malacology/RGBEPP
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polish: adjust some parameters

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kuoi 2025-02-14 14:08:21 +11:00
parent a09fd55086
commit 1c73eb1479
2 changed files with 5 additions and 5 deletions
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6
RGBEPP.d
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@ -289,7 +289,7 @@ void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcT
string inputFileR2 = buildPath(DirQcTrim, baseName ~ "_R2.fastq.gz");
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, "--ultra-sensitive", "--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[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex];
string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string];
@ -341,7 +341,7 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string
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[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", referFasta, "--check-ref", "s", "-Oz"];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "-Oz", "-o", outputVcf];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}
@ -580,7 +580,7 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
string inputBackTransNT = buildPath(DirNT_out, gene ~ ".fasta");
string outputFastaNT = buildPath(DirTrimNT, gene ~ ".fasta");
if (exists(inputFastaAA) && exists(inputBackTransNT)) {
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"];
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-gt", "0.7"];
executeCommand(cmdTrim);
} else {
writeln("Skipping gene: ", gene, " as files are missing.");

4
RGBEPP_refmix.d
View file

@ -397,7 +397,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, stri
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, "--check-ref", "s", "-Oz"];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "-Oz", "-o", outputVcf];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}
@ -687,7 +687,7 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
string inputBackTransNT = buildPath(DirNT_out, gene ~ ".fasta");
string outputFastaNT = buildPath(DirTrimNT, gene ~ ".fasta");
if (exists(inputFastaAA) && exists(inputBackTransNT)) {
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"];
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-gt", "0.7"];
executeCommand(cmdTrim);
} else {
writeln("Skipping gene: ", gene, " as files are missing.");