malacology/RGBEPP
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add: consensu and split and convert fasta

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This commit is contained in:
kuoi 2024-09-09 01:17:57 +10:00
parent 765294f017
commit 7dcef7bba1
1 changed files with 72 additions and 23 deletions
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95
RGBEPP.d
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@ -165,25 +165,15 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
string[] cmdFixmate = ["samtools", "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
string[] cmdSort = ["samtools", "sort", "-@", ARG_T.to!string, "-"];
string[] cmdMarkdup = ["samtools", "markdup", "-@", ARG_T.to!string, "-", outputBam];
executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
string [] cmdIndexBam = ["samtools", "index", "-@", ARG_T.to!string, outputBam];
executeCommand(cmdIndexBam);
}
writeln("PostMapping::End");
}
void processIndexBam(string[] ARG_L, int ARG_T, string DirBam){
writeln("Indexing::Start");
//samtools index bam after markdup
foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
string [] cmdIndexBam = ["samtools", "index", "-@", ARG_T.to!string, inputBam];
executeCommand(cmdIndexBam);
}
writeln("Indexing::End");
}
void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, string DirVcf, string DirMap) {
writeln("VarCalling::Start");
@ -210,16 +200,22 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, stri
}
void processCon(string[] ARG_L, string ARG_R, int ARG_T, string DirVcf, string DirConsensus, string DirMap) {
void processCon(string[] ARG_L, string ARG_R, int ARG_T, string[] ARG_G, string DirVcf, string DirConsensus, string DirMap) {
createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
createDir(DirConTaxa);
string[] Refs = getRef(ARG_R, DirMap);
string ARG_R_refer = Refs[1]; //reference_in fasta file
writeln("Consensus::Start");
// Extract fasta from vcf file
foreach (string file; ARG_L) {
string baseName = getBaseName(file);
string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
string outputFasta = DirConsensus ~ "/" ~ baseName ~ ".fasta";
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
// index vcf.gz
string[] cmdIndexVcf = ["bcftools", "index", inputVcf];
@ -229,11 +225,59 @@ void processCon(string[] ARG_L, string ARG_R, int ARG_T, string DirVcf, string D
string[] cmdCon = ["bcftools", "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
executeCommand(cmdCon);
}
// Recombine the sequences based on genes
writeln("Consensus::End");
}
void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
string DirConGene = DirConsensus ~ "/" ~ "gene";
// create a dictory
string[string] geneSequences;
// read first
foreach (file; ARG_L) {
string inputFile = DirConTaxa ~ "/" ~ file ~ ".fas";
if (!exists(inputFile)) {
writeln("File not found: ", inputFile);
continue;
}
string content = cast(string) readText(inputFile);
bool inSequence = false;
string currentGene;
foreach (line; content.splitter("\n")) {
if (line.empty) continue;
if (line[0] == '>') {
string header = line[1 .. $];
if (ARG_G.canFind(header)) {
currentGene = header;
geneSequences[currentGene] ~= ">" ~ file ~ "\n";
inSequence = true;
} else {
inSequence = false;
}
} else if (inSequence) {
geneSequences[currentGene] ~= line ~ "\n";
}
}
}
// write different files
foreach (gene; ARG_G) {
string outputFile = DirConGene ~ "/" ~ gene ~ ".fasta";
File output = File(outputFile, "a");
if (gene in geneSequences) {
output.write(geneSequences[gene]);
}
}
}
void main(string[] args) {
string pkgver = "0.0.2";
string pkgver = "0.0.3";
string DirHome = std.file.getcwd();
string DirRaw = DirHome ~ "/00_raw";
@ -247,6 +291,7 @@ void main(string[] args) {
string PathMacse = "/usr/share/java/macse.jar";
int ARG_T = 8;
string[] ARG_G;
string[] ARG_L;
string ARG_F;
string ARG_R;
@ -258,12 +303,16 @@ void main(string[] args) {
i++;
ARG_F = args[i];
break;
case "-g", "--gene":
i++;
ARG_G ~= readArrFromFile(args[i]);
break;
case "-h", "--help":
show_help(pkgver);
return;
case "-l", "--list":
i++;
ARG_L ~= readArrFromFile( DirHome ~ "/" ~ args[i]);
ARG_L ~= readArrFromFile(args[i]);
break;
case "-r", "--reference":
i++;
@ -300,18 +349,18 @@ void main(string[] args) {
processPostMap(ARG_L, ARG_T, DirMap, DirBam);
}
if (ARG_F == "all" || ARG_F == "indexbam") {
processIndexBam(ARG_L, ARG_T, DirBam);
}
if (ARG_F == "all" || ARG_F == "varcall") {
processVarCall(ARG_L, ARG_R, ARG_T, DirBam, DirVcf, DirMap);
}
if (ARG_F == "all" || ARG_F == "consen") {
processCon(ARG_L, ARG_R, ARG_T, DirVcf, DirConsensus,DirMap);
processCon(ARG_L, ARG_R, ARG_T, ARG_G, DirVcf, DirConsensus,DirMap);
processCombFasta(ARG_L, ARG_G, DirConsensus);
}
if (ARG_F == "all" || ARG_F == "align") {
}
writeln("RGBEPP::End");
}