Updated Biomart and Emboss workflow

Script

fasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq;

Script

List HSOut = new ArrayList();
List RatOut = new ArrayList();
List MouseOut = new ArrayList();

Map hsToMouse = new HashMap();
Iterator j = MouseGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
  String id = (String)i.next();
  hsToMouse.put(id, j.next());
}
Map hsToRat = new HashMap();
j = RatGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
  String id = (String)i.next();
  hsToRat.put(id, j.next());
}

// Build the unique outputs
for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
  String hsID = (String)i.next();
  String ratID = (String)hsToRat.get(hsID);
  // Remove version number
  // ratID = (ratID.split("."))[0];
  String mouseID = (String)hsToMouse.get(hsID);
  // Remove version number
  //mouseId = (mouseID.split("."))[0];
  if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
    HSOut.add(hsID);
    RatOut.add(ratID.split("\\.")[0]);
    MouseOut.add(mouseID.split("\\.")[0]);
  }
}

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Endpoint

Endpoint

Endpoint