add: get arg_g
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7dcef7bba1
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c423431a65
1 changed files with 33 additions and 8 deletions
39
RGBEPP.d
39
RGBEPP.d
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@ -94,7 +94,20 @@ string[] getRef(string ARG_R, string DirMap){
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return Refs;
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}
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void performQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) {
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string[] getARG_G(string ARG_R){
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string[] ARG_G;
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// if ARG_G is empty
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if (ARG_G.length == 0) {
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auto file = File(ARG_R, "r");
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ARG_G = file.byLine
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.filter!(line => line.startsWith(">")) // flitering
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.map!(line => line[1..$].idup) // convert to word
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.array;
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}
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return ARG_G;
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}
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void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) {
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// Prepare directory
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createDir(DirQcTrim);
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@ -117,7 +130,7 @@ void performQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int
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}
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void performMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) {
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void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) {
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writeln("Mapping::Start");
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// Prepare directory
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@ -233,13 +246,15 @@ void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
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string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
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string DirConGene = DirConsensus ~ "/" ~ "gene";
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createDir(DirConGene);
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// create a dictory
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string[string] geneSequences;
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writeln("ConvertFasta::Start");
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// read first
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foreach (file; ARG_L) {
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string inputFile = DirConTaxa ~ "/" ~ file ~ ".fas";
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string inputFile = DirConTaxa ~ "/" ~ file ~ ".fasta";
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if (!exists(inputFile)) {
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writeln("File not found: ", inputFile);
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continue;
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@ -268,14 +283,19 @@ void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
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// write different files
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foreach (gene; ARG_G) {
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string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta";
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File output = File(outputFile, "a");
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File output = File(outputFile, "w");
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if (gene in geneSequences) {
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output.write(geneSequences[gene]);
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}
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}
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writeln("ConvertFasta::End");
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}
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void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){
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}
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void main(string[] args) {
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string pkgver = "0.0.3";
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@ -335,14 +355,19 @@ void main(string[] args) {
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return;
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}
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// get gene from ARG_R reference fasta
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if (ARG_R.length != 0 ){
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ARG_G = getARG_G(ARG_R);
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}
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writeln("RGBEPP::Start");
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// Perform steps based on provided function argument
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if (ARG_F == "all" || ARG_F == "clean") {
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performQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T);
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processQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T);
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}
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if (ARG_F == "all" || ARG_F == "map") {
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performMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T);
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processMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T);
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}
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if (ARG_F == "all" || ARG_F == "postmap") {
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@ -359,7 +384,7 @@ void main(string[] args) {
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}
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if (ARG_F == "all" || ARG_F == "align") {
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processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
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}
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writeln("RGBEPP::End");
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