malacology/RGBEPP
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update: fix the first two steps

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This commit is contained in:
kuoi 2024-10-23 18:26:22 +11:00
parent 1227280755
commit 50f99a9575
1 changed files with 45 additions and 5 deletions
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50
RGBEPP.d
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@ -175,15 +175,51 @@ void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, s
writeln("QcTrimming::End");
}
void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){
void processAssemMv(string[] ARG_L,string DirAssembly){
// Prepare
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
string DirAssemblyCont = DirAssembly ~ "/" ~ "contigs";
writeln("Assembly_Move::Start");
createDir(DirAssemblySca);
createDir(DirAssemblyCont);
foreach (string file; ARG_L ){
string baseName = getBaseName(file);
string DirAssemblyInd = DirAssembly ~ "/" ~ baseName;
string inputSca = DirAssemblyInd ~ "/" ~ "scaffolds.fasta";
string inputCont = DirAssemblyInd ~ "/" ~ "contigs.fasta";
string outputSca = DirAssemblySca ~ "/" ~ baseName ~ ".fasta";
string outputCont = DirAssemblyCont ~ "/" ~ baseName ~ ".fasta";
if (!exists(inputSca)) {
writeln("File not found: ", inputSca);
continue;
} else {
copy(inputSca, outputSca);
}
if (!exists(inputCont)) {
writeln("File not found: ", inputCont);
continue;
} else {
copy(inputCont, outputCont);
}
}
writeln("Assembly_Move::End");
}
void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){
// Prepare directory
writeln("Mapping::Start");
createDir(DirMap);
createDir(DirMap ~ "/index");
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta";
createDir(DirAssemblySca);
createDir(DirAssemblyFas);
string ReferDmnd = DirAssemblySca ~ "/" ~ "Reference.dmnd";
string ARG_R_Base = getBaseName(ARG_R);
string ARG_R_Ref = DirAssemblyFas ~ "/" ~ ARG_R_Base ~ ".fasta";
copy(ARG_R, ARG_R_Ref);
string [] cmdDmMakeDB = [ "diamond", "makedb", "--db", "Reference", "--in", ARG_R_Ref];
executeCommand(cmdDmMakeDB);
string ReferDmnd = DirAssemblyFas ~ "/" ~ "Reference.dmnd";
string PathBowtie2_build = PathBowtie2 ~ "-build";
foreach (string file; ARG_L) {
@ -207,6 +243,7 @@ void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string Di
executeCommandPipe([cmdMap, cmdSam2Bam]);
}
writeln("Mapping::End");
}
void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
@ -628,16 +665,18 @@ void main(string[] args) {
}
}
if (ARG_F == "assembly") {
if (ARG_F == "all" || ARG_F == "assembly") {
if(testFiles([PathSpades])){
processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades);
processAssemMv(ARG_L, DirAssembly);
}
}
if (ARG_F == "all" || ARG_F == "map") {
if(testFiles([PathBowtie2, PathSamtools])){
//processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
processMappingDenovo(ARG_L, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
}
}
@ -653,6 +692,7 @@ void main(string[] args) {
processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools);
}
}
if (ARG_F == "all" || ARG_F == "consen") {