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polish: use buildPath instead of /; add: codon only

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kuoi 2024-12-09 15:23:55 +11:00
parent 78d7aad869
commit 4d3b5c2001
3 changed files with 204 additions and 445 deletions
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275
RGBEPP.d
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@ -25,13 +25,15 @@ void show_help(string pkgver) {
-m\t--memory\tmemory settings (optional, default 16 GB) -m\t--memory\tmemory settings (optional, default 16 GB)
-r\t--reference\treference genome path -r\t--reference\treference genome path
-t\t--threads\tthreads setting (optional, default 8 threads) -t\t--threads\tthreads setting (optional, default 8 threads)
--codon\t\tOnly use the codon region (optional)
--fastp\t\tFastp path (optional) --fastp\t\tFastp path (optional)
--spades\t\tSpades python path (optional) --spades\t\tSpades python path (optional)
--diamond\t\tDiamond python path (optional) --diamond\t\tDiamond python path (optional)
--sortdiamond\t\tSortDiamond python path (optional) --sortdiamond\tSortDiamond python path (optional)
--bowtie2\t\tBowtie2 path (optional) --bowtie2\t\tBowtie2 path (optional)
--samtools\t\tSamtools path (optional) --samtools\t\tSamtools path (optional)
--bcftools\t\tBcftools path (optional) --bcftools\t\tBcftools path (optional)
--exonerate\t\tExonerate path (optional)
--macse\t\tMacse jarfile path (optional) --macse\t\tMacse jarfile path (optional)
--delstop\t\tDelstop path (optional) --delstop\t\tDelstop path (optional)
--trimal\t\tTrimal path (optional) --trimal\t\tTrimal path (optional)
@ -73,6 +75,15 @@ void createDir(string path) {
} }
} }
void moveDir (string oldPath, string newPath) {
try {
rename(oldPath, newPath);
writeln("Directory renamed successfully.");
} catch (Exception e) {
writeln("Error renaming directory: ", e.msg);
}
}
void executeCommand(string[] cmd) { void executeCommand(string[] cmd) {
auto process = spawnProcess(cmd); auto process = spawnProcess(cmd);
@ -81,6 +92,27 @@ void executeCommand(string[] cmd) {
} }
} }
void executeCommandToFile(string[] cmd, string outputFile) {
// Create a pipe for the command's output
auto pipe = pipe();
// Spawn the process
auto pid = spawnProcess(cmd, stdin, pipe.writeEnd);
// Close the write end of the pipe to signal EOF
pipe.writeEnd.close();
// Read the output from the pipe
auto output = cast(string) pipe.readEnd.byChunk(4096).joiner.array;
// Wait for the process to finish
wait(pid);
// Write the output to the specified file
std.file.write(outputFile, cast(ubyte[])output);
}
void executeCommandPipe(string[][] cmds) { void executeCommandPipe(string[][] cmds) {
Pid[] pids; Pid[] pids;
@ -128,7 +160,7 @@ string getBaseName(string ARG_R){
string[] getRef(string ARG_R, string DirMap){ string[] getRef(string ARG_R, string DirMap){
string baseNameRef = getBaseName(ARG_R); string baseNameRef = getBaseName(ARG_R);
string ARG_R_index = DirMap ~ "/index/" ~ baseNameRef; // bt2_index_base string ARG_R_index = buildPath(DirMap, "index", baseNameRef); // bt2_index_base
string ARG_R_refer = ARG_R_index ~ ".fasta"; //reference_in fasta file string ARG_R_refer = ARG_R_index ~ ".fasta"; //reference_in fasta file
string[] Refs = [ARG_R_index, ARG_R_refer]; string[] Refs = [ARG_R_index, ARG_R_refer];
return Refs; return Refs;
@ -168,12 +200,12 @@ void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, s
writeln("QcTrimming::Start"); 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 = buildPath(DirRaw, baseName ~ "_R1.fastq.gz");
string inputFileR2 = DirRaw ~ "/" ~ baseName ~ "_R2.fastq.gz"; string inputFileR2 = buildPath(DirRaw, baseName ~ "_R2.fastq.gz");
string outputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz"; string outputFileR1 = buildPath(DirQcTrim, baseName ~ "_R1.fastq.gz");
string outputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string outputFileR2 = buildPath(DirQcTrim, baseName ~ "_R2.fastq.gz");
