//**********************************************************************************************************************
vector<string> RemoveOtuLabelsCommand::setParameters(){
try {
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
- CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
- CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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); }
string RemoveOtuLabelsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
- helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n";
+ helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes. It can also be used to select a set of otus from a shared or list file.\n";
+ helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, shared, list, label and accnos.\n";
helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
helpString += "The otucorr parameter is input the results of the otu.association command.\n";
helpString += "The corraxes parameter is input the results of the corr.axes command.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input. \n";
helpString += "The remove.otulabels commmand should be in the following format: \n";
helpString += "remove.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
return helpString;
}
}
//**********************************************************************************************************************
-string RemoveOtuLabelsCommand::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 == "constaxonomy") { outputFileName = "pick.taxonomy"; }
- else if (type == "otucorr") { outputFileName = "pick.corr"; }
- else if (type == "corraxes") { outputFileName = "pick.axes"; }
- 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, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
- exit(1);
- }
+string RemoveOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "corraxes") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[distance],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[distance],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["contaxonomy"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
outputTypes["otucorr"] = tempOutNames;
outputTypes["corraxes"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["otucorr"] = inputDir + it->second; }
}
+
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
}
vector<string> tempOutNames;
outputTypes["constaxonomy"] = tempOutNames;
outputTypes["otucorr"] = tempOutNames;
outputTypes["corraxes"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+
//check for parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
else if (otucorrfile == "not found") { otucorrfile = ""; }
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
- if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; }
+ if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "") && (sharedfile == "") && (listfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes, otucorr, shared or list."); m->mothurOutEndLine(); abort = true; }
+
+ if ((sharedfile != "") || (listfile != "")) {
+ 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=""; }
+ }
}
}
//get labels you want to keep
labels = m->readAccnos(accnosfile);
+ //simplfy labels
+ set<string> newLabels;
+ for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) { newLabels.insert(m->getSimpleLabel(*it)); }
+ labels = newLabels;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: numlabels = " + toString(labels.size()) + "\n"); }
if (m->control_pressed) { return 0; }
if (constaxonomyfile != "") { readClassifyOtu(); }
if (corraxesfile != "") { readCorrAxes(); }
if (otucorrfile != "") { readOtuAssociation(); }
+ if (listfile != "") { readList(); }
+ if (sharedfile != "") { readShared(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+ variables["[extension]"] = m->getExtension(constaxonomyfile);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
int removedCount = 0;
//read headers
- string headers = m->getline(in);
+ string headers = m->getline(in); m->gobble(in);
out << headers << endl;
while (!in.eof()) {
in >> otu >> size >> tax; m->gobble(in);
- if (labels.count(otu) == 0) {
+ if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }
+
+ if (labels.count(m->getSimpleLabel(otu)) == 0) {
wroteSomething = true;
out << otu << '\t' << size << '\t' << tax << endl;
}else { removedCount++; }
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+ variables["[extension]"] = m->getExtension(otucorrfile);
+ string outputFileName = getOutputFileName("otucorr", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
int removedCount = 0;
//read headers
- string headers = m->getline(in);
+ string headers = m->getline(in); m->gobble(in);
out << headers << endl;
while (!in.eof()) {
in >> otu1 >> otu2;
string line = m->getline(in); m->gobble(in);
- if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
+ if ((labels.count(m->getSimpleLabel(otu1)) == 0) && (labels.count(m->getSimpleLabel(otu2)) == 0)){
wroteSomething = true;
out << otu1 << '\t' << otu2 << '\t' << line << endl;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+ variables["[extension]"] = m->getExtension(corraxesfile);
+ string outputFileName = getOutputFileName("corraxes", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
int removedCount = 0;
//read headers
- string headers = m->getline(in);
+ string headers = m->getline(in); m->gobble(in);
out << headers << endl;
while (!in.eof()) {
in >> otu;
string line = m->getline(in); m->gobble(in);
- if (labels.count(otu) == 0) {
+ if (labels.count(m->getSimpleLabel(otu)) == 0) {
wroteSomething = true;
out << otu << '\t' << line << endl;
}
}
//**********************************************************************************************************************
+int RemoveOtuLabelsCommand::readShared(){
+ try {
+
+ getShared();
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+
+ vector<string> newLabels;
+
+ //create new "filtered" lookup
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(lookup[i]->getLabel());
+ temp->setGroup(lookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ bool wroteSomething = false;
+ int numRemoved = 0;
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) {
+
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
+
+ //is this otu on the list
+ if (labels.count(m->getSimpleLabel(m->currentSharedBinLabels[i])) == 0) {
+ wroteSomething = true;
+ newLabels.push_back(m->currentSharedBinLabels[i]);
+ for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
+ newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
+ }
+ }else { numRemoved++; }
+ }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
+
+ m->currentSharedBinLabels = newLabels;
+
+ newLookup[0]->printHeaders(out);
+
+ for (int i = 0; i < newLookup.size(); i++) {
+ out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
+ newLookup[i]->print(out);
+ }
+ out.close();
+
+ for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine(); }
+
+ m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "readShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveOtuLabelsCommand::readList(){
+ try {
+ getListVector();
+
+ if (m->control_pressed) { delete list; return 0;}
+
+ ListVector newList;
+ newList.setLabel(list->getLabel());
+ int removedCount = 0;
+ bool wroteSomething = false;
+ string snumBins = toString(list->getNumBins());
+
+ for (int i = 0; i < list->getNumBins(); i++) {
+
+ if (m->control_pressed) { delete list; return 0;}
+
+ //create a label for this otu
+ string otuLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { otuLabel += "0"; }
+ }
+ otuLabel += sbinNumber;
+
+ if (labels.count(m->getSimpleLabel(otuLabel)) == 0) {
+ newList.push_back(list->get(i));
+ }else { removedCount++; }
+ }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ variables["[distance]"] = list->getLabel();
+ string outputFileName = getOutputFileName("list", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ delete list;
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only OTUs from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
+
+ m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveOtuLabelsCommand::getListVector(){
+ try {
+ InputData input(listfile, "list");
+ list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ if (label == "") { label = lastLabel; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return 0; }
+
+ if(labels.count(list->getLabel()) == 1){
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = list->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ delete list;
+ list = input.getListVector();
+ }
+
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ delete list;
+ list = input.getListVector(lastLabel);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "getListVector");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveOtuLabelsCommand::getShared(){
+ try {
+ InputData input(sharedfile, "sharedfile");
+ lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (label == "") { label = lastLabel; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return 0; }
+
+ if(labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+ }
+
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "getShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff