malacology/RGBEPP
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add: get arg_g

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kuoi 2024-09-09 02:04:36 +10:00
parent 7dcef7bba1
commit c423431a65
1 changed files with 33 additions and 8 deletions
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41
RGBEPP.d
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@ -94,7 +94,20 @@ string[] getRef(string ARG_R, string DirMap){
return Refs; return Refs;
} }
void performQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) { string[] getARG_G(string ARG_R){
string[] ARG_G;
// if ARG_G is empty
if (ARG_G.length == 0) {
auto file = File(ARG_R, "r");
ARG_G = file.byLine
.filter!(line => line.startsWith(">")) // flitering
.map!(line => line[1..$].idup) // convert to word
.array;
}
return ARG_G;
}
void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) {
// Prepare directory // Prepare directory
createDir(DirQcTrim); createDir(DirQcTrim);
@ -117,7 +130,7 @@ void performQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int
} }
void performMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) { void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) {
writeln("Mapping::Start"); writeln("Mapping::Start");
// Prepare directory // Prepare directory
@ -233,13 +246,15 @@ void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
string DirConTaxa = DirConsensus ~ "/" ~ "taxa"; string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
string DirConGene = DirConsensus ~ "/" ~ "gene"; string DirConGene = DirConsensus ~ "/" ~ "gene";
createDir(DirConGene);
// create a dictory // create a dictory
string[string] geneSequences; string[string] geneSequences;
writeln("ConvertFasta::Start");
// read first // read first
foreach (file; ARG_L) { foreach (file; ARG_L) {
string inputFile = DirConTaxa ~ "/" ~ file ~ ".fas"; string inputFile = DirConTaxa ~ "/" ~ file ~ ".fasta";
if (!exists(inputFile)) { if (!exists(inputFile)) {
writeln("File not found: ", inputFile); writeln("File not found: ", inputFile);
continue; continue;
@ -268,14 +283,19 @@ void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
// write different files // write different files
foreach (gene; ARG_G) { foreach (gene; ARG_G) {
string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta"; string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta";
File output = File(outputFile, "a"); File output = File(outputFile, "w");
if (gene in geneSequences) { if (gene in geneSequences) {
output.write(geneSequences[gene]); output.write(geneSequences[gene]);
} }
} }
writeln("ConvertFasta::End");
}
void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){
} }
void main(string[] args) { void main(string[] args) {
string pkgver = "0.0.3"; string pkgver = "0.0.3";
@ -335,14 +355,19 @@ void main(string[] args) {
return; return;
} }
// get gene from ARG_R reference fasta
if (ARG_R.length != 0 ){
ARG_G = getARG_G(ARG_R);
}
writeln("RGBEPP::Start"); writeln("RGBEPP::Start");
// Perform steps based on provided function argument // Perform steps based on provided function argument
if (ARG_F == "all" || ARG_F == "clean") { if (ARG_F == "all" || ARG_F == "clean") {
performQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T); processQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T);
} }
if (ARG_F == "all" || ARG_F == "map") { if (ARG_F == "all" || ARG_F == "map") {
performMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T); processMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T);
} }
if (ARG_F == "all" || ARG_F == "postmap") { if (ARG_F == "all" || ARG_F == "postmap") {
@ -359,7 +384,7 @@ void main(string[] args) {
} }
if (ARG_F == "all" || ARG_F == "align") { if (ARG_F == "all" || ARG_F == "align") {
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
} }
writeln("RGBEPP::End"); writeln("RGBEPP::End");