malacology/RGBEPP
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polish: trimming methods

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kuoi 2024-09-10 15:09:05 +10:00
parent 1752e785b4
commit 28ef396afd
1 changed files with 20 additions and 8 deletions
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28
RGBEPP.d
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@ -336,18 +336,22 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
} }
void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){
createDir(DirAlign ~ "/" ~ "AA_out"); writeln("Trimming::End");
createDir(DirAlign ~ "/" ~ "NT_out");
string DirAA = DirAlign ~ "/" ~ "AA"; string DirAA = DirAlign ~ "/" ~ "AA";
string DirNT = DirAlign ~ "/" ~ "NT"; string DirNT = DirAlign ~ "/" ~ "NT";
string DirAA_out = DirAlign ~ "/" ~ "AA_out";
string DirNT_out = DirAlign ~ "/" ~ "NT_out";
createDir(DirAA_out);
createDir(DirNT_out);
// copy file firstly // copy file firstly
foreach (gene; ARG_G){ foreach (gene; ARG_G){
string inputFastaAA = DirAA ~ "/" ~ gene ~ ".fasta"; string inputFastaAA = DirAA ~ "/" ~ gene ~ ".fasta";
string outputFastaAA = DirAA ~ "_out" ~ "/" ~ gene ~ ".fasta"; string outputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta";
string inputFastaNT = DirNT ~ "/" ~ gene ~ ".fasta"; string inputFastaNT = DirNT ~ "/" ~ gene ~ ".fasta";
string outputFastaNT = DirNT ~ "_out" ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = DirNT_out ~ "/" ~ gene ~ ".fasta";
copy(inputFastaNT, outputFastaNT); copy(inputFastaNT, outputFastaNT);
copy(inputFastaAA, outputFastaAA); copy(inputFastaAA, outputFastaAA);
@ -356,15 +360,19 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat
executeCommand(cmdDelStop); executeCommand(cmdDelStop);
} }
string DirTrimNT = DirTrim ~ "/" ~ "NT";
createDir(DirTrim); createDir(DirTrim);
createDir(DirTrimNT);
foreach (gene; ARG_G){ foreach (gene; ARG_G){
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 = DirTrim ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = DirTrimNT ~ "/" ~ gene ~ ".fasta";
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-gappyout"]; string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"];
executeCommand(cmdTrim); executeCommand(cmdTrim);
} }
writeln("Trimming::End");
} }
void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){ void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){
@ -467,6 +475,10 @@ void main(string[] args) {
i++; i++;
PathTrimal = args[i]; PathTrimal = args[i];
break; break;
case "--delstop":
i++;
PathDelstop = args[i];
break;
case "--spades": case "--spades":
i++; i++;
PathSpades = args[i]; PathSpades = args[i];