int SharedCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//getting output filename
filename = listfile;
if (outputDir == "") { outputDir += m->hasPath(filename); }
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
m->openOutputFile(filename, out);
pickedGroups = false;
//if hte user has not specified any groups then use them all
if (Groups.size() == 0) {
Groups = groupMap->getNamesOfGroups(); m->setGroups(Groups);
}else { pickedGroups = true; }
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
for (i=0; i<Groups.size(); i++) {
temp = new ofstream;
filehandles[Groups[i]] = temp;
}
//set fileroot
fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
m->mothurRemove((fileroot + Groups[i] + ".rabund"));
outputNames.push_back((fileroot + Groups[i] + ".rabund"));
outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
}
//lookup.clear();
string errorOff = "no error";
//errorOff = "";
//if user provided an order file containing the order the shared file should be in read it
if (ordergroupfile != "") { readOrderFile(); }
input = new InputData(listfile, "shared");
SharedList = input->getSharedListVector();
string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//sanity check
int error = ListGroupSameSeqs();
if ((!pickedGroups) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
m->mothurRemove(filename); //remove blank shared file you made
createMisMatchFile();
//delete memory
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete SharedList; delete groupMap;
return 0;
}
if (error == 1) { m->control_pressed = true; }
//if user has specified groups make new groupfile for them
if (pickedGroups) { //make new group file
string groups = "";
if (m->getNumGroups() < 4) {
for (int i = 0; i < m->getNumGroups(); i++) {
groups += (m->getGroups())[i] + ".";
}
}else { groups = "merge"; }
string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
m->openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, m->getGroups())) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun == true) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete SharedList;
}
out.close();
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete groupMap;
if (m->control_pressed) {
m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//set rabund file as new current rabundfile
string current = "";
itTypes = outputTypes.find("rabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOut(filename); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "execute");
exit(1);
}
}
int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
vector<string> setNames = designMap->getCategory();
if (method == "average") {
//create sharedRabundFloatVectors
vector<SharedRAbundFloatVector*> temp = thisLookUp[0]->getSharedRAbundFloatVectors(thisLookUp);
//follow code below
map<string, SharedRAbundFloatVector> merged;
map<string, SharedRAbundFloatVector>::iterator it;
for (int i = 0; i < setNames.size(); i++) {
SharedRAbundFloatVector myLookup(thisLookUp[0]->getNumBins());
myLookup.setLabel(thisLookUp[0]->getLabel());
merged[setNames[i]] = myLookup;
}
map<string, vector<int> > clearGroupAbunds;
map<string, vector<int> >::iterator itAbunds;
for (int i = 0; i < temp.size(); i++) {
if (m->control_pressed) { return 0; }
//what grouping does this group belong to
string grouping = designMap->get(temp[i]->getGroup());
if (grouping == "not found") { m->mothurOut("[ERROR]: " + temp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
else {
//do we already have a member of this grouping?
it = merged.find(grouping);
if (it == merged.end()) { //nope, so create it
merged[grouping] = *temp[i];
merged[grouping].setGroup(grouping);
vector<int> temp;
clearGroupAbunds[grouping] = temp;
}
}
}
for (int j = 0; j < temp[0]->getNumBins(); j++) {
if (m->control_pressed) { return 0; }
map<string, vector<int> > otusGroupAbunds = clearGroupAbunds;
for (int i = 0; i < temp.size(); i++) {
string grouping = designMap->get(temp[i]->getGroup());
if (grouping == "not found") { m->mothurOut("[ERROR]: " + temp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
else {
otusGroupAbunds[grouping].push_back(temp[i]->getAbundance(j));
}
}
for (itAbunds = otusGroupAbunds.begin(); itAbunds != otusGroupAbunds.end(); itAbunds++) {
int abund = mergeAbund(itAbunds->second);
merged[itAbunds->first].set(j, abund, itAbunds->first);
}
}
if (method == "median") {
vector<SharedRAbundFloatVector*> temp2;
for (it = merged.begin(); it != merged.end(); it++) { temp2.push_back(&(it->second)); }
eliminateZeroOTUS(temp2);
}
//print new file
for (it = merged.begin(); it != merged.end(); it++) {
if (!m->printedSharedHeaders) { (it->second).printHeaders(out); }
out << (it->second).getLabel() << '\t' << it->first << '\t';
(it->second).print(out);
}
}else {
map<string, SharedRAbundVector> merged;
map<string, SharedRAbundVector>::iterator it;
for (int i = 0; i < setNames.size(); i++) {
SharedRAbundVector myLookup(thisLookUp[0]->getNumBins());
myLookup.setLabel(thisLookUp[0]->getLabel());
merged[setNames[i]] = myLookup;
}
map<string, vector<int> > clearGroupAbunds;
map<string, vector<int> >::iterator itAbunds;
for (int i = 0; i < thisLookUp.size(); i++) {
if (m->control_pressed) { return 0; }
//what grouping does this group belong to
string grouping = designMap->get(thisLookUp[i]->getGroup());
if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
else {
//do we already have a member of this grouping?
