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polish: get diamond and sortdiamond done

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This commit is contained in:
kuoi 2024-12-08 17:15:43 +11:00
parent 50f99a9575
commit e89a83a542
1 changed files with 49 additions and 125 deletions
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174
RGBEPP.d
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@ -26,13 +26,15 @@ void show_help(string pkgver) {
-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)
--fastp\t\tFastp path (optional) --fastp\t\tFastp path (optional)
--spades\t\tSpades python path (optional)
--diamond\t\tDiamond python path (optional)
--sortdiamond\t\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)
--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)
--spades\t\tSpades python path (optional)
for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n"); for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n");
} }
@ -175,6 +177,21 @@ void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, s
writeln("QcTrimming::End"); writeln("QcTrimming::End");
} }
void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){
writeln("Assembly::Start");
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);
}
writeln("Assembly::End");
}
void processAssemMv(string[] ARG_L,string DirAssembly){ void processAssemMv(string[] ARG_L,string DirAssembly){
// Prepare // Prepare
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds"; string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
@ -205,7 +222,7 @@ void processAssemMv(string[] ARG_L,string DirAssembly){
writeln("Assembly_Move::End"); writeln("Assembly_Move::End");
} }
void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathDiamond, string PathSamtools, string PathSortDiamond){
// Prepare directory // Prepare directory
writeln("Mapping::Start"); writeln("Mapping::Start");
createDir(DirMap); createDir(DirMap);
@ -217,7 +234,7 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
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 = DirAssemblyFas ~ "/" ~ ARG_R_Base ~ ".fasta";
copy(ARG_R, ARG_R_Ref); copy(ARG_R, ARG_R_Ref);
string [] cmdDmMakeDB = [ "diamond", "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 = DirAssemblyFas ~ "/" ~ "Reference.dmnd";
string PathBowtie2_build = PathBowtie2 ~ "-build"; string PathBowtie2_build = PathBowtie2 ~ "-build";
@ -232,8 +249,8 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
string outputBam = DirMap ~ "/" ~ baseName ~ ".bam"; string outputBam = DirMap ~ "/" ~ baseName ~ ".bam";
string[] cmdDiamond = ["diamond", "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 = ["sortdiamond", inputM8, outputSort]; string[] cmdSortDiamond = [PathSortDiamond, inputM8, outputSort];
string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex]; string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex];
string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string]; string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string];
string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam]; string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
@ -246,40 +263,6 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
writeln("Mapping::End"); writeln("Mapping::End");
} }
void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
writeln("Mapping::Start");
// Prepare directory
createDir(DirMap);
createDir(DirMap ~ "/index");
string PathBowtie2_build = PathBowtie2 ~ "-build";
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);
string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, ARG_R_refer, ARG_R_index];
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
string[] cmdMap = [PathBowtie2, "-x", ARG_R_index, "-1", inputFileR1, "-2", inputFileR2,
"-p", ARG_T.to!string];
string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
executeCommandPipe([cmdMap, cmdSam2Bam]);
}
writeln("Mapping::End");
}
void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) { void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) {
createDir(DirBam); createDir(DirBam);
@ -327,31 +310,6 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string
} }
void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirBam, string DirVcf, string PathBcftools) {
writeln("VarCalling::Start");
string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_refer = Refs[1]; //reference_in fasta file
createDir(DirVcf);
foreach (string file; parallel(ARG_L, 1)) {
string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
// Variant calling using bcftools
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];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}
