*/
#include "sharedcommand.h"
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
+ return (left->getGroup() < right->getGroup());
+}
//**********************************************************************************************************************
-SharedCommand::SharedCommand(){
+SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
//getting output filename
filename = globaldata->inputFileName;
- filename = getRootName(filename);
+ if (outputDir == "") { outputDir += m->hasPath(filename); }
+
+ filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
- openOutputFile(filename, out);
+
+ m->openOutputFile(filename, out);
+ pickedGroups = false;
groupMap = globaldata->gGroupmap;
+ //if hte user has not specified any groups then use them all
+ if (globaldata->Groups.size() == 0) {
+ groups = groupMap->namesOfGroups;
+ }else{ //they have specified groups
+ groups = globaldata->Groups;
+ pickedGroups = true;
+ }
+
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
- for (i=0; i<groupMap->getNumGroups(); i++) {
+ for (i=0; i<groups.size(); i++) {
temp = new ofstream;
- filehandles[groupMap->namesOfGroups[i]] = temp;
+ filehandles[groups[i]] = temp;
}
//set fileroot
- fileroot = getRootName(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<groupMap->getNumGroups(); i++) {
- remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+ for (int i=0; i<groups.size(); i++) {
+ remove((fileroot + groups[i] + ".rabund").c_str());
+ outputNames.push_back((fileroot + groups[i] + ".rabund"));
}
}
catch(exception& e) {
- errorOut(e, "SharedCommand", "SharedCommand");
+ m->errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
}
try {
//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 (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
+ delete read;
input = globaldata->ginput;
SharedList = globaldata->gSharedList;
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
+ 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
+
+ createMisMatchFile();
+
+ //delete memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+ delete input;
+ globaldata->ginput = NULL;
+ delete SharedList;
+ globaldata->gSharedList = NULL;
+
+ return 1;
+ }
+
+ //if user has specified groups make new groupfile for them
+ if (globaldata->Groups.size() != 0) { //make new group file
+ string groups = "";
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups += globaldata->Groups[i] + ".";
+ }
+
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
+ 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, globaldata->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;
-
+ 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;
+ }
- 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(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
+ 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; 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]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
- userLines.erase(count);
}
- 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();
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ 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; 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]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
+
+ //restore real lastlabel to save below
+ SharedList->setLabel(saveLabel);
}
delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
-
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete SharedList;
+ if (SharedList != NULL) { delete SharedList; }
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ 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; 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]; }
}
globaldata->gSharedList = NULL;
- delete read;
out.close();
}
+ //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;
+ }
+
+ 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
+ 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();
+
+ //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) {
+ m->errorOut(e, "SharedCommand", "printSharedData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
for (int i = 0; i < thislookup.size(); i++) {
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
+ 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; }
+ }
- openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
- (*filehandles[thislookup[i]->getGroup()]) << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(*(filehandles[thislookup[i]->getGroup()]));
- (*(filehandles[thislookup[i]->getGroup()])).close();
+ //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) {
- errorOut(e, "SharedCommand", "printSharedData");
+ m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SharedCommand::createMisMatchFile() {
+ try {
+ ofstream outMisMatch;
+ 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";
+ 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);
}
}
}
-
//**********************************************************************************************************************
+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) {
+ 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