convertdb module

src/leb/main/EzAAI.java

@@ -36,11 +36,13 @@ public class EzAAI {
  + " Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity.\n"
  + " J Microbiol. 59, 476–480 (2021).\n"
  + " DOI: 10.1007/s12275-021-1154-0";
+ public static final boolean STABLE = false;
 
  final static int MODULE_CONVERT = 1,
  MODULE_EXTRACT = 2,
  MODULE_CALCULATE = 3,
  MODULE_CLUSTER = 4,
+ MODULE_CONVERTDB = 5,
  MODULE_INVALID = 0;
 
  final static int PROGRAM_MMSEQS = 1,
@@ -56,6 +58,7 @@ public EzAAI(String module) {
  if(module.equals("extract")) this.module = MODULE_EXTRACT;
  if(module.equals("calculate")) this.module = MODULE_CALCULATE;
  if(module.equals("cluster")) this.module = MODULE_CLUSTER;
+ if(module.equals("convertdb")) this.module = MODULE_CONVERTDB;
  }
 
  // Argument variables
@@ -84,6 +87,7 @@ private int parseArguments(String[] args) {
  case MODULE_EXTRACT: modstr = "extract"; break;
  case MODULE_CALCULATE: modstr = "calculate"; break;
  case MODULE_CLUSTER: modstr = "cluster"; break;
+ case MODULE_CONVERTDB: modstr = "convertdb"; break;
  }
 
  Arguments arg = new Arguments(args);
@@ -176,7 +180,7 @@ else if(!arg.get("-s").equals("nucl")) {
  if(module == MODULE_CLUSTER) {
  if(arg.get("-u") != null) useid = true;
  }
- 
+
  if(arg.get("-prodigal") != null) path_prodigal = arg.get("-prodigal");
  if(arg.get("-mmseqs") != null) path_mmseqs = arg.get("-mmseqs");
  if(arg.get("-diamond") != null) path_diamond = arg.get("-diamond");
@@ -216,7 +220,7 @@ private int checkDependency(int module, int program) {
  Prompt.talk("Checking dependencies...");
 
  switch(module) {
- case MODULE_CONVERT:
+ case MODULE_CONVERT: case MODULE_CONVERTDB:
  if(checkProgram(PROGRAM_MMSEQS)) return PROGRAM_MMSEQS;
  break;
  case MODULE_EXTRACT:
@@ -581,6 +585,14 @@ private int runCluster() {
  Prompt.print("Task finished.");
  return 0;
  }
+
+ private int runConvertDB() {
+ int ret;
+ if((ret = dbToFaa(input1, output)) == 0) {
+ Prompt.print("Task finished.");
+ }
+ return ret;
+ }
 
  private int run(String[] args) {
  if(parseArguments(args) < 0) return -1;
@@ -607,6 +619,7 @@ private int run(String[] args) {
  case MODULE_EXTRACT: return runExtract();
  case MODULE_CALCULATE: return runCalculate();
  case MODULE_CLUSTER: return runCluster();
+ case MODULE_CONVERTDB: return runConvertDB();
  default: return -1;
  }
  }
@@ -639,6 +652,7 @@ else if(ezAAI.module == MODULE_INVALID) {
  GenericConfig.setHeaderLength(7);
  GenericConfig.setHeader("EzAAI");
  Prompt.print(String.format("EzAAI - %s [%s]", VERSION, RELEASE));
+ if(!STABLE) Prompt.warning("This is an unstable version. Please use with caution and report any bugs to the developer.");
  if(ezAAI.run(args) < 0) {
  Prompt.error("Program terminated with error.");
  }
@@ -660,6 +674,7 @@ private static void printHelp(int module) {
  System.out.println(ANSIHandler.wrapper(" Module\t\tDescription", 'c'));
  System.out.printf(" %s\t%s%n", "extract", "Extract protein DB from genome using Prodigal");
  System.out.printf(" %s\t%s%n", "convert", "Convert CDS FASTA file into protein DB");
+ System.out.printf(" %s\t%s%n", "convertdb", "Convert protein DB into FASTA file");
  System.out.printf(" %s\t%s%n", "calculate", "Calculate AAI value from protein databases using MMSeqs2");
  System.out.printf(" %s\t%s%n", "cluster", "Hierarchical clustering of taxa with AAI values");
  System.out.println();
@@ -762,5 +777,24 @@ private static void printHelp(int module) {
  System.out.printf(" %s\t\t%s%n", "-u", "Use ID instead of label for tree");
  System.out.println();
  }
+ if(module == MODULE_CONVERTDB) {
+ System.out.println(ANSIHandler.wrapper("\n EzAAI - convertdb", 'G'));
+ System.out.println(ANSIHandler.wrapper(" Convert protein DB into FASTA file", 'g'));
+ System.out.println();
+
+ System.out.println(ANSIHandler.wrapper("\n USAGE:", 'Y') + " java -jar EzAAI.jar convertdb -i <IN_DB> -o <OUT_FA>");
+ System.out.println();
+
+ System.out.println(ANSIHandler.wrapper("\n Required options", 'Y'));
+ System.out.println(ANSIHandler.wrapper(" Argument\tDescription", 'c'));
+ System.out.printf(" %s\t\t%s%n", "-i", "Input protein DB");
+ System.out.printf(" %s\t\t%s%n", "-o", "Output FASTA file");
+ System.out.println();
+
+ System.out.println(ANSIHandler.wrapper("\n Additional options", 'y'));
+ System.out.println(ANSIHandler.wrapper(" Argument\tDescription", 'c'));
+ System.out.printf(" %s\t%s%n", "-mmseqs", "Custom path to MMSeqs2 binary (default: mmseqs)");
+ System.out.println();
+ }
  }
 }