writeln("VarCalling::End");
}
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);
@ -379,35 +337,6 @@ void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssem
} }
void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
createDir(DirConTaxa);
string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_refer = Refs[1]; //reference_in fasta file
writeln("Consensus::Start");
// Extract fasta from vcf file
foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
// index vcf.gz
string[] cmdIndexVcf = [PathBcftools, "index", inputVcf];
executeCommand(cmdIndexVcf);
// Generate consensus sequences using bcftools
string[] cmdCon = [PathBcftools, "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
executeCommand(cmdCon);
}
// Recombine the sequences based on genes
writeln("Consensus::End");
}
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 = DirConsensus ~ "/" ~ "taxa";
@ -521,21 +450,6 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
} }
void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){
writeln("Assembly::Start");
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);
}
writeln("Assembly::End");
}
void main(string[] args) { void main(string[] args) {
string pkgver = "0.0.3"; string pkgver = "0.0.3";
@ -543,22 +457,24 @@ void main(string[] args) {
string DirRaw = DirHome ~ "/00_raw"; string DirRaw = DirHome ~ "/00_raw";
string DirQcTrim = DirHome ~ "/01_fastp"; string DirQcTrim = DirHome ~ "/01_fastp";
string DirMap = DirHome ~ "/02_bowtie2"; string DirMap = DirHome ~ "/02_bowtie2";
string DirAssembly = DirHome ~ "/02_spades"; string DirAssembly = DirHome ~ "/03_spades";
string DirBam = DirHome ~ "/03_bam"; string DirBam = DirHome ~ "/04_bam";
string DirVcf = DirHome ~ "/04_vcf"; string DirVcf = DirHome ~ "/05_vcf";
string DirConsensus = DirHome ~ "/05_consen"; string DirConsensus = DirHome ~ "/06_consen";
string DirConsensus1 = DirHome ~ "/05_consen1"; string DirConsensus1 = DirHome ~ "/07_consen1";
string DirAlign = DirHome ~ "/06_macse"; string DirAlign = DirHome ~ "/08_macse";
string DirTrim = DirHome ~ "/07_trimal"; string DirTrim = DirHome ~ "/09_trimal";
string PathFastp = "/usr/bin/fastp"; string PathFastp = "/usr/bin/fastp";
string PathSpades = "/usr/bin/spades.py";
string PathDiamond = "/usr/bin/diamond";
string PathSortDiamond = "/usr/bin/sortdiamond";
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 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";
string PathSpades = "/usr/bin/spades.py";
int ARG_T = 8; int ARG_T = 8;
int ARG_M = 16; int ARG_M = 16;
@ -602,6 +518,18 @@ void main(string[] args) {
i++; i++;
PathFastp = args[i]; PathFastp = args[i];
break; break;
case "--spades":
i++;
PathSpades = args[i];
break;
case "--diamond":
i++;
PathDiamond = args[i];
break;
case "--sortdiamond":
i++;
PathSortDiamond = args[i];
break;
case "--bowtie2": case "--bowtie2":
i++; i++;
PathBowtie2 = args[i]; PathBowtie2 = args[i];
@ -626,10 +554,6 @@ void main(string[] args) {
i++; i++;
PathDelstop = args[i]; PathDelstop = args[i];
break; break;
case "--spades":
i++;
PathSpades = args[i];
break;
default: default:
break; break;
} }
@ -648,6 +572,9 @@ void main(string[] args) {
if (ARG_C != ""){ if (ARG_C != ""){
PathFastp = getValueFromConfig(ARG_C, "fastp"); PathFastp = getValueFromConfig(ARG_C, "fastp");
PathSpades = getValueFromConfig(ARG_C, "spades");
PathDiamond = getValueFromConfig(ARG_C, "diamond");
PathSortDiamond = getValueFromConfig(ARG_C, "sortdiamond");
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");
@ -674,9 +601,8 @@ void main(string[] args) {
} }
if (ARG_F == "all" || ARG_F == "map") { if (ARG_F == "all" || ARG_F == "map") {
if(testFiles([PathBowtie2, PathSamtools])){ if(testFiles([PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond])){
//processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools); processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond);
processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
} }
} }
@ -688,7 +614,6 @@ void main(string[] args) {
if (ARG_F == "all" || ARG_F == "varcall") { if (ARG_F == "all" || ARG_F == "varcall") {
if(testFiles([PathBcftools])){ if(testFiles([PathBcftools])){
//processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools); processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools);
} }
@ -697,7 +622,6 @@ void main(string[] args) {
if (ARG_F == "all" || ARG_F == "consen") { if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){ if(testFiles([PathBcftools])){
//processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools); processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus); processCombFasta(ARG_G, ARG_L, DirConsensus);
} }