malacology/RGBEPP
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add: trimming

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kuoi 2024-09-10 02:37:06 +10:00
parent f220da124e
commit 1752e785b4
2 changed files with 45 additions and 2 deletions
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42
RGBEPP.d
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@ -335,7 +335,40 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
} }
void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string PathDelstop, string PathTrimal){
createDir(DirAlign ~ "/" ~ "AA_out");
createDir(DirAlign ~ "/" ~ "NT_out");
string DirAA = DirAlign ~ "/" ~ "AA";
string DirNT = DirAlign ~ "/" ~ "NT";
// copy file firstly
foreach (gene; ARG_G){
string inputFastaAA = DirAA ~ "/" ~ gene ~ ".fasta";
string outputFastaAA = DirAA ~ "_out" ~ "/" ~ gene ~ ".fasta";
string inputFastaNT = DirNT ~ "/" ~ gene ~ ".fasta";
string outputFastaNT = DirNT ~ "_out" ~ "/" ~ gene ~ ".fasta";
copy(inputFastaNT, outputFastaNT);
copy(inputFastaAA, outputFastaAA);
// del stop codon
string[] cmdDelStop = [PathDelstop, outputFastaAA, outputFastaNT, "--delete"];
executeCommand(cmdDelStop);
}
createDir(DirTrim);
foreach (gene; ARG_G){
string inputFastaAA = DirAA ~ "_out" ~ "/" ~ gene ~ ".fasta";
string inputBackTransNT = DirNT ~ "_out" ~ "/" ~ gene ~ ".fasta";
string outputFastaNT = DirTrim ~ "/" ~ gene ~ ".fasta";
string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-gappyout"];
executeCommand(cmdTrim);
}
}
void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){ void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, string DirAssembly, string PathSpades){
writeln("Assembly::Start");
createDir(DirAssembly); createDir(DirAssembly);
foreach (string file; ARG_L) { foreach (string file; ARG_L) {
string baseName = getBaseName(file); string baseName = getBaseName(file);
@ -346,6 +379,7 @@ void processAssembly(string[] ARG_L, int ARG_M, int ARG_T, string DirQcTrim, str
string[] cmdAssembly = [PathSpades, "--pe1-1", inputFileR1, "--pe1-2", inputFileR2, "-t", ARG_T.to!string, "-m", ARG_M.to!string, "--careful", "--phred-offset", "33", "-o", DirAss]; string[] cmdAssembly = [PathSpades, "--pe1-1", inputFileR1, "--pe1-2", inputFileR2, "-t", ARG_T.to!string, "-m", ARG_M.to!string, "--careful", "--phred-offset", "33", "-o", DirAss];
executeCommand(cmdAssembly); executeCommand(cmdAssembly);
} }
writeln("Assembly::End");
} }
void main(string[] args) { void main(string[] args) {
@ -359,13 +393,15 @@ void main(string[] args) {
string DirBam = DirHome ~ "/03_bam"; string DirBam = DirHome ~ "/03_bam";
string DirVcf = DirHome ~ "/04_vcf"; string DirVcf = DirHome ~ "/04_vcf";
string DirConsensus = DirHome ~ "/05_consen"; string DirConsensus = DirHome ~ "/05_consen";
string DirAlign = DirHome ~ "/06_macse"; string DirAlign = DirHome ~ "/06_macse";
string DirTrim = DirHome ~ "/07_trimal";
string PathFastp = "/usr/bin/fastp"; string PathFastp = "/usr/bin/fastp";
string PathBowtie2 = "/usr/bin/bowtie2"; string PathBowtie2 = "/usr/bin/bowtie2";
string PathSamtools = "/usr/bin/samtools"; string PathSamtools = "/usr/bin/samtools";
string PathBcftools = "/usr/bin/bcftools"; string PathBcftools = "/usr/bin/bcftools";
string PathMacse = "/usr/share/java/macse.jar"; string PathMacse = "/usr/share/java/macse.jar";
string PathDelstop = "/usr/bin/delstop";
string PathTrimal = "/usr/bin/trimal"; string PathTrimal = "/usr/bin/trimal";
string PathSpades = "/usr/bin/spades.py"; string PathSpades = "/usr/bin/spades.py";
@ -492,7 +528,9 @@ void main(string[] args) {
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse); processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
} }
if (ARG_F == "all" || ARG_F == "trim") {
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal);
}
writeln("RGBEPP::End"); writeln("RGBEPP::End");
} }

5
dub.sdl Normal file
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@ -0,0 +1,5 @@
name "rgbepp"
description "Reference Genome based Exon Phylogeny Pipeline"
authors "Guoyi Zhang"
copyright "Copyright © 2024, Guoyi Zhang"
license "GPL-2.0-only"