*/
#include "indicatorcommand.h"
+#include "sharedutilities.h"
+
//**********************************************************************************************************************
vector<string> IndicatorCommand::getValidParameters(){
try {
- string Array[] = {"tree","shared","relabund","label","groups","outputdir","inputdir"};
+ string Array[] = {"tree","shared","relabund","design","label","groups","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string Array[] = {"tree","shared","relabund","groups","label","outputdir","inputdir"};
+ string Array[] = {"tree","shared","design","relabund","groups","label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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 = ""; }
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); }
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 indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n");
+ m->mothurOut("The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n");
+ m->mothurOut("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");
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");
if (abort == true) { return 0; }
+ //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
+ globaldata->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 != "") { globaldata->Groups = Groups; }
/***************************************************/
// reading tree info //
globaldata->setGroupFile(groupfile);
treeMap = new TreeMap();
bool mismatch = false;
+
for (int i = 0; i < globaldata->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(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;
+ }
+ treeMap->addSeq(globaldata->Treenames[i], "Group1");
+ }else{
+ vector<string> myGroups; myGroups.push_back(globaldata->Treenames[i]);
+ vector<string> myNames = designMap->getNamesSeqs(myGroups);
+
+ for(int k = 0; k < myNames.size(); k++) {
+ if (!(m->inUsersGroups(myNames[k], globaldata->gGroupmap->namesOfGroups))) {
+ m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ }
+ treeMap->addSeq(globaldata->Treenames[i], "Group1");
}
- treeMap->addSeq(globaldata->Treenames[i], "Group1");
}
+
+ if ((designfile != "") && (globaldata->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;
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]; } globaldata->gTree.clear();
- 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;
/***************************************************/
GetIndicatorSpecies(outputTree);
+ if (designfile != "") { delete designMap; }
+
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]; } }
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";
}
if (groupsAlreadyAdded.size() != lookup.size()) { 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; }
- //}
-
+
indicatorValues = getValues(groupings);
}else {
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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