*/
#include "indicatorcommand.h"
+#include "sharedutilities.h"
+
+
//**********************************************************************************************************************
-vector<string> IndicatorCommand::getValidParameters(){
+vector<string> IndicatorCommand::setParameters(){
try {
- string Array[] = {"tree","shared","relabund","label","groups","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "IndicatorCommand", "getValidParameters");
+ m->errorOut(e, "IndicatorCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> IndicatorCommand::getRequiredParameters(){
+string IndicatorCommand::getHelpString(){
try {
- string Array[] = {"tree"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \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 design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\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";
+ helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
+ helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "IndicatorCommand", "getRequiredParameters");
+ m->errorOut(e, "IndicatorCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
exit(1);
}
}
-
-//**********************************************************************************************************************
-vector<string> IndicatorCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "IndicatorCommand", "getRequiredFiles");
- exit(1);
- }
-}
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//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
- string Array[] = {"tree","shared","relabund","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- globaldata->newRead();
+ m->runParse = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
if (path == "") { parameters["relabund"] = inputDir + it->second; }
}
+ it = parameters.find("design");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["design"] = inputDir + it->second; }
+ }
}
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (treefile == "not open") { abort = true; }
- else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the indicator command."); m->mothurOutEndLine(); abort = true; }
- else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; }
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; Groups.push_back("all"); }
else { m->splitAtDash(groups, Groups); }
- globaldata->Groups = Groups;
+ m->Groups = 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=""; }
- if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true; }
+ if ((relabundfile == "") && (sharedfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then relabund
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
}
//**********************************************************************************************************************
-void IndicatorCommand::help(){
- try {
- m->mothurOut("The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n");
- m->mothurOut("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");
- m->mothurOut("The summary file lists the indicator value for each OTU for each node.\n");
- m->mothurOut("The indicator command parameters are tree, groups, shared, relabund and label. The tree parameter is required as well as either shared or relabund.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed. The groups may be entered separated by dashes.\n");
- m->mothurOut("The label parameter indicates at what distance your tree relates to the shared or relabund.\n");
- m->mothurOut("The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "IndicatorCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-IndicatorCommand::~IndicatorCommand(){}
-
-//**********************************************************************************************************************
-
int IndicatorCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //read designfile if given and set up globaldatas 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;
+
+ //loop through the Groups and fill Globaldata's Groups with the design file info
+ m->Groups = designMap->getNamesSeqs(Groups);
+ }
/***************************************************/
// use smart distancing to get right sharedRabund //
/***************************************************/
if (sharedfile != "") {
getShared();
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
}else {
getSharedFloat();
- if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
}
+
+ //reset Globaldatas groups if needed
+ if (designfile != "") { m->Groups = Groups; }
/***************************************************/
// reading tree info //
/***************************************************/
string groupfile = "";
Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
-
- globaldata->setGroupFile(groupfile);
treeMap = new TreeMap();
bool mismatch = false;
- for (int i = 0; i < globaldata->Treenames.size(); i++) {
+
+ for (int i = 0; i < m->Treenames.size(); i++) {
//sanity check - is this a group that is not in the sharedfile?
- if (!(m->inUsersGroups(globaldata->Treenames[i], globaldata->gGroupmap->namesOfGroups))) {
- m->mothurOut("[ERROR]: " + globaldata->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
- mismatch = true;
+ if (designfile == "") {
+ if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
+ 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");
+ }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))) {
+ 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");
}
- treeMap->addSeq(globaldata->Treenames[i], "Group1");
}
+
+ if ((designfile != "") && (m->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
if (mismatch) { //cleanup and exit
+ 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;
return 0;
}
-
- globaldata->gTreemap = treeMap;
read = new ReadNewickTree(treefile);
- int readOk = read->read();
+ int readOk = read->read(treeMap);
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; delete read; return 0; }
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
- vector<Tree*> T = globaldata->gTree;
+ vector<Tree*> T = read->getTrees();
delete read;
- if (m->control_pressed) {
+ 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]; } }
- for (int i = 0; i < T.size(); i++) { delete T[i]; } globaldata->gTree.clear(); delete globaldata->gTreemap; return 0;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