string jsonFile = DirQcTrim ~ "/" ~ baseName ~ ".json"; string jsonFile = buildPath(DirQcTrim, baseName ~ ".json");
string htmlFile = DirQcTrim ~ "/" ~ baseName ~ ".html"; string htmlFile = buildPath(DirQcTrim, baseName ~ ".html");
// Perform quality control and trimming using external program `fastp` // Perform quality control and trimming using external program `fastp`
string[] cmdQcTrim = [PathFastp, "-i", inputFileR1, "-I", inputFileR2, string[] cmdQcTrim = [PathFastp, "-i", inputFileR1, "-I", inputFileR2,
@ -190,10 +222,10 @@ void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, str
createDir(DirAssembly); createDir(DirAssembly);
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string DirAss = DirAssembly ~ "/" ~ baseName; string DirAss = buildPath(DirAssembly, baseName);
createDir(DirAss); createDir(DirAss);
string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz"; string inputFileR1 = buildPath(DirQcTrim, baseName ~ "_R1.fastq.gz");
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string inputFileR2 = buildPath(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]; 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); executeCommand(cmdAssembly);
} }
@ -202,18 +234,18 @@ void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, str
void processAssemMv(string[] ARG_L,string DirAssembly){ void processAssemMv(string[] ARG_L,string DirAssembly){
// Prepare // Prepare
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds"; string DirAssemblySca = buildPath(DirAssembly, "scaffolds");
string DirAssemblyCont = DirAssembly ~ "/" ~ "contigs"; string DirAssemblyCont = buildPath(DirAssembly, "contigs");
writeln("Assembly_Move::Start"); writeln("Assembly_Move::Start");
createDir(DirAssemblySca); createDir(DirAssemblySca);
createDir(DirAssemblyCont); createDir(DirAssemblyCont);
foreach (string file; ARG_L ){ foreach (string file; ARG_L ){
string baseName = getBaseName(file); string baseName = getBaseName(file);
string DirAssemblyInd = DirAssembly ~ "/" ~ baseName; string DirAssemblyInd = buildPath(DirAssembly, baseName);
string inputSca = DirAssemblyInd ~ "/" ~ "scaffolds.fasta"; string inputSca = buildPath(DirAssemblyInd, "scaffolds.fasta");
string inputCont = DirAssemblyInd ~ "/" ~ "contigs.fasta"; string inputCont = buildPath(DirAssemblyInd, "contigs.fasta");
string outputSca = DirAssemblySca ~ "/" ~ baseName ~ ".fasta"; string outputSca = buildPath(DirAssemblySca, baseName ~ ".fasta");
string outputCont = DirAssemblyCont ~ "/" ~ baseName ~ ".fasta"; string outputCont = buildPath(DirAssemblyCont, baseName ~ ".fasta");
if (!exists(inputSca)) { if (!exists(inputSca)) {
writeln("File not found: ", inputSca); writeln("File not found: ", inputSca);
continue; continue;
@ -234,28 +266,28 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
// Prepare directory // Prepare directory
writeln("Mapping::Start"); writeln("Mapping::Start");
createDir(DirMap); createDir(DirMap);
createDir(DirMap ~ "/index"); createDir(buildPath(DirMap, "index"));
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds"; string DirAssemblySca = buildPath(DirAssembly, "scaffolds");
string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta"; string DirAssemblyFas = buildPath(DirAssembly, "fasta");
createDir(DirAssemblyFas); createDir(DirAssemblyFas);
string ARG_R_Base = getBaseName(ARG_R); string ARG_R_Base = getBaseName(ARG_R);
string ARG_R_Ref = DirAssemblyFas ~ "/" ~ ARG_R_Base ~ ".fasta"; string ARG_R_Ref = buildPath(DirAssemblyFas, ARG_R_Base ~ ".fasta");
copy(ARG_R, ARG_R_Ref); copy(ARG_R, ARG_R_Ref);
string [] cmdDmMakeDB = [ PathDiamond, "makedb", "--db", "Reference", "--in", ARG_R_Ref]; string [] cmdDmMakeDB = [ PathDiamond, "makedb", "--db", "Reference", "--in", ARG_R_Ref];
executeCommand(cmdDmMakeDB); executeCommand(cmdDmMakeDB);
