string IndicatorCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The indicator command reads a shared or relabund file and a tree or design file, and outputs a .indicator.tre and .indicator.summary file. \n";
+ helpString += "The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. \n";
+ helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n";
helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
helpString += "The summary file lists the indicator value for each OTU for each node.\n";
- helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
+ helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. \n";
helpString += "The design parameter allows you to relate the tree to the shared or relabund file, if your tree contains the grouping names, or if no tree is provided to group your groups into groupings.\n";
helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n";
helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "tree") { outputFileName = "indicator.tre"; }
+ else if (type == "summary") { outputFileName = "indicator.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
}
m->runParse = true;
- m->Groups.clear();
- m->namesOfGroups.clear();
+ m->clearGroups();
+ m->clearAllGroups();
m->Treenames.clear();
- m->names.clear();
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; Groups.push_back("all"); }
else { m->splitAtDash(groups, Groups); }
- m->Groups = Groups;
+ m->setGroups(Groups);
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if ((relabundfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
int start = time(NULL);
- //read designfile if given and set up globaldatas groups for read of sharedfiles
+ //read designfile if given and set up groups for read of sharedfiles
if (designfile != "") {
designMap = new GroupMap(designfile);
designMap->readDesignMap();
//fill Groups - checks for "all" and for any typo groups
- SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, designMap->namesOfGroups);
- delete util;
+ SharedUtil util;
+ vector<string> nameGroups = designMap->getNamesOfGroups();
+ util.setGroups(Groups, nameGroups);
+ designMap->setNamesOfGroups(nameGroups);
- //loop through the Groups and fill Globaldata's Groups with the design file info
- m->Groups = designMap->getNamesSeqs(Groups);
+ vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
+ m->setGroups(namesSeqs);
}
/***************************************************/
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
}
- //reset Globaldatas groups if needed
- if (designfile != "") { m->Groups = Groups; }
+ //reset groups if needed
+ if (designfile != "") { m->setGroups(Groups); }
/***************************************************/
// reading tree info //
string groupfile = "";
m->setTreeFile(treefile);
Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- treeMap = new TreeMap();
+ ct = new CountTable();
bool mismatch = false;
-
- for (int i = 0; i < m->Treenames.size(); i++) {
- //sanity check - is this a group that is not in the sharedfile?
+
+ set<string> nameMap;
+ map<string, string> groupMap;
+ set<string> gps;
+ for (int i = 0; i < m->Treenames.size(); i++) {
+ nameMap.insert(m->Treenames[i]);
+ //sanity check - is this a group that is not in the sharedfile?
if (designfile == "") {
- if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
+ if (i == 0) { gps.insert("Group1"); }
+ if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
mismatch = true;
}
- treeMap->addSeq(m->Treenames[i], "Group1");
+ groupMap[m->Treenames[i]] = "Group1";
}else{
vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
vector<string> myNames = designMap->getNamesSeqs(myGroups);
for(int k = 0; k < myNames.size(); k++) {
- if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
+ if (!(m->inUsersGroups(myNames[k], m->getAllGroups()))) {
m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
mismatch = true;
}
}
- treeMap->addSeq(m->Treenames[i], "Group1");
+ groupMap[m->Treenames[i]] = "Group1";
}
- }
+ }
+ ct->createTable(nameMap, groupMap, gps);
if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete treeMap;
+ delete ct;
return 0;
}
read = new ReadNewickTree(treefile);
- int readOk = read->read(treeMap);
+ int readOk = read->read(ct);
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete ct; delete read; return 0; }
vector<Tree*> T = read->getTrees();
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete ct; return 0;
}
-
+
T[0]->assembleTree();
/***************************************************/
// create ouptut tree - respecting pickedGroups //
/***************************************************/
- Tree* outputTree = new Tree(m->Groups.size(), treeMap);
+ Tree* outputTree = new Tree(m->getNumGroups(), ct);
- outputTree->getSubTree(T[0], m->Groups);
+ outputTree->getSubTree(T[0], m->getGroups());
outputTree->assembleTree();
//no longer need original tree, we have output tree to use and label
for (int i = 0; i < T.size(); i++) { delete T[i]; }
-
if (m->control_pressed) {
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete outputTree; delete treeMap; return 0;
+ delete outputTree; delete ct; return 0;
}
/***************************************************/
// get indicator species values //
/***************************************************/
GetIndicatorSpecies(outputTree);
- delete outputTree; delete treeMap;
+ delete outputTree; delete ct;
}else { //run with design file only
//get indicator species
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//set tree file as new current treefile
if (treefile != "") {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
vector<SharedRAbundVector*> subset;
//for each grouping
- for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
for (int k = 0; k < lookup.size(); k++) {
//are you from this grouping?
- if (designMap->getGroup(lookup[k]->getGroup()) == designMap->namesOfGroups[i]) {
+ if (designMap->getGroup(lookup[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
subset.push_back(lookup[k]);
groupsAlreadyAdded.insert(lookup[k]->getGroup());
}
vector<SharedRAbundFloatVector*> subset;
//for each grouping
- for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
for (int k = 0; k < lookupFloat.size(); k++) {
//are you from this grouping?
- if (designMap->getGroup(lookupFloat[k]->getGroup()) == designMap->namesOfGroups[i]) {
+ if (designMap->getGroup(lookupFloat[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
subset.push_back(lookupFloat[k]);
groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
}
if (m->control_pressed) { out.close(); return 0; }
- out << (j+1) << '\t' << indicatorValues[j] << '\t';
+ out << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; }
else { out << "<" << (1/(float)iters) << endl; }
if (pValues[j] <= 0.05) {
- cout << "OTU" << j+1 << '\t' << indicatorValues[j] << '\t';
+ cout << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
string pValueString = "<" + toString((1/(float)iters));
if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
else { cout << "<" << (1/(float)iters); }
- m->mothurOutJustToLog("OTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
m->mothurOutEndLine();
}
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
//print headings
out << "TreeNode\t";
- for (int i = 0; i < numBins; i++) { out << "OTU" << (i+1) << "_IndValue" << '\t' << "pValue" << '\t'; }
+ for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
out << endl;
m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n");
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+ string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
}
if (pValues[j] <= 0.05) {
- cout << i+1 << "\tOTU" << j+1 << '\t' << indicatorValues[j] << '\t';
+ cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
string pValueString = "<" + toString((1/(float)iters));
if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
else { cout << "<" << (1/(float)iters); }
- m->mothurOutJustToLog(toString(i) + "\tOTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
m->mothurOutEndLine();
}
}
try {
vector<float> pvalues;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
in >> numTemp; m->gobble(in);
pvalues[j] += numTemp;
}
- in.close(); remove(tempFile.c_str());
+ in.close(); m->mothurRemove(tempFile);
}
for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
}
try {
vector<float> pvalues;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
in >> numTemp; m->gobble(in);
pvalues[j] += numTemp;
}
- in.close(); remove(tempFile.c_str());
+ in.close(); m->mothurRemove(tempFile);
}
for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
}
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