}
T[0]->assembleTree();
/***************************************************/
// create ouptut tree - respecting pickedGroups //
/***************************************************/
- Tree* outputTree = new Tree(globaldata->Groups.size());
+ Tree* outputTree = new Tree(m->Groups.size(), treeMap);
- outputTree->getSubTree(T[0], globaldata->Groups);
+ outputTree->getSubTree(T[0], m->Groups);
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]; } globaldata->gTree.clear();
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
- if (m->control_pressed) {
+ 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 globaldata->gTreemap; return 0;
+ delete outputTree; delete treeMap; return 0;
}
/***************************************************/
/***************************************************/
GetIndicatorSpecies(outputTree);
- if (m->control_pressed) {
- 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 < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- delete outputTree; delete globaldata->gTreemap; return 0;
+ 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;
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //set tree file as new current treefile
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
}
m->mothurOutEndLine();
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
+
+ int numBins = 0;
+ if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
+ else { numBins = lookupFloat[0]->getNumBins(); }
+
+ //print headings
+ out << "TreeNode\t";
+ for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
+ out << endl;
+
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
//you need the distances to leaf to decide grouping below
//this will also set branch lengths if the tree does not include them
- map<int, float> distToLeaf = getLengthToLeaf(T);
+ map<int, float> distToRoot = getDistToRoot(T);
//for each node
for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
//get nodes that will be a valid grouping
//you are valid if you are not one of my descendants
- //AND your distToLeaf is <= mine
- //AND your distToLeaf is >= my smallest childs
- //AND you were not added as part of a larger groupings
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
set<string> groupsAlreadyAdded;
//create a grouping with my grouping
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
- if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
+
+
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
vector<SharedRAbundVector*> subset;
int count = 0;
int doneCount = nodeToDescendants[j].size();
}
}
- if (groupsAlreadyAdded.size() != lookup.size()) { cout << i << '\t' << groupsAlreadyAdded.size() << '\t' << lookup.size() << endl; m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
- for (int k = 0; k < lookup.size(); k++) {
- if (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0) { cout << lookup[k]->getGroup() << endl; }
- }
-
+ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
indicatorValues = getValues(groupings);
}else {
//get nodes that will be a valid grouping
//you are valid if you are not one of my descendants
- //AND your distToLeaf is <= mine
- //AND your distToLeaf is >= my smallest childs
- //AND you were not added as part of a larger grouping
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
set<string> groupsAlreadyAdded;
//create a grouping with my grouping
if (subset.size() != 0) { groupings.push_back(subset); }
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
- if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
vector<SharedRAbundFloatVector*> subset;
int count = 0;
int doneCount = nodeToDescendants[j].size();
}
}
//**********************************************************************************************************************
-//you need the distances to leaf to decide groupings
+//you need the distances to root to decide groupings
//this will also set branch lengths if the tree does not include them
-map<int, float> IndicatorCommand::getLengthToLeaf(Tree*& T){
+map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
try {
map<int, float> dists;
if (T->tree[i].getBranchLength() > 0.0) { hasBranchLengths = true; break; }
}
- for (int i = 0; i < T->getNumNodes(); i++) {
-
- int lc = T->tree[i].getLChild();
- int rc = T->tree[i].getRChild();
-
- //if you have no branch length, set it then calc
- if (!hasBranchLengths) {
+ //set branchlengths if needed
+ if (!hasBranchLengths) {
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ int lc = T->tree[i].getLChild();
+ int rc = T->tree[i].getRChild();
+
if (lc == -1) { // you are a leaf
//if you are a leaf set you priliminary length to 1.0, this may adjust later
T->tree[i].setBranchLength(1.0);
float rdist = dists[rc];
float greater = ldist;
- if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0; }
+ if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
else { dists[i] = rdist + 1.0; }
+
//branch length = difference + 1
T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
}
-
- }else{
- if (lc == -1) { dists[i] = T->tree[i].getBranchLength(); }
- else { //smaller of my two children distances plus my branch length
- //look at your children's length to leaf
- float ldist = dists[lc];
- float rdist = dists[rc];
-
- float smaller = ldist;
- if (rdist < smaller) { smaller = rdist; }
-
- dists[i] = smaller + T->tree[i].getBranchLength();
+ }
+ }
+
+ dists.clear();
+
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ double sum = 0.0;
+ int index = i;
+
+ while(T->tree[index].getParent() != -1){
+ if (T->tree[index].getBranchLength() != -1) {
+ sum += abs(T->tree[index].getBranchLength());
}
+ index = T->tree[index].getParent();
}
+ dists[i] = sum;
}
return dists;
if (lc == -1) { //you are a leaf your only descendant is yourself
set<int> temp; temp.insert(i);
- names.insert(T->tree[i].getName());
nodes[i] = temp;
+
+ if (designfile == "") {
+ names.insert(T->tree[i].getName());
+ }else {
+ vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
+ vector<string> myReps = designMap->getNamesSeqs(myGroup);
+ for (int k = 0; k < myReps.size(); k++) {
+ names.insert(myReps[k]);
+ }
+ }
+
}else{ //your descedants are the combination of your childrens descendants
names = descendants[lc];
nodes[i] = nodes[lc];
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