string ReferDmnd = DirAssemblyFas ~ "/" ~ "Reference.dmnd"; string ReferDmnd = buildPath(DirAssemblyFas, "Reference.dmnd");
string PathBowtie2_build = PathBowtie2 ~ "-build"; string PathBowtie2_build = PathBowtie2 ~ "-build";
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string inputM8 = DirAssemblySca ~ "/" ~ baseName ~ ".m8"; string inputM8 = buildPath(DirAssemblySca, baseName ~ ".m8");
string inputFasta = DirAssemblySca ~ "/" ~ baseName ~ ".fasta"; string inputFasta = buildPath(DirAssemblySca, baseName ~ ".fasta");
string outputSort = DirAssemblyFas ~ "/" ~ baseName ~ ".fasta"; string outputSort = buildPath(DirAssemblyFas, baseName ~ ".fasta");
string outputIndex = DirAssemblyFas ~ "/" ~ baseName; string outputIndex = buildPath(DirAssemblyFas, baseName);
string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz"; string inputFileR1 = buildPath(DirQcTrim, baseName ~ "_R1.fastq.gz");
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string inputFileR2 = buildPath(DirQcTrim, baseName ~ "_R2.fastq.gz");
string outputBam = DirMap ~ "/" ~ baseName ~ ".bam"; string outputBam = buildPath(DirMap, baseName ~ ".bam");
string[] cmdDiamond = [PathDiamond, "blastx", "-d", "Reference.dmnd", "-q", inputFasta, "-o", inputM8, "--outfmt", "6", "qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore", "qlen", "slen", "gaps", "ppos", "qframe", "qseq"]; string[] cmdDiamond = [PathDiamond, "blastx", "-d", "Reference.dmnd", "-q", inputFasta, "-o", inputM8, "--outfmt", "6", "qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore", "qlen", "slen", "gaps", "ppos", "qframe", "qseq"];
string[] cmdSortDiamond = [PathSortDiamond, inputM8, outputSort]; string[] cmdSortDiamond = [PathSortDiamond, inputM8, outputSort];
@ -278,8 +310,8 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, str
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string inputBam = DirMap ~ "/" ~ baseName ~ ".bam"; string inputBam = buildPath(DirMap, baseName ~ ".bam");
string outputBam = DirBam ~ "/" ~ baseName ~ ".bam"; string outputBam = buildPath(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 = [PathSamtools, "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"]; string[] cmdFixmate = [PathSamtools, "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
@ -297,14 +329,14 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, str
void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string DirMap, string DirBam, string DirVcf, string PathBcftools) { void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string DirMap, string DirBam, string DirVcf, string PathBcftools) {
writeln("VarCalling::Start"); writeln("VarCalling::Start");
string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta"; string DirAssemblyFas = buildPath(DirAssembly, "fasta");
createDir(DirVcf); createDir(DirVcf);
foreach (string file; parallel(ARG_L, 1)) { foreach (string file; parallel(ARG_L, 1)) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam"; string inputBam = buildPath(DirBam, baseName ~ ".bam");
string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz"; string outputVcf = buildPath(DirVcf, baseName ~ ".vcf.gz");
string referFasta = DirAssemblyFas ~ "/" ~ baseName ~ ".fasta"; string referFasta = buildPath(DirAssemblyFas, baseName ~ ".fasta");
// Variant calling using bcftools // Variant calling using bcftools
string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", referFasta, inputBam]; string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", referFasta, inputBam];
string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string]; string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
@ -321,17 +353,17 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string
void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssembly, string DirVcf, string DirConsensus, string PathBcftools) { void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssembly, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus); createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa"; string DirConTaxa = buildPath(DirConsensus, "taxa");
