*/
#include "sharedcommand.h"
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
+ return (left->getGroup() < right->getGroup());
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getValidParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){
+ try {
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "SharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
//getting output filename
filename = globaldata->inputFileName;
- if (outputDir == "") { outputDir += hasPath(filename); }
+ if (outputDir == "") { outputDir += m->hasPath(filename); }
- filename = outputDir + getRootName(getSimpleName(filename));
+ filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
+ outputTypes["shared"].push_back(filename);
- openOutputFile(filename, out);
+ m->openOutputFile(filename, out);
pickedGroups = false;
groupMap = globaldata->gGroupmap;
}
//set fileroot
- fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
+ fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
//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"));
}
}
catch(exception& e) {
- errorOut(e, "SharedCommand", "SharedCommand");
+ m->errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
}
//lookup.clear();
string errorOff = "no error";
//errorOff = "";
-cout << globaldata->inputFileName << endl;
+
+ //if user provided an order file containing the order the shared file should be in read it
+ if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ 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 1;
+ }
+
if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
- mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
+ m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
remove(filename.c_str()); //remove blank shared file you made
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
+ delete input;
+ globaldata->ginput = NULL;
delete SharedList;
globaldata->gSharedList = NULL;
groups += globaldata->Groups[i] + ".";
}
- string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
ofstream outGroups;
- openOutputFile(newGroupFile, outGroups);
+ m->openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
set<string> userLabels = globaldata->labels;
while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ 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 1;
+ }
if(globaldata->allLines == 1 || globaldata->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);
}
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ 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 1;
+ }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
userLabels.erase(SharedList->getLabel());
}
- if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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);
}
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ 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 1;
+ }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
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);
}
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ if (m->control_pressed) {
+ delete input; globaldata->ginput = NULL;
+ 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 1;
+ }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete it3->second;
}
+
+ //change format to shared to speed up commands
+ globaldata->setFormat("sharedfile");
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
globaldata->setSharedFile(filename);
+
+ if (m->control_pressed) {
+ delete input; globaldata->ginput = NULL;
+ remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ //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); }
+ }
+
+ 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) {
- errorOut(e, "SharedCommand", "execute");
+ m->errorOut(e, "SharedCommand", "execute");
exit(1);
}
}
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
try {
- //initialize bin values
- for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
+ if (order.size() == 0) { //user has not specified an order so do aplabetically
+ sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+
+ globaldata->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);
+
+ globaldata->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];
+ }
+
+ globaldata->Groups.clear();
- RAbundVector rav = thislookup[i]->getRAbundVector();
- openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
- rav.print(*(filehandles[thislookup[i]->getGroup()]));
- (*(filehandles[thislookup[i]->getGroup()])).close();
+ //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);
+
+ globaldata->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) {
- errorOut(e, "SharedCommand", "printSharedData");
+ m->errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
}
//**********************************************************************************************************************
-void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
try {
vector<SharedRAbundVector*> newLookup;
//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++) { delete thislookup[j]; }
thislookup = newLookup;
-
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+ m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
exit(1);
}
}
//**********************************************************************************************************************
-void SharedCommand::createMisMatchFile() {
+int SharedCommand::createMisMatchFile() {
try {
ofstream outMisMatch;
- string outputMisMatchName = getRootName(globaldata->inputFileName);
+ string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
//you have sequences in your list file that are not in your group file
if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
outputMisMatchName += "missing.group";
- mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+ 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();
- openOutputFile(outputMisMatchName, outMisMatch);
+ 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);
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; }
+ 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";
- mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+ 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);
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;
}
map<string, string>::iterator itMatch;
- openOutputFile(outputMisMatchName, outMisMatch);
+ 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]);
}
outMisMatch.close();
}
-
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "SharedCommand", "createMisMatchFile");
+ m->errorOut(e, "SharedCommand", "createMisMatchFile");
exit(1);
}
}
}
-
+//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+ try {
+ //remove old names
+ order.clear();
+
+ ifstream in;
+ m->openInputFile(globaldata->getOrderGroupFile(), 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) {
return false;
}
catch(exception& e) {
- errorOut(e, "SharedCommand", "isValidGroup");
+ m->errorOut(e, "SharedCommand", "isValidGroup");
exit(1);
}
}
projects / mothur.git / blobdiff