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