add: consensu and split and convert fasta
This commit is contained in:
parent
765294f017
commit
7dcef7bba1
1 changed files with 72 additions and 23 deletions
95
RGBEPP.d
95
RGBEPP.d
|
|
@ -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");
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue