2-build", "--threads", ARG_T.to!string, ARG_R_refer, ARG_R_index]; string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, ARG_R_refer, ARG_R_index];
executeCommand(cmdBuildDB); executeCommand(cmdBuildDB);
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
@ -154,9 +155,9 @@ void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMa
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
// Perform mapping using Bowtie2 and converted to Bam using samtools // Perform mapping using Bowtie2 and converted to Bam using samtools
string[] cmdMap = ["bowtie2", "-x", ARG_R_index, "-1", inputFileR1, "-2", inputFileR2, string[] cmdMap = [PathBowtie2, "-x", ARG_R_index, "-1", inputFileR1, "-2", inputFileR2,
"-p", ARG_T.to!string]; "-p", ARG_T.to!string];
string[] cmdSam2Bam = ["samtools", "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam]; string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
executeCommandPipe([cmdMap, cmdSam2Bam]); executeCommandPipe([cmdMap, cmdSam2Bam]);
@ -164,7 +165,7 @@ void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMa
writeln("Mapping::End"); writeln("Mapping::End");
} }
void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) { void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) {
createDir(DirBam); createDir(DirBam);
writeln("PostMapping::Start"); writeln("PostMapping::Start");
@ -175,12 +176,12 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
string outputBam = DirBam ~ "/" ~ baseName ~ ".bam"; string outputBam = DirBam ~ "/" ~ baseName ~ ".bam";
// Convert SAM to BAM, sort and remove duplicates using Samtools // Convert SAM to BAM, sort and remove duplicates using Samtools
string[] cmdFixmate = ["samtools", "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"]; string[] cmdFixmate = [PathSamtools, "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
string[] cmdSort = ["samtools", "sort", "-@", ARG_T.to!string, "-"]; string[] cmdSort = [PathSamtools, "sort", "-@", ARG_T.to!string, "-"];
string[] cmdMarkdup = ["samtools", "markdup", "-@", ARG_T.to!string, "-", outputBam]; string[] cmdMarkdup = [PathSamtools, "markdup", "-@", ARG_T.to!string, "-", outputBam];
executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]); executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
string [] cmdIndexBam = ["samtools", "index", "-@", ARG_T.to!string, outputBam]; string [] cmdIndexBam = [PathSamtools, "index", "-@", ARG_T.to!string, outputBam];
executeCommand(cmdIndexBam); executeCommand(cmdIndexBam);
} }
@ -188,7 +189,7 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
} }
void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, string DirVcf, string DirMap) { void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirBam, string DirVcf, string PathBcftools) {
writeln("VarCalling::Start"); writeln("VarCalling::Start");
string[] Refs = getRef(ARG_R, DirMap); string[] Refs = getRef(ARG_R, DirMap);
@ -202,10 +203,10 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, stri
string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz"; string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
// Variant calling using bcftools // Variant calling using bcftools
string[] cmdPileup = ["bcftools", "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam]; string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
string[] cmdVarCall = ["bcftools", "call", "-mv", "-Oz", "--threads", ARG_T.to!string]; string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
string[] cmdNorm = ["bcftools", "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"]; string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
string[] cmdFilter = ["bcftools", "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf]; string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]); executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
} }
@ -213,7 +214,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, stri
} }
void processCon(string[] ARG_L, string ARG_R, int ARG_T, string[] ARG_G, string DirVcf, string DirConsensus, string DirMap) { void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus); createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa"; string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
@ -231,18 +232,18 @@ void processCon(string[] ARG_L, string ARG_R, int ARG_T, string[] ARG_G, string
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta"; string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
// index vcf.gz // index vcf.gz
string[] cmdIndexVcf = ["bcftools", "index", inputVcf]; string[] cmdIndexVcf = [PathBcftools, "index", inputVcf];
executeCommand(cmdIndexVcf); executeCommand(cmdIndexVcf);
// Generate consensus sequences using bcftools // Generate consensus sequences using bcftools
string[] cmdCon = ["bcftools", "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta]; string[] cmdCon = [PathBcftools, "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
executeCommand(cmdCon); executeCommand(cmdCon);
} }
// Recombine the sequences based on genes // Recombine the sequences based on genes
writeln("Consensus::End"); writeln("Consensus::End");
} }
void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) { void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
string DirConTaxa = DirConsensus ~ "/" ~ "taxa"; string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
string DirConGene = DirConsensus ~ "/" ~ "gene"; string DirConGene = DirConsensus ~ "/" ~ "gene";
@ -305,13 +306,28 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta"; string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta";
string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta"; string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta";
string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta"; string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta";
string[] cmd = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ]; string[] cmdAlign = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
executeCommand(cmd); executeCommand(cmdAlign);
} }
writeln("Align::End"); writeln("Align::End");
} }
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 main(string[] args) { void main(string[] args) {
string pkgver = "0.0.3"; string pkgver = "0.0.3";
@ -325,17 +341,27 @@ void main(string[] args) {
string DirConsensus = DirHome ~ "/05_consen"; string DirConsensus = DirHome ~ "/05_consen";
string DirAlign = DirHome ~ "/06_macse"; string DirAlign = DirHome ~ "/06_macse";
string PathFastp = "/usr/bin/fastp";
string PathBowtie2 = "/usr/bin/bowtie2";
string PathSamtools = "/usr/bin/samtools";
string PathBcftools = "/usr/bin/bcftools";
string PathMacse = "/usr/share/java/macse.jar"; string PathMacse = "/usr/share/java/macse.jar";
string PathTrimal = "/usr/bin/trimal";
int ARG_T = 8; int ARG_T = 8;
string[] ARG_G; string[] ARG_G;
string[] ARG_L; string[] ARG_L;
string ARG_C;
string ARG_F; string ARG_F;
string ARG_R; string ARG_R;
if (args.length > 1){ if (args.length > 1){
foreach (int i; 0 .. cast(int)args.length) { foreach (int i; 0 .. cast(int)args.length) {
switch (args[i]) { switch (args[i]) {
case "-c", "--config":
i++;
ARG_C = args[i];
break;
case "-f", "--functions": case "-f", "--functions":
i++; i++;
ARG_F = args[i]; ARG_F = args[i];
@ -377,27 +403,39 @@ void main(string[] args) {
ARG_G = getARG_G(ARG_R); ARG_G = getARG_G(ARG_R);
} }
// get pathXXX form config file
if (ARG_C != ""){
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");
PathTrimal = getValueFromConfig(ARG_C, "trimal");
}
writeln("RGBEPP::Start"); writeln("RGBEPP::Start");
// Perform steps based on provided function argument // Perform steps based on provided function argument
if (ARG_F == "all" || ARG_F == "clean") { if (ARG_F == "all" || ARG_F == "clean") {
processQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T); processQualityControl(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
} }
if (ARG_F == "all" || ARG_F == "map") { if (ARG_F == "all" || ARG_F == "map") {
processMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T); processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
} }
if (ARG_F == "all" || ARG_F == "postmap") { if (ARG_F == "all" || ARG_F == "postmap") {
processPostMap(ARG_L, ARG_T, DirMap, DirBam); processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
} }
if (ARG_F == "all" || ARG_F == "varcall") { if (ARG_F == "all" || ARG_F == "varcall") {
processVarCall(ARG_L, ARG_R, ARG_T, DirBam, DirVcf, DirMap); processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
} }
if (ARG_F == "all" || ARG_F == "consen") { if (ARG_F == "all" || ARG_F == "consen") {
processCon(ARG_L, ARG_R, ARG_T, ARG_G, DirVcf, DirConsensus,DirMap); processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_L, ARG_G, DirConsensus); processCombFasta(ARG_G, ARG_L, DirConsensus);
} }
if (ARG_F == "all" || ARG_F == "align") { if (ARG_F == "all" || ARG_F == "align") {