string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta"; string DirAssemblyFas = buildPath(DirAssembly, "fasta");
createDir(DirConTaxa); createDir(DirConTaxa);
writeln("Consensus::Start"); writeln("Consensus::Start");
// Extract fasta from vcf file // Extract fasta from vcf file
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz"; string inputVcf = buildPath(DirVcf, baseName ~ ".vcf.gz");
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta"; string outputFasta = buildPath(DirConTaxa, baseName ~ ".fasta");
string referFasta = DirAssemblyFas ~ "/" ~ baseName ~ ".fasta"; string referFasta = buildPath(DirAssemblyFas, baseName ~ ".fasta");
// index vcf.gz // index vcf.gz
string[] cmdIndexVcf = [PathBcftools, "index", inputVcf]; string[] cmdIndexVcf = [PathBcftools, "index", inputVcf];
executeCommand(cmdIndexVcf); executeCommand(cmdIndexVcf);
@ -347,8 +379,8 @@ void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssem
void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) { void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
string DirConTaxa = DirConsensus ~ "/" ~ "taxa"; string DirConTaxa = buildPath(DirConsensus, "taxa");
string DirConGene = DirConsensus ~ "/" ~ "gene"; string DirConGene = buildPath(DirConsensus, "gene");
createDir(DirConGene); createDir(DirConGene);
// create a dictory // create a dictory
@ -357,7 +389,7 @@ void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
writeln("ConvertFasta::Start"); writeln("ConvertFasta::Start");
// read first // read first
foreach (file; ARG_L) { foreach (file; ARG_L) {
string inputFile = DirConTaxa ~ "/" ~ file ~ ".fasta"; string inputFile = buildPath(DirConTaxa, file ~ ".fasta");
if (!exists(inputFile)) { if (!exists(inputFile)) {
writeln("File not found: ", inputFile); writeln("File not found: ", inputFile);
continue; continue;
@ -385,7 +417,7 @@ void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
} }
// write different files // write different files
foreach (gene; ARG_G) { foreach (gene; ARG_G) {
string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta"; string outputFile = buildPath(DirConGene, gene ~ ".fasta");
File output = File(outputFile, "w"); File output = File(outputFile, "w");
if (gene in geneSequences) { if (gene in geneSequences) {
output.write(geneSequences[gene]); output.write(geneSequences[gene]);
@ -394,20 +426,99 @@ void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
writeln("ConvertFasta::End"); writeln("ConvertFasta::End");
} }
void splitFasta(const string inputFasta) {
File infile;
try {
infile = File(inputFasta, "r");
} catch (FileException e) {
stderr.writeln("Error: Unable to open input file ", inputFasta);
return;
}
string line;
string seqName;
File outfile;
bool in_sequence = false;
foreach (lineContent; infile.byLine()) {
if (lineContent.empty) continue;
if (lineContent[0] == '>') {
// New sequence header
if (in_sequence) { // if found new sequence, close
outfile.close(); // previous output file
}
seqName = cast(string)lineContent[1 .. $]; // Remove '>'
string outputFile = seqName ~ ".fasta"; // suitable to many os
outfile = File(outputFile, "w");
outfile.writeln(">", getBaseName(inputFasta));
// will enter sequence
in_sequence = true;
} else if (in_sequence) {
// Inside sequence content
outfile.writeln(lineContent);
}
}
if (in_sequence) {
outfile.close();
}
if (infile.eof) {
writeln("Sequences have been split into individual files.");
} else {
stderr.writeln("Error occurred while reading file.");
}
infile.close();
}
void processCodon(string[] ARG_G, string ARG_R, string DirConsensus, string PathExonerate){
string DirConGene = buildPath(DirConsensus , "gene");
string ARG_R_Base = getBaseName(ARG_R);
string ARG_R_Ref = buildPath(DirConsensus, ARG_R_Base ~ ".fasta");
copy(ARG_R, ARG_R_Ref);
splitFasta(ARG_R_Ref);
