*/
#include "sharedcommand.h"
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
+ return (left->getGroup() < right->getGroup());
+}
//**********************************************************************************************************************
-
-SharedCommand::SharedCommand(){
+vector<string> SharedCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+ CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- //getting output filename
- filename = globaldata->inputFileName;
- filename = getRootName(filename);
- filename = filename + "shared";
- openOutputFile(filename, out);
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedCommand", "setParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string SharedCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The make.shared command reads a list and group file and creates a shared file, as well as a rabund file for each group.\n";
+ helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
+ helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
+ helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
+ helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "SharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ 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("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("ordergroup");
+ //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["ordergroup"] = inputDir + it->second; }
+ }
+ }
+
+
+ //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 = ""; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+ if (ordergroupfile == "not open") { abort = true; }
+ else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") {
+ m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ m->namesOfGroups = groupMap->namesOfGroups;
+ }
+ else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else {
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ m->namesOfGroups = groupMap->namesOfGroups;
+ m->setGroupFile(groupfile);
+ }
+
+ string groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
-
}
//**********************************************************************************************************************
int SharedCommand::execute(){
try {
- globaldata = GlobalData::getInstance();
+
+ 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->namesOfGroups; m->Groups = 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++) {
+ remove((fileroot + Groups[i] + ".rabund").c_str());
+ outputNames.push_back((fileroot + Groups[i] + ".rabund"));
+ outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
+ }
+
//lookup.clear();
- int count = 1;
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(); remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
+ }
+
+ if ((m->Groups.size() == 0) && (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();
- //read in listfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- SharedListVector* lastList = SharedList;
- //lookup = SharedList->getSharedRAbundVector();
- //vector<SharedRAbundVector*> lastLookup = lookup;
+ out.close();
+ remove(filename.c_str()); //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 user has specified groups make new groupfile for them
+ if (pickedGroups) { //make new group file
+ string groups = "";
+ if (m->Groups.size() < 4) {
+ for (int i = 0; i < m->Groups.size(); i++) {
+ groups += m->Groups[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->Groups)) {
+ 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 = globaldata->labels;
- set<int> userLines = globaldata->lines;
-
- shared = new Shared();
+ 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(); remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
+ }
- while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
-
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+ 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(); remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
+ }
- shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
-
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->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(); remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
+ }
+
+ 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);
}
- if (count != 1) { delete lastList; }
- lastList = SharedList;
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
-
- //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- //lastLookup = lookup;
- //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- //cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- //cout << ". I will use " << lastList->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
- }else {
- //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
+ 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(); remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
+ }
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ delete SharedList;
}
- delete lastList;
- delete shared;
out.close();
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+
+ delete input; delete groupMap;
+
+ if (m->control_pressed) {
+ remove(filename.c_str());
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
+ try {
+
+ if (order.size() == 0) { //user has not specified an order so do aplabetically
+ sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+
+ m->Groups.clear();
+
+ //initialize bin values
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+
+ m->Groups.push_back(thislookup[i]->getGroup());
+
+ RAbundVector rav = thislookup[i]->getRAbundVector();
+ m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ rav.print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
