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add: command check and the config example file

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This commit is contained in:
kuoi 2024-09-11 12:13:14 +10:00
parent 967960f5bc
commit 2968698cda
2 changed files with 56 additions and 9 deletions
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57
RGBEPP.d
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@ -30,11 +30,33 @@ void show_help(string pkgver) {
--samtools\t\tSamtools path (optional)
--bcftools\t\tBcftools path (optional)
--macse\t\tMacse jarfile path (optional)
--delstop\t\tDelstop path (optional)
--trimal\t\tTrimal path (optional)
--spades\t\tSpades python path (optional)
for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n");
}
bool testJava() {
bool pass = true;
auto result = execute(["java", "-version"]);
if (result.status != 0) {
pass = false;
writeln("Error: Java is not found");
}
return pass;
}
bool testFiles(string[] filePaths) {
bool pass = true;
foreach(filePath; filePaths){
if (!exists(filePath) && filePath != "") {
writeln("Error: " ~ filePath ~ " does not exists.");
pass = false;
}
}
return pass;
}
void createDir(string path) {
if (!exists(path)) {
mkdir(path);
@ -505,6 +527,7 @@ void main(string[] args) {
PathSamtools = getValueFromConfig(ARG_C, "samtools");
PathBcftools = getValueFromConfig(ARG_C, "bcftools");
PathMacse = getValueFromConfig(ARG_C, "macse");
PathDelstop = getValueFromConfig(ARG_C, "delstop");
PathTrimal = getValueFromConfig(ARG_C, "trimal");
}
@ -512,36 +535,52 @@ void main(string[] args) {
writeln("RGBEPP::Start");
// Perform steps based on provided function argument
if (ARG_F == "all" || ARG_F == "clean") {
processQcTrim(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
if(testFiles([PathFastp])){
processQcTrim(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
}
}
if (ARG_F == "assembly") {
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
if(testFiles([PathSpades])){
processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades);
}
}
if (ARG_F == "all" || ARG_F == "map") {
processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
if(testFiles([PathBowtie2, PathSamtools])){
processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
}
}
if (ARG_F == "all" || ARG_F == "postmap") {
processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
if(testFiles([PathSamtools])){
processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
}
}
if (ARG_F == "all" || ARG_F == "varcall") {
processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
if(testFiles([PathBcftools])){
processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
}
}
if (ARG_F == "all" || ARG_F == "consen") {
processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus);
if(testFiles([PathBcftools])){
processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus);
}
}
if (ARG_F == "all" || ARG_F == "align") {
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
if(testFiles([PathMacse]) && testJava){
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
}
}
if (ARG_F == "all" || ARG_F == "trim") {
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal);
if(testFiles([PathTrimal])){
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal);
}
}
writeln("RGBEPP::End");

8
config.example Normal file
View file

@ -0,0 +1,8 @@
fastp = /usr/bin/fastp
bowtie2 = /usr/bin/bowtie2
samtools = /usr/bin/samtools
bcftools = /usr/bin/bcftools
macse = /usr/share/java/macse.jar
delstop = /usr/bin/delstop
trimal = /usr/bin/trimal
spades = /usr/bin/spades.py