polish: get diamond and sortdiamond done
This commit is contained in:
parent
50f99a9575
commit
e89a83a542
1 changed files with 49 additions and 125 deletions
174
RGBEPP.d
174
RGBEPP.d
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@ -26,13 +26,15 @@ void show_help(string pkgver) {
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-r\t--reference\treference genome path
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-t\t--threads\tthreads setting (optional, default 8 threads)
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--fastp\t\tFastp path (optional)
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--spades\t\tSpades python path (optional)
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--diamond\t\tDiamond python path (optional)
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--sortdiamond\t\tSortDiamond python path (optional)
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--bowtie2\t\tBowtie2 path (optional)
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--samtools\t\tSamtools path (optional)
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--bcftools\t\tBcftools path (optional)
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--macse\t\tMacse jarfile path (optional)
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--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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}
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@ -175,6 +177,21 @@ void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, s
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writeln("QcTrimming::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);
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string DirAss = DirAssembly ~ "/" ~ baseName;
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createDir(DirAss);
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string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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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];
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executeCommand(cmdAssembly);
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}
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writeln("Assembly::End");
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}
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void processAssemMv(string[] ARG_L,string DirAssembly){
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// Prepare
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string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
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@ -205,7 +222,7 @@ void processAssemMv(string[] ARG_L,string DirAssembly){
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writeln("Assembly_Move::End");
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}
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void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){
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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){
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// Prepare directory
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writeln("Mapping::Start");
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createDir(DirMap);
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@ -217,7 +234,7 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
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string ARG_R_Base = getBaseName(ARG_R);
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string ARG_R_Ref = DirAssemblyFas ~ "/" ~ ARG_R_Base ~ ".fasta";
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copy(ARG_R, ARG_R_Ref);
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string [] cmdDmMakeDB = [ "diamond", "makedb", "--db", "Reference", "--in", ARG_R_Ref];
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string [] cmdDmMakeDB = [ PathDiamond, "makedb", "--db", "Reference", "--in", ARG_R_Ref];
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executeCommand(cmdDmMakeDB);
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string ReferDmnd = DirAssemblyFas ~ "/" ~ "Reference.dmnd";
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string PathBowtie2_build = PathBowtie2 ~ "-build";
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@ -232,8 +249,8 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
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string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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string outputBam = DirMap ~ "/" ~ baseName ~ ".bam";
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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"];
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string[] cmdSortDiamond = ["sortdiamond", inputM8, outputSort];
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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"];
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string[] cmdSortDiamond = [PathSortDiamond, inputM8, outputSort];
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string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex];
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string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string];
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string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
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@ -246,40 +263,6 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
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writeln("Mapping::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");
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// Prepare directory
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createDir(DirMap);
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createDir(DirMap ~ "/index");
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string PathBowtie2_build = PathBowtie2 ~ "-build";
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_index = Refs[0]; // bt2_index_base
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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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);
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foreach (string file; ARG_L) {
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string baseName = baseName(file, ".fastq.gz");
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string outputBam = DirMap ~ "/" ~ baseName ~ ".bam";
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string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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// 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]);
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}
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writeln("Mapping::End");
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}
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void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) {
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createDir(DirBam);
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@ -327,31 +310,6 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string
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}
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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");
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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createDir(DirVcf);
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foreach (string file; parallel(ARG_L, 1)) {
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string baseName = getBaseName(file);
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string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
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string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
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// Variant calling using bcftools
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string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
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string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
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string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
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string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
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executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
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}
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writeln("VarCalling::End");
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}
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void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssembly, string DirVcf, string DirConsensus, string PathBcftools) {
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createDir(DirConsensus);
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@ -379,35 +337,6 @@ void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssem
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}
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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);
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string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
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createDir(DirConTaxa);
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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writeln("Consensus::Start");
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// Extract fasta from vcf file
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
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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);
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// 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);
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}
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// Recombine the sequences based on genes
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writeln("Consensus::End");
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}
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void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
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string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
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@ -521,21 +450,6 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
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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);
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string DirAss = DirAssembly ~ "/" ~ baseName;
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createDir(DirAss);
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string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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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];
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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) {
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string pkgver = "0.0.3";
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@ -543,22 +457,24 @@ void main(string[] args) {
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string DirRaw = DirHome ~ "/00_raw";
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string DirQcTrim = DirHome ~ "/01_fastp";
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string DirMap = DirHome ~ "/02_bowtie2";
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string DirAssembly = DirHome ~ "/02_spades";
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string DirBam = DirHome ~ "/03_bam";
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string DirVcf = DirHome ~ "/04_vcf";
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string DirConsensus = DirHome ~ "/05_consen";
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string DirConsensus1 = DirHome ~ "/05_consen1";
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string DirAlign = DirHome ~ "/06_macse";
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string DirTrim = DirHome ~ "/07_trimal";
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string DirAssembly = DirHome ~ "/03_spades";
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string DirBam = DirHome ~ "/04_bam";
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string DirVcf = DirHome ~ "/05_vcf";
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string DirConsensus = DirHome ~ "/06_consen";
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string DirConsensus1 = DirHome ~ "/07_consen1";
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string DirAlign = DirHome ~ "/08_macse";
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string DirTrim = DirHome ~ "/09_trimal";
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string PathFastp = "/usr/bin/fastp";
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string PathSpades = "/usr/bin/spades.py";
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string PathDiamond = "/usr/bin/diamond";
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string PathSortDiamond = "/usr/bin/sortdiamond";
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string PathBowtie2 = "/usr/bin/bowtie2";
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string PathSamtools = "/usr/bin/samtools";
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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;
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@ -602,6 +518,18 @@ void main(string[] args) {
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i++;
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PathFastp = args[i];
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break;
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case "--spades":
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i++;
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PathSpades = args[i];
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break;
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case "--diamond":
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i++;
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PathDiamond = args[i];
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break;
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case "--sortdiamond":
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i++;
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PathSortDiamond = args[i];
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break;
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case "--bowtie2":
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i++;
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PathBowtie2 = args[i];
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@ -626,10 +554,6 @@ void main(string[] args) {
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i++;
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PathDelstop = args[i];
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break;
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case "--spades":
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i++;
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PathSpades = args[i];
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break;
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default:
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break;
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}
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@ -648,6 +572,9 @@ void main(string[] args) {
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if (ARG_C != ""){
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PathFastp = getValueFromConfig(ARG_C, "fastp");
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PathSpades = getValueFromConfig(ARG_C, "spades");
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PathDiamond = getValueFromConfig(ARG_C, "diamond");
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PathSortDiamond = getValueFromConfig(ARG_C, "sortdiamond");
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PathBowtie2 = getValueFromConfig(ARG_C, "bowtie2");
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PathSamtools = getValueFromConfig(ARG_C, "samtools");
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PathBcftools = getValueFromConfig(ARG_C, "bcftools");
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@ -674,9 +601,8 @@ void main(string[] args) {
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}
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if (ARG_F == "all" || ARG_F == "map") {
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if(testFiles([PathBowtie2, PathSamtools])){
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//processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
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processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
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if(testFiles([PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond])){
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processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond);
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}
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}
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@ -688,7 +614,6 @@ void main(string[] args) {
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if (ARG_F == "all" || ARG_F == "varcall") {
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if(testFiles([PathBcftools])){
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//processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
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processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools);
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}
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@ -697,7 +622,6 @@ void main(string[] args) {
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if (ARG_F == "all" || ARG_F == "consen") {
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if(testFiles([PathBcftools])){
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//processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
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processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools);
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processCombFasta(ARG_G, ARG_L, DirConsensus);
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}
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