malacology/RGBEPP
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add: align with parallel

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kuoi 2024-09-09 03:19:42 +10:00
parent c423431a65
commit 9ae0c38656
1 changed files with 23 additions and 6 deletions
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29
RGBEPP.d
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@ -7,6 +7,7 @@ import std.algorithm;
import std.conv; import std.conv;
import std.array; import std.array;
import std.path; import std.path;
import std.parallelism;
void show_help(string pkgver) { void show_help(string pkgver) {
writeln("\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m writeln("\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m
@ -14,17 +15,16 @@ void show_help(string pkgver) {
Version: ", pkgver, " Version: ", pkgver, "
License: GPL-2.0-only License: GPL-2.0-only
Author: Guoyi Zhang Author: Guoyi Zhang
-c\t--contigs\tcontigs type: scaffolds or contigs -g\t--genes\t\tgene file path (optional, if -r is specified)
-g\t--genes\t\tgene file path -f\t--functions\tfunctions type (optional): all clean map
-f\t--functions\tfunctions type (optional): all clean map postmap varcall consen \t \tpostmap varcall consen align
-h\t--help\t\tshow this information -h\t--help\t\tshow this information
-l\t--list\t\tlist file path -l\t--list\t\tlist file path
-m\t--memory\tmemory settings (optional, default 16 GB) -m\t--memory\tmemory settings (optional, default 16 GB)
-r\t--reference\treference genome path -r\t--reference\treference genome path
-t\t--threads\tthreads setting (optional, default 8 threads) -t\t--threads\tthreads setting (optional, default 8 threads)
--macse\t\tMacse jarfile path --macse\t\tMacse jarfile path
for example: ./your_program -c scaffolds -f all -l list -g genes \\ for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n");
-r reference.fasta \n");
} }
void createDir(string path) { void createDir(string path) {
@ -33,7 +33,7 @@ void createDir(string path) {
} }
} }
void executeCommand(string[] cmd, string workingDir = "") { void executeCommand(string[] cmd) {
auto process = spawnProcess(cmd); auto process = spawnProcess(cmd);
if (wait(process) != 0) { if (wait(process) != 0) {
@ -293,6 +293,23 @@ void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string PathMacse){
string DirConGene = DirConsensus ~ "/" ~ "gene";
string DirAlignAA = DirAlign ~ "/" ~ "AA";
string DirAlignNT = DirAlign ~ "/" ~ "NT";
writeln("Align::Start");
createDir(DirAlign);
createDir(DirAlignAA);
createDir(DirAlignNT);
foreach (gene; parallel(ARG_G, 1)) {
string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta";
string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta";
string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta";
string[] cmd = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
executeCommand(cmd);
}
writeln("Align::End");
} }