it = merged.find(grouping);
if (it == merged.end()) { //nope, so create it
merged[grouping] = *thisLookUp[i];
merged[grouping].setGroup(grouping);
vector<int> temp;
clearGroupAbunds[grouping] = temp;
}
}
}
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
if (m->control_pressed) { return 0; }
map<string, vector<int> > otusGroupAbunds = clearGroupAbunds;
for (int i = 0; i < thisLookUp.size(); i++) {
string grouping = designMap->get(thisLookUp[i]->getGroup());
if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
else {
otusGroupAbunds[grouping].push_back(thisLookUp[i]->getAbundance(j));
}
}
for (itAbunds = otusGroupAbunds.begin(); itAbunds != otusGroupAbunds.end(); itAbunds++) {
int abund = mergeAbund(itAbunds->second);
merged[itAbunds->first].set(j, abund, itAbunds->first);
}
}
if (method == "median") {
vector<SharedRAbundVector*> temp;
for (it = merged.begin(); it != merged.end(); it++) { temp.push_back(&(it->second)); }
eliminateZeroOTUS(temp);
}
//print new file
for (it = merged.begin(); it != merged.end(); it++) {
if (!m->printedSharedHeaders) { (it->second).printHeaders(out); }
out << (it->second).getLabel() << '\t' << it->first << '\t';
(it->second).print(out);
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "process");
exit(1);
}
}
int CorrAxesCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
/*************************************************************************************/
// use smart distancing to get right sharedRabund and convert to relabund if needed //
/************************************************************************************/
if (sharedfile != "") {
InputData* input = new InputData(sharedfile, "sharedfile");
getSharedFloat(input);
delete input;
if (m->control_pressed) { 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; }
}else if (relabundfile != "") {
InputData* input = new InputData(relabundfile, "relabund");
getSharedFloat(input);
delete input;
if (m->control_pressed) { 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; }
}else if (metadatafile != "") {
getMetadata(); //reads metadata file and store in lookupFloat, saves column headings in metadataLabels for later
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading metadata file."); m->mothurOutEndLine(); return 0; }
if (pickedGroups) { eliminateZeroOTUS(lookupFloat); }
}else { m->mothurOut("[ERROR]: no file given."); m->mothurOutEndLine(); return 0; }
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
//this is for a sanity check to make sure the axes file and shared file match
for (int i = 0; i < lookupFloat.size(); i++) { names.insert(lookupFloat[i]->getGroup()); }
/*************************************************************************************/
// read axes file and check for file mismatches with shared or relabund file //
/************************************************************************************/
//read axes file
map<string, vector<float> > axes = readAxes();
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
//sanity check, the read only adds groups that are in the shared or relabund file, but we want to make sure the axes file isn't missing anyone
if (axes.size() != lookupFloat.size()) {
map<string, vector<float> >::iterator it;
for (int i = 0; i < lookupFloat.size(); i++) {
it = axes.find(lookupFloat[i]->getGroup());
if (it == axes.end()) { m->mothurOut(lookupFloat[i]->getGroup() + " is in your shared of relabund file but not in your axes file, please correct."); m->mothurOutEndLine(); }
}
m->control_pressed = true;
}
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
/*************************************************************************************/
// calc the r values //
/************************************************************************************/
string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes";
outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//output headings
if (metadatafile == "") { out << "OTU"; }
else { out << "Feature"; }
for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1) << "\tp-value"; }
out << "\tlength" << endl;
if (method == "pearson") { calcPearson(axes, out); }
else if (method == "spearman") { calcSpearman(axes, out); }
else if (method == "kendall") { calcKendall(axes, out); }
else { m->mothurOut("[ERROR]: Invalid method."); m->mothurOutEndLine(); }
out.close();
for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
if (m->control_pressed) { return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "execute");
exit(1);
}
}
