malacology/RGBEPP
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fix: skip genes

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This commit is contained in:
kuoi 2024-09-19 13:48:13 +10:00
parent 56c0293057
commit 1227280755
1 changed files with 6 additions and 3 deletions
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9
RGBEPP.d
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@ -473,9 +473,12 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
string inputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta"; string inputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta";
string inputBackTransNT = DirNT_out ~ "/" ~ gene ~ ".fasta"; string inputBackTransNT = DirNT_out ~ "/" ~ gene ~ ".fasta";
string outputFastaNT = DirTrimNT ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = 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, "-automated1"];
executeCommand(cmdTrim); executeCommand(cmdTrim);
} else {
writeln("Skipping gene: ", gene, " as files are missing.");
}
} }
writeln("Trimming::End"); writeln("Trimming::End");