#18 - add option to indicate self-comparison

src/leb/main/EzAAI.java

@@ -77,6 +77,7 @@ public EzAAI(String module) {
 
  String label = null; // convert, extract
  String input2 = null, matchout = null, mtxout = null; int thread = 10; double identity = 0.4, coverage = 0.5; // calculate
+ boolean self = false; // calculate
  int program = PROGRAM_MMSEQS; // calculate
  boolean useid = false; // cluster
 
@@ -188,6 +189,13 @@ else if(!arg.get("-s").equals("nucl")) {
  return -1;
  }
  }
+ if(arg.get("-self") != null) {
+ self = Integer.parseInt(arg.get("-self")) != 0;
+ if(self && !input1.equals(input2)) {
+ Prompt.error("Self-comparison with different input files is not allowed.");
+ return -1;
+ }
+ }
  if(arg.get("-id") != null) identity = Double.parseDouble(arg.get("-id"));
  if(arg.get("-cov") != null) coverage = Double.parseDouble(arg.get("-cov"));
  if(arg.get("-match") != null) matchout = arg.get("-match");
@@ -407,6 +415,11 @@ private int runCalculate() {
  jnames = new String[1];
  jnames[0] = jfile.getAbsolutePath();
  }
+
+ if(self && inames.length <= 1) {
+ Prompt.error("Self-comparison requires directory with at least two files.");
+ return -1;
+ }
 
  // convert profiles into FASTA files
  List<String> ilist = new ArrayList<>(), jlist = new ArrayList<>();
@@ -450,10 +463,12 @@ else if(!faaDir.isDirectory()) {
  Double[][] aaiTable = new Double[ilist.size()][jlist.size()];
  Integer[][] hitTable = new Integer[ilist.size()][jlist.size()];
  Integer[] ilens = new Integer[ilist.size()], jlens = new Integer[jlist.size()];
-
+
+ int it = 0, sz = self ? (ilist.size() * (ilist.size() - 1) / 2) : (ilist.size() * jlist.size());
  for(int i = 0; i < ilist.size(); i++) {
  for(int j = 0; j < jlist.size(); j++) {
- Prompt.print(String.format("Calculating AAI... [Task %d/%d]", i*jlist.size()+j+1, ilist.size()*jlist.size()));
+ if(self && i >= j) { continue; }
+ Prompt.print(String.format("Calculating AAI... [Task %d/%d]", ++it, sz));
  ProcCalcPairwiseAAI procAAI = new ProcCalcPairwiseAAI();
 
  switch(program) {
@@ -479,11 +494,25 @@ else if(!faaDir.isDirectory()) {
  List<String> res = procAAI.calculateProteomePairWithDetails(ilabs.get(i), jlabs.get(j), ilist.get(i), jlist.get(j));
  hitTable[i][j] = Integer.parseInt(res.get(4));
  aaiTable[i][j] = Double.parseDouble(res.get(6));
- if(j == 0) ilens[i] = Integer.parseInt(res.get(0));
- if(i == 0) jlens[j] = Integer.parseInt(res.get(1));
+ if(ilens[i] == null) ilens[i] = Integer.parseInt(res.get(0));
+ if(jlens[j] == null) jlens[j] = Integer.parseInt(res.get(1));
  }
  }
  if(maw != null) maw.close();
+
+ // if self, fill the remaining cells
+ if(self) {
+ for(int i = 0; i < ilist.size(); i++) {
+ if(jlens[i] == null) jlens[i] = ilens[i];
+ if(ilens[i] == null) ilens[i] = jlens[i];
+ aaiTable[i][i] = 100.0;
+ hitTable[i][i] = ilens[i];
+ for(int j = i+1; j < jlist.size(); j++) {
+ aaiTable[j][i] = aaiTable[i][j];
+ hitTable[j][i] = hitTable[i][j];
+ }
+ }
+ }
 
  // print result into output file
  BufferedWriter bw = new BufferedWriter(new FileWriter(output, outExists));
@@ -782,6 +811,7 @@ private static void printHelp(int module) {
  System.out.printf(" %-"+indent+"s%s%n", "-p ", "Customize calculation program [mmseqs / diamond / blastp] (default: mmseqs)");
  System.out.printf(" %-"+indent+"s%s%n", "-t ", "Number of CPU threads to use (default: 10)");
  System.out.printf(" %-"+indent+"s%s%n", "-tmp ", "Custom temporary directory (default: /tmp)");
+ System.out.printf(" %-"+indent+"s%s%n", "-self ", "Assume self-comparison; -i and -j must be identical [0 / 1] (default: 0)");
  System.out.printf(" %-"+indent+"s%s%n", "-id ", "Minimum identity threshold for AAI calculations [0 - 1.0] (default: 0.4)");
  System.out.printf(" %-"+indent+"s%s%n", "-cov ", "Minimum query coverage threshold for AAI calculations [0 - 1.0] (default: 0.5)");
  System.out.printf(" %-"+indent+"s%s%n", "-match ", "Path to write a result of matched CDS names");