outputTypes["weighted"] = tempOutNames;
outputTypes["wsummary"] = tempOutNames;
outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
outputTypes["weighted"] = tempOutNames;
outputTypes["wsummary"] = tempOutNames;
outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
if (globaldata->gTree.size() == 0) {//no trees were read
m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; }
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
- string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
- phylip = m->isTrue(temp);
-
+ string temp = validParameter.validFile(parameters, "distance", false);
+ if (temp == "not found") { phylip = false; outputForm = ""; }
+ else{
+ if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; }
+ else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+ }
+
temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "F"; }
random = m->isTrue(temp);
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
//for each tree
for (int i = 0; i < T.size(); i++) {
- string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist";
- outputNames.push_back(phylipFileName);
- outputTypes["phylip"].push_back(phylipFileName);
+ string phylipFileName;
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.phylip.dist";
+ outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
+ }else { //column
+ phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.column.dist";
+ outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
+ }
+
ofstream out;
m->openOutputFile(phylipFileName, out);
- //output numSeqs
- out << globaldata->Groups.size() << endl;
-
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ //output numSeqs
+ out << globaldata->Groups.size() << endl;
+ }
+
//make matrix with scores in it
vector< vector<float> > dists; dists.resize(globaldata->Groups.size());
for (int i = 0; i < globaldata->Groups.size(); i++) {
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
- out << name << '\t';
- //output distances
- for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
- out << endl;
+ if (outputForm == "lt") {
+ out << name << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }else if (outputForm == "square") {
+ out << name << '\t';
+
+ //output distances
+ for (int l = 0; l < globaldata->Groups.size(); l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }else{
+ //output distances
+ for (int l = 0; l < r; l++) {
+ string otherName = globaldata->Groups[l];
+ if (otherName.length() < 10) { //pad with spaces to make compatible
+ while (otherName.length() < 10) { otherName += " "; }
+ }
+
+ out << name << '\t' << otherName << dists[r][l] << endl;
+ }
+ }
}
out.close();
}