malacology/RGBEPP
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fix: skip the missing gene

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This commit is contained in:
kuoi 2024-12-12 10:37:49 +11:00
parent 5a504bcdfd
commit 0d8ca08d9e
1 changed files with 20 additions and 5 deletions
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25
RGBEPP.d
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@ -525,8 +525,13 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
string inputFasta = buildPath(DirConGene, gene ~ ".fasta");
string outAA = buildPath(DirAlignAA, gene ~ ".fasta");
string outNT = buildPath(DirAlignNT, gene ~ ".fasta");
string[] cmdAlign = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
executeCommand(cmdAlign);
if (!exists(inputFasta)) {
writeln("File not found: ", inputFasta);
continue;
} else{
string[] cmdAlign = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
executeCommand(cmdAlign);
}
}
writeln("Align::End");
@ -549,9 +554,19 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
string outputFastaAA = buildPath(DirAA_out, gene ~ ".fasta");
string inputFastaNT = buildPath(DirNT, gene ~ ".fasta");
string outputFastaNT = buildPath(DirNT_out, gene ~ ".fasta");
copy(inputFastaNT, outputFastaNT);
copy(inputFastaAA, outputFastaAA);
if (!exists(inputFastaNT)) {
writeln("File not found: ", inputFastaNT);
continue;
} else{
copy(inputFastaNT, outputFastaNT);
}
if (!exists(inputFastaAA)) {
writeln("File not found: ", inputFastaAA);
continue;
} else{
copy(inputFastaAA, outputFastaAA);
}
// del stop codon
string[] cmdDelStop = [PathDelstop, outputFastaAA, outputFastaNT, "--delete"];
executeCommand(cmdDelStop);