moveDir(DirConGene, DirConGene ~ "_bak");
writeln("GetCodon::Start");
foreach (gene; ARG_G) {
string inputFile = buildPath(DirConGene ~ "_bak", gene ~ ".fasta");
string outputFile = buildPath(DirConGene, gene ~ ".fasta");
string referFile = buildPath(DirConsensus, gene ~ ".fasta");
if (!exists(inputFile)) {
writeln("File not found: ", inputFile);
continue;
} else {
string[] cmdExonerate = [PathExonerate, inputFile, referFile, "--showalignment", "no", "--showvulgar", "no", "--showtargetgff", "no", "--ryo", "\">%qi\n%qcs\n\"", "--verbose", "0"];
executeCommandToFile(cmdExonerate, outputFile);
}
std.file.remove(referFile);
}
rmdirRecurse(DirConGene ~ "_bak");
writeln("GetCodon::End");
}
void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){
string DirConGene = DirConsensus ~ "/" ~ "gene"; string DirConGene = buildPath(DirConsensus, "gene");
string DirAlignAA = DirAlign ~ "/" ~ "AA"; string DirAlignAA = buildPath(DirAlign, "AA");
string DirAlignNT = DirAlign ~ "/" ~ "NT"; string DirAlignNT = buildPath(DirAlign, "NT");
writeln("Align::Start"); writeln("Align::Start");
createDir(DirAlign); createDir(DirAlign);
createDir(DirAlignAA); createDir(DirAlignAA);
createDir(DirAlignNT); createDir(DirAlignNT);
foreach (gene; parallel(ARG_G, 1)) { foreach (gene; parallel(ARG_G, 1)) {
string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta"; string inputFasta = buildPath(DirConGene, gene ~ ".fasta");
string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta"; string outAA = buildPath(DirAlignAA, gene ~ ".fasta");
string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta"; string outNT = buildPath(DirAlignNT, gene ~ ".fasta");
string[] cmdAlign = ["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(cmdAlign); executeCommand(cmdAlign);
} }
@ -418,20 +529,20 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){
writeln("Trimming::Start"); writeln("Trimming::Start");
string DirAA = DirAlign ~ "/" ~ "AA"; string DirAA = buildPath(DirAlign, "AA");
string DirNT = DirAlign ~ "/" ~ "NT"; string DirNT = buildPath(DirAlign, "NT");
string DirAA_out = DirAlign ~ "/" ~ "AA_out"; string DirAA_out = buildPath(DirAlign, "AA_out");
string DirNT_out = DirAlign ~ "/" ~ "NT_out"; string DirNT_out = buildPath(DirAlign, "NT_out");
createDir(DirAA_out); createDir(DirAA_out);
createDir(DirNT_out); createDir(DirNT_out);
// copy file firstly // copy file firstly
foreach (gene; parallel(ARG_G,1)){ foreach (gene; parallel(ARG_G,1)){
string inputFastaAA = DirAA ~ "/" ~ gene ~ ".fasta"; string inputFastaAA = buildPath(DirAA, gene ~ ".fasta");
string outputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta"; string outputFastaAA = buildPath(DirAA_out, gene ~ ".fasta");
string inputFastaNT = DirNT ~ "/" ~ gene ~ ".fasta"; string inputFastaNT = buildPath(DirNT, gene ~ ".fasta");
string outputFastaNT = DirNT_out ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = buildPath(DirNT_out, gene ~ ".fasta");
copy(inputFastaNT, outputFastaNT); copy(inputFastaNT, outputFastaNT);
copy(inputFastaAA, outputFastaAA); copy(inputFastaAA, outputFastaAA);
@ -440,13 +551,13 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
executeCommand(cmdDelStop); executeCommand(cmdDelStop);
} }
string DirTrimNT = DirTrim ~ "/" ~ "NT"; string DirTrimNT = buildPath(DirTrim, "NT");
createDir(DirTrim); createDir(DirTrim);
createDir(DirTrimNT); createDir(DirTrimNT);
foreach (gene; parallel(ARG_G,1)){ foreach (gene; parallel(ARG_G,1)){
string inputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta"; string inputFastaAA = buildPath(DirAA_out, gene ~ ".fasta");
string inputBackTransNT = DirNT_out ~ "/" ~ gene ~ ".fasta"; string inputBackTransNT = buildPath(DirNT_out, gene ~ ".fasta");
string outputFastaNT = DirTrimNT ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = buildPath(DirTrimNT, gene ~ ".fasta");
if (exists(inputFastaAA) && exists(inputBackTransNT)) { if (exists(inputFastaAA) && exists(inputBackTransNT)) {
