malacology/RGBEPP
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fix: use method3 to polish consen

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This commit is contained in:
kuoi 2024-09-15 13:48:19 +10:00
parent 1697e38b97
commit b63668504d
1 changed files with 29 additions and 1 deletions
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30
RGBEPP.d
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@ -332,6 +332,33 @@ void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string Pa
writeln("Consensus::End"); writeln("Consensus::End");
} }
void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssembly, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus);
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta";
createDir(DirConTaxa);
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 = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
string referFasta = DirAssemblyFas ~ "/" ~ baseName ~ ".fasta";
// index vcf.gz
string[] cmdIndexVcf = [PathBcftools, "index", inputVcf];
executeCommand(cmdIndexVcf);
// Generate consensus sequences using bcftools
string[] cmdCon = [PathBcftools, "consensus", "-f", referFasta, inputVcf, "-o", outputFasta];
executeCommand(cmdCon);
}
// Recombine the sequences based on genes
writeln("Consensus::End");
}
void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) { void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus); createDir(DirConsensus);
@ -644,8 +671,9 @@ void main(string[] args) {
if (ARG_F == "all" || ARG_F == "consen") { if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){ if(testFiles([PathBcftools])){
processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools); //processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
//processConSam(ARG_L, DirBam, DirConsensus, PathSamtools); //processConSam(ARG_L, DirBam, DirConsensus, PathSamtools);
processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus); processCombFasta(ARG_G, ARG_L, DirConsensus);
} }
} }