+ }
+ }else{
+ //create a map from groupName to each sharedrabund
+ map<string, SharedRAbundVector*> myMap;
+ map<string, SharedRAbundVector*>::iterator myIt;
+
+ for (int i = 0; i < thislookup.size(); i++) {
+ myMap[thislookup[i]->getGroup()] = thislookup[i];
+ }
+
+ m->Groups.clear();
+
+ //loop through ordered list and print the rabund
+ for (int i = 0; i < order.size(); i++) {
+ myIt = myMap.find(order[i]);
+
+ if(myIt != myMap.end()) { //we found it
+ out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
+ (myIt->second)->print(out);
+
+ m->Groups.push_back((myIt->second)->getGroup());
+
+ RAbundVector rav = (myIt->second)->getRAbundVector();
+ m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+ rav.print(*(filehandles[(myIt->second)->getGroup()]));
+ (*(filehandles[(myIt->second)->getGroup()])).close();
+ }else{
+ m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+ }
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
-
}
//**********************************************************************************************************************
-void SharedCommand::printSharedData() {
+int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
try {
-
- ///for (int i = 0; i < thislookup.size(); i++) {
- // out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
-//cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- // thislookup[i]->print(out);
- // }
- //prints out horizontally
- for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
- out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
- it->second->print(out); // prints sharedrabundvector
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ //else{ cout << "bin # " << i << " is all zeros" << endl; }
}
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+ thislookup = newLookup;
+
+ return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+int SharedCommand::createMisMatchFile() {
+ try {
+ ofstream outMisMatch;
+ string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
+
+ //you have sequences in your list file that are not in your group file
+ if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
+ outputMisMatchName += "missing.group";
+ m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
+
+ m->openOutputFile(outputMisMatchName, outMisMatch);
+
+ map<string, string> listNames;
+ map<string, string>::iterator itList;
+
+ //go through list and if group returns "not found" output it
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
+ if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ string group = groupMap->getGroup(name);
+
+ if(group == "not found") { outMisMatch << name << endl; }
+
+ itList = listNames.find(name);
+ if (itList != listNames.end()) { m->mothurOut(name + " is in your list file more than once. Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+ else { listNames[name] = name; }
+ }
+
+ //get last name
+ string group = groupMap->getGroup(names);
+ if(group == "not found") { outMisMatch << names << endl; }
+
+ itList = listNames.find(names);
+ if (itList != listNames.end()) { m->mothurOut(names + " is in your list file more than once. Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+ else { listNames[names] = names; }
+
+ }
+
+ outMisMatch.close();
+
+
+ }else {//you have sequences in your group file that are not in you list file
+
+ outputMisMatchName += "missing.name";
+ m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
+
+ map<string, string> namesInList;
+ map<string, string>::iterator itList;
+
+ //go through listfile and get names
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+
+ itList = namesInList.find(name);
+ if (itList != namesInList.end()) { m->mothurOut(name + " is in your list file more than once. Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+
+ namesInList[name] = name;
+
+ }
+
+ itList = namesInList.find(names);
+ if (itList != namesInList.end()) { m->mothurOut(names + " is in your list file more than once. Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
+
+ //get last name
+ namesInList[names] = names;
+ }
+
+ //get names of sequences in groupfile
+ vector<string> seqNames = groupMap->getNamesSeqs();
+
+ map<string, string>::iterator itMatch;
+
+ m->openOutputFile(outputMisMatchName, outMisMatch);
+
+ //loop through names in seqNames and if they aren't in namesIn list output them
+ for (int i = 0; i < seqNames.size(); i++) {
+ if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
+
+ itMatch = namesInList.find(seqNames[i]);
+
+ if (itMatch == namesInList.end()) {
+
+ outMisMatch << seqNames[i] << endl;
+ }
+ }
+ outMisMatch.close();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "createMisMatchFile");
exit(1);
}
-
}
//**********************************************************************************************************************
SharedCommand::~SharedCommand(){
//delete list;
- delete read;
+
}
-
//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+ try {
+ //remove old names
+ order.clear();
+
+ ifstream in;
+ m->openInputFile(ordergroupfile, in);
+ string thisGroup;
+
+ while(!in.eof()){
+ in >> thisGroup; m->gobble(in);
+
+ order.push_back(thisGroup);
+
+ if (m->control_pressed) { order.clear(); break; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "readOrderFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
+ try {
+ for (int i = 0; i < groups.size(); i++) {
+ if (groupname == groups[i]) { return true; }
+ }
+
+ return false;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "isValidGroup");
+ exit(1);
+ }
+}
+/************************************************************/
+
+
projects / mothur.git / blobdiff