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"]; string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"];
executeCommand(cmdTrim); executeCommand(cmdTrim);
@ -462,16 +573,16 @@ void main(string[] args) {
string pkgver = "0.0.3"; string pkgver = "0.0.3";
string DirHome = std.file.getcwd(); string DirHome = std.file.getcwd();
string DirRaw = DirHome ~ "/00_raw"; string DirRaw = buildPath(DirHome, "00_raw");
string DirQcTrim = DirHome ~ "/01_fastp"; string DirQcTrim = buildPath(DirHome, "01_fastp");
string DirMap = DirHome ~ "/02_bowtie2"; string DirMap = buildPath(DirHome, "02_bowtie2");
string DirAssembly = DirHome ~ "/03_spades"; string DirAssembly = buildPath(DirHome, "03_spades");
string DirBam = DirHome ~ "/04_bam"; string DirBam = buildPath(DirHome, "04_bam");
string DirVcf = DirHome ~ "/05_vcf"; string DirVcf = buildPath(DirHome, "05_vcf");
string DirConsensus = DirHome ~ "/06_consen"; string DirConsensus = buildPath(DirHome, "06_consen");
string DirConsensus1 = DirHome ~ "/07_consen1"; string DirConsensus1 = buildPath(DirHome, "07_consen1");
string DirAlign = DirHome ~ "/08_macse"; string DirAlign = buildPath(DirHome, "08_macse");
string DirTrim = DirHome ~ "/09_trimal"; string DirTrim = buildPath(DirHome, "09_trimal");
string PathFastp = "/usr/bin/fastp"; string PathFastp = "/usr/bin/fastp";
string PathSpades = "/usr/bin/spades.py"; string PathSpades = "/usr/bin/spades.py";
@ -480,6 +591,7 @@ void main(string[] args) {
string PathBowtie2 = "/usr/bin/bowtie2"; string PathBowtie2 = "/usr/bin/bowtie2";
string PathSamtools = "/usr/bin/samtools"; string PathSamtools = "/usr/bin/samtools";
string PathBcftools = "/usr/bin/bcftools"; string PathBcftools = "/usr/bin/bcftools";
string PathExonerate = "/usr/bin/exonerate";
string PathMacse = "/usr/share/java/macse.jar"; string PathMacse = "/usr/share/java/macse.jar";
string PathDelstop = "/usr/bin/delstop"; string PathDelstop = "/usr/bin/delstop";
string PathTrimal = "/usr/bin/trimal"; string PathTrimal = "/usr/bin/trimal";
@ -491,6 +603,7 @@ void main(string[] args) {
string ARG_C; string ARG_C;
string ARG_F; string ARG_F;
string ARG_R; string ARG_R;
bool enableCodon = false;
if (args.length > 1){ if (args.length > 1){
foreach (int i; 0 .. cast(int)args.length) { foreach (int i; 0 .. cast(int)args.length) {
@ -522,6 +635,9 @@ void main(string[] args) {
i++; i++;
ARG_T = args[i].to!int; ARG_T = args[i].to!int;
break; break;
case "--codon":
enableCodon = true;
break;
case "--fastp": case "--fastp":
i++; i++;
PathFastp = args[i]; PathFastp = args[i];
@ -550,6 +666,10 @@ void main(string[] args) {
i++; i++;
PathBcftools = args[i]; PathBcftools = args[i];
break; break;
case "--exonerate":
i++;
PathExonerate = args[i];
break;
case "--macse": case "--macse":
i++; i++;
PathMacse = args[i]; PathMacse = args[i];
@ -586,6 +706,7 @@ void main(string[] args) {
PathBowtie2 = getValueFromConfig(ARG_C, "bowtie2"); PathBowtie2 = getValueFromConfig(ARG_C, "bowtie2");
PathSamtools = getValueFromConfig(ARG_C, "samtools"); PathSamtools = getValueFromConfig(ARG_C, "samtools");
PathBcftools = getValueFromConfig(ARG_C, "bcftools"); PathBcftools = getValueFromConfig(ARG_C, "bcftools");
PathExonerate = getValueFromConfig(ARG_C, "exonerate");
PathMacse = getValueFromConfig(ARG_C, "macse"); PathMacse = getValueFromConfig(ARG_C, "macse");
PathDelstop = getValueFromConfig(ARG_C, "delstop"); PathDelstop = getValueFromConfig(ARG_C, "delstop");
PathTrimal = getValueFromConfig(ARG_C, "trimal"); PathTrimal = getValueFromConfig(ARG_C, "trimal");
@ -644,6 +765,14 @@ void main(string[] args) {
} }
} }
if (ARG_F == "all" && enableCodon) {
if(testFiles([PathExonerate]) && testStringArray(ARG_G) && testString(ARG_R)){
processCodon(ARG_G, ARG_R, DirConsensus, PathExonerate); //ARG_G
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "align") { if (ARG_F == "all" || ARG_F == "align") {
if(testFiles([PathMacse]) && testJava && testStringArray(ARG_G)){ if(testFiles([PathMacse]) && testJava && testStringArray(ARG_G)){
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse); //ARG_G processAlign(ARG_G, DirConsensus, DirAlign, PathMacse); //ARG_G

371
RGBEPP.sh
View file

@ -1,371 +0,0 @@
#!/bin/bash
### Environment Setting
pkgver=0.0.2
DirHome=$(pwd)
DirRaw=$DirHome/00_raw
DirQcTrim=$DirHome/01_fastp
DirAssembly=$DirHome/02_spades
DirFasta=$DirHome/03_assemblied
DirMap=$DirHome/04_diamond
DirPre=$DirHome/05_pre
DirSplit=$DirHome/06_split
DirMerge=$DirHome/07_merge
DirAlign=$DirHome/08_macse
PathSplitfsata=/usr/bin/splitfasta-cpp
PathMacse=/usr/share/java/macse.jar
PathSortdiamond=/usr/bin/sortdiamond
ARG_C='scaffolds'
ARG_M=16
ARG_T=8
### Get some arrays
show_help(){
# echo -e "\t\t\t\t\t\t\t\033[0;31mR\033[0m\033[0;92mG\033[0m\033[0;94mB\033[0m \033[0;33mE\033[0m\033[0;94mP\033[0m\033[0;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
echo -e "\t\t\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\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
Version: $pkgver\n \
License: GPL-2.0-only\n \
Author: Guoyi Zhang\n \
-c\t--contigs\tcontings type: scaffolds or contigs\n \
-g\t--genes\t\tgene file path\n \
-f\t--functions\tfunctions type (optional): all clean \n \
\t \t\tassembly fasta map pre split merge align\n \
-h\t--help\t\tshow this information\n \
-l\t--list\t\tlist file path\n \
-m\t--memory\tmemory settings (optional, default 16 GB)\n \
-r\t--reference\treference genome path\n \
-t\t--threads\tthreads setting (optional, default 8 threads)\n \
\t--macse\t\tMacse jarfile path\n \
\t--sortdiamond\tsortdiamond file path\n \
\t--splitfasta\tsplitfasta file path\n \
for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
\t -r reference.aa.fas \n"
}
if [ $# -eq 0 ]; then
show_help
exit 1
else
ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads:,macse:,sortdiamond:,splitfasta: -n 'RGBEPP.sh' -- "$@")
if [ $? != 0 ]; then
echo "Failed to parse options." >&2
exit 1
fi
eval set -- "$ARGS"
while true; do
case "$1" in
-c|--contigs)
case "$2" in
"") shift 2 ;;
*) ARG_C=$2; shift 2 ;;
esac ;;
-g|--genes)
case "$2" in
"") shift 2 ;;
*) ARG_G=$2; shift 2 ;;
esac ;;
-f|--functions)
case "$2" in
"") shift 2 ;;
*) ARG_F=$2; shift 2 ;;
esac ;;
-h|--help)
show_help
shift ;;
-l|--list)
case "$2" in
"") shift 2 ;;
*) ARG_L=$2; shift 2 ;;
esac ;;
-m|--memory)
case "$2" in
"") shift 2 ;;
*) ARG_M=$2; shift 2 ;;
esac ;;
-r|--reference)
case "$2" in
"") shift 2 ;;
*) ARG_R=$2; shift 2 ;;
esac ;;
-t|--threads)
case "$2" in
"") shift 2 ;;
*) ARG_T=$2; shift 2 ;;
esac ;;
--macse)
case "$2" in
"") shift 2 ;;
*) PathMacse=$2; shift 2 ;;
esac ;;
--sortdiamond)
case "$2" in
"") shift 2 ;;
*) PathSortdiamond=$2; shift 2 ;;
esac ;;
--splitfasta)
case "$2" in
"") shift 2 ;;
*) PathSplitfsata=$2; shift 2 ;;
esac ;;
--)
shift; break ;;
*) echo "Unknown option: $1"
exit 1
;;
esac
done
fi
### Get and check some arguments
check_var() {
local var_name="$1"
local var_value="${!var_name}" # get value
if [ -z "$var_value" ]; then
echo "Error: $var_name is not set or is empty"
exit 1
else
echo "$var_name is set to: $var_value"
case "$var_name" in
"ARG_G")
readarray -t genes < "$var_value"
length_gn=${#genes[@]}
;;
"ARG_L")
readarray -t full_names < "$var_value"
length_fn=${#full_names[@]}
;;
"ARG_F")
check_command "cp"
check_command "cd"
check_command "mv"
check_command "find"
check_command "mkdir"
;;
esac
fi
}
check_path(){
local path_name="$1"
local path_value="${!path_name}" # get value
# expand ~
path_value=$(eval echo "$path_value")
if [ -e "$path_value" ]; then
echo "$path_name exists at: $path_value"
else
echo "Error: $path_name does not exist at: $path_value"
exit 1
fi
}
check_command() {
local cmd_name="$1"
if command -v "$cmd_name" >/dev/null 2>&1; then
echo "$cmd_name command exists."
else
echo "Error: $cmd_name command not found."
