X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=subsamplecommand.cpp;h=7a857e8df70d4ab99328e3988e1f23faf9837a49;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=036341ff48f9de13d6684fe9632da08742ee7d82;hpb=89f19f9c6ab89c2f6c7c6921a328ae87bce6f8e3;p=mothur.git diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp index 036341f..7a857e8 100644 --- a/subsamplecommand.cpp +++ b/subsamplecommand.cpp @@ -8,6 +8,7 @@ */ #include "subsamplecommand.h" +#include "sharedutilities.h" //********************************************************************************************************************** vector SubSampleCommand::getValidParameters(){ @@ -226,6 +227,9 @@ SubSampleCommand::SubSampleCommand(string option) { if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) { m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; } + if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) { + m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; } + } } @@ -270,10 +274,20 @@ int SubSampleCommand::execute(){ if (abort == true) { return 0; } if (sharedfile != "") { getSubSampleShared(); } - //if (listfile != "") { getSubSampleList(); } - //if (rabund != "") { getSubSampleRabund(); } - //if (sabundfile != "") { getSubSampleSabund(); } - //if (fastafile != "") { getSubSampleFasta(); } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } + + if (listfile != "") { getSubSampleList(); } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } + + if (rabundfile != "") { getSubSampleRabund(); } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } + + if (sabundfile != "") { getSubSampleSabund(); } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } + + if (fastafile != "") { getSubSampleFasta(); } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -288,6 +302,269 @@ int SubSampleCommand::execute(){ } } //********************************************************************************************************************** +int SubSampleCommand::getSubSampleFasta() { + try { + + if (namefile != "") { readNames(); } //fills names with all names in namefile. + else { getNames(); }//no name file, so get list of names to pick from + + GroupMap* groupMap; + if (groupfile != "") { + + groupMap = new GroupMap(groupfile); + groupMap->readMap(); + + //takes care of user setting groupNames that are invalid or setting groups=all + SharedUtil* util = new SharedUtil(); + util->setGroups(Groups, groupMap->namesOfGroups); + delete util; + + //file mismatch quit + if (names.size() != groupMap->getNumSeqs()) { + m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct."); + m->mothurOutEndLine(); + delete groupMap; + return 0; + } + } + + if (m->control_pressed) { return 0; } + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName); + + //make sure that if your picked groups size is not too big + + if (pickedGroups) { + int total = 0; + for(int i = 0; i < Groups.size(); i++) { + total += groupMap->getNumSeqs(Groups[i]); + } + + if (size == 0) { //user has not set size, set size = 10% samples size + size = int (total * 0.10); + } + + if (total < size) { + if (size != 0) { + m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine(); + } + size = int (total * 0.10); + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine(); + } + + if (size == 0) { //user has not set size, set size = 10% samples size + size = int (names.size() * 0.10); + } + + int thisSize = names.size(); + if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine(); + size = thisSize; + } + + random_shuffle(names.begin(), names.end()); + + if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); } + + //randomly select a subset of those names to include in the subsample + set subset; //dont want repeat sequence names added + for (int j = 0; j < size; j++) { + + if (m->control_pressed) { return 0; } + + //get random sequence to add, making sure we have not already added it + bool done = false; + int myrand; + while (!done) { + myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1)); + + if (subset.count(names[myrand]) == 0) { + + if (groupfile != "") { //if there is a groupfile given fill in group info + string group = groupMap->getGroup(names[myrand]); + if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; } + + if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups + if (m->inUsersGroups(group, Groups)) { + subset.insert(names[myrand]); break; + } + }else{ + subset.insert(names[myrand]); break; + } + }else{ //save everyone, group + subset.insert(names[myrand]); break; + } + } + } + } + + //read through fasta file outputting only the names on the subsample list + ifstream in; + m->openInputFile(fastafile, in); + + string thisname; + int count = 0; + map >::iterator itNameMap; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + Sequence currSeq(in); + thisname = currSeq.getName(); + + if (thisname != "") { + + //does the subset contain a sequence that this sequence represents + itNameMap = nameMap.find(thisname); + if (itNameMap != nameMap.end()) { + vector nameRepresents = itNameMap->second; + + for (int i = 0; i < nameRepresents.size(); i++){ + if (subset.count(nameRepresents[i]) != 0) { + out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl; + count++; + } + } + }else{ + m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine(); + } + } + m->gobble(in); + } + in.close(); + out.close(); + + if (count != subset.size()) { + m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine(); + } + + //if a groupfile is provided read through the group file only outputting the names on the subsample list + if (groupfile != "") { + + string groupOutputDir = outputDir; + if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); } + string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile); + + ofstream outGroup; + m->openOutputFile(groupOutputFileName, outGroup); + outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName); + + ifstream inGroup; + m->openInputFile(groupfile, inGroup); + string name, group; + + while(!inGroup.eof()){ + + if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; } + + inGroup >> name; m->gobble(inGroup); //read from first column + inGroup >> group; //read from second column + + //if this name is in the accnos file + if (subset.count(name) != 0) { + outGroup << name << '\t' << group << endl; + subset.erase(name); + } + + m->gobble(inGroup); + } + inGroup.close(); + outGroup.close(); + + //sanity check + if (subset.size() != 0) { + m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine(); + for (set::iterator it = subset.begin(); it != subset.end(); it++) { + m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine(); + } + } + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getSubSampleFasta"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::getNames() { + try { + + ifstream in; + m->openInputFile(fastafile, in); + + string thisname; + while(!in.eof()){ + + if (m->control_pressed) { in.close(); return 0; } + + Sequence currSeq(in); + thisname = currSeq.getName(); + + if (thisname != "") { + vector temp; temp.push_back(thisname); + nameMap[thisname] = temp; + names.push_back(thisname); + } + m->gobble(in); + } + in.close(); + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getNames"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::readNames() { + try { + + ifstream in; + m->openInputFile(namefile, in); + + string thisname, repnames; + map >::iterator it; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); return 0; } + + in >> thisname; m->gobble(in); //read from first column + in >> repnames; //read from second column + + it = nameMap.find(thisname); + if (it == nameMap.end()) { + + vector splitRepNames; + m->splitAtComma(repnames, splitRepNames); + + nameMap[thisname] = splitRepNames; + for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); } + + }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); } + + m->gobble(in); + } + in.close(); + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "readNames"); + exit(1); + } +} +//********************************************************************************************************************** int SubSampleCommand::getSubSampleShared() { try { @@ -302,31 +579,41 @@ int SubSampleCommand::getSubSampleShared() { InputData* input = new InputData(sharedfile, "sharedfile"); vector lookup = input->getSharedRAbundVectors(); string lastLabel = lookup[0]->getLabel(); - + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - - + + if (size == 0) { //user has not set size, set size = smallest samples size + size = lookup[0]->getNumSeqs(); + for (int i = 1; i < lookup.size(); i++) { + int thisSize = lