//**********************************************************************************************************************
UnifracWeightedCommand::UnifracWeightedCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["weighted"] = tempOutNames;
outputTypes["wsummary"] = tempOutNames;
outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
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);
int UnifracWeightedCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
}
if (random) {
- vector<double> sums = weighted->getBranchLengthSums(T[i]);
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
vector< vector<string> > namesOfGroupCombos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
}else{
- createProcesses(T[i], namesOfGroupCombos, sums, rScores);
+ createProcesses(T[i], namesOfGroupCombos, rScores);
}
#else
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
#endif
if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//report progress
- m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
+// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
lines.clear();
}
/**************************************************************************************************/
-int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
vector<int> processIDS;
EstOutput results;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, scores);
//pass numSeqs to parent
ofstream out;
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, sums, scores);
+ driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
}
/**************************************************************************************************/
-int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector< vector<double> >& scores) {
try {
Tree* randT = new Tree();
if (m->control_pressed) { delete randT; return 0; }
//get wscore of random tree
- EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
+ EstOutput randomData = weighted->getValues(randT, groupA, groupB);
if (m->control_pressed) { delete randT; return 0; }
//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++) {
//flip it so you can print it
for (int r=0; r<globaldata->Groups.size(); r++) {
- for (int l = r+1; l < globaldata->Groups.size(); l++) {
+ for (int l = 0; l < r; l++) {
dists[r][l] = utreeScores[count];
dists[l][r] = utreeScores[count];
count++;
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();
}
projects / mothur.git / blobdiff