exit 1
fi
}
### Quality control && Trimming
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "clean" ]; then
## Prepare
mkdir -p $DirQcTrim
check_var "ARG_L"
check_command "fastp"
readarray -t full_names < "$ARG_L"
length_fn=${#full_names[@]}
readarray -t genes < "$ARG_G"
length_gn=${#genes[@]}
## Quality control and trimming using fastp
for (( i=0; i<$length_fn; i++ )); do
fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j $DirQcTrim/${full_names[$i]}.json -h $DirQcTrim/${full_names[$i]}.html -o $DirQcTrim/${full_names[$i]}_R1.fastq.gz -O $DirQcTrim/${full_names[$i]}_R2.fastq.gz -w $ARG_T
done
fi
### De novo assembly
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "assembly" ]; then
## Prepare
mkdir -p $DirAssembly
check_var "ARG_L"
check_command "spades.py"
## De novo assembly using spades
for (( i=0; i<$length_fn; i++ )); do
mkdir -p $DirAssembly/${full_names[$i]}
spades.py --pe1-1 $DirQcTrim/${full_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${full_names[$i]}_R2.fastq.gz -t $ARG_T -m $ARG_M --careful --phred-offset 33 -o $DirAssembly/${full_names[$i]}
# -k 96,107,117,127 \
done
fi
### Moving scaffords or Contigs out
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "fasta" ]; then
## Check if the contigs type is specified
check_var "ARG_C"
check_var "ARG_L"
## Prepare
mkdir -p $DirFasta
## Move the assemblied fasta file to the folder
if [ "$ARG_C" = "scaffolds" ] || [ "$ARG_C" = "contigs" ] ; then
for (( i=0; i<$length_fn; i++ )); do
cp $DirAssembly/${full_names[$i]}/$ARG_C.fasta $DirFasta/$ARG_C/${full_names[$i]}.fasta
done
fi
fi
### Mapping
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
## Check if the reference or contigs type is specified
check_var "ARG_C"
check_var "ARG_R"
check_command "diamond"
## Prepare
mkdir -p $DirMap
## Index reference database
cd $DirFasta/$ARG_C
diamond makedb --db Reference --in $ARG_R
cd -
## Blastx for mapping DNA sequences to protein reference sequence
cd $DirFasta/$ARG_C
for (( i=0; i<$length_fn; i++ )); do
diamond blastx -d Reference.dmnd -q ${full_names[$i]}.fasta -o ${full_names[$i]}.m8 \
--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen gaps ppos qframe qseq
# subject: reference; query: align-aimed
#1: qseqid: Query Seq-id
#2: sseqid: Subject Seq - id
#3: pident: Percentage of identical matches
#4: length: Alignment length
#5: mismatch: Number of mismatches
#6: gapopen: Number of gap openings
#7: qstart: Start of alignment in query
#8: qend: End of alignment in query
#9: sstart: Start of alignment in subject
#10: send: End of alignment in subject
#11: evalue: Expect value
#12: bitscore: Bit score
#13: qlen: Query sequence length
#14: slen: Subject sequence length
#15: gaps: Total number of gaps
#16: ppos: Percentage of positive - scoring matches
#17: qframe: Query frame (frames in blast?)
#18: qseq: Aligned part of query sequence
done
cd -
mv $DirFasta/$ARG_C/*.m8 $DirMap
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
mkdir -p $DirPre
check_var "ARG_L"
check_path "PathSortdiamond"
# extract fasta file from diamond balst style output
for (( i=0; i<$length_fn; i++ )); do
$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
done
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
mkdir -p $DirSplit
cd $DirPre
check_var "ARG_L"
check_path "PathSplitfasta"
# split fasta into different folders based on sequence names
for (( i=0; i<$length_fn; i++ )); do
$PathSplitfsata ${full_names[$i]}.fasta
done
# mv to destdir
find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
cd -
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
## Check if the genes is specified
check_var "ARG_G"
mkdir -p $DirMerge
cd $DirSplit
# merge different taxa sequences in same gene to one fasta
for (( i=0; i<$length_gn; i++ ))
do
cd ${genes[$i]}
cat * > ../${genes[$i]}.fasta
cd ..
done
# mv to destdir
mv *.fasta ../$DirMerge
cd -
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
## Check if the genes is specified
check_var "ARG_G"
check_command "java"
check_command "parallel"
check_path "PathMacse"
# current_thread=0
mkdir -p $DirAlign
mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
cd $DirMerge
# align the sequence based on codon
parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
cd -
fi

1
config.example
View file

@ -5,6 +5,7 @@ sortdiamond = /usr/bin/sortdiamond
bowtie2 = /usr/bin/bowtie2 bowtie2 = /usr/bin/bowtie2
samtools = /usr/bin/samtools samtools = /usr/bin/samtools
bcftools = /usr/bin/bcftools bcftools = /usr/bin/bcftools
exonerate = /usr/bin/exonerate
macse = /usr/share/java/macse.jar macse = /usr/share/java/macse.jar
delstop = /usr/bin/delstop delstop = /usr/bin/delstop
trimal = /usr/bin/trimal trimal = /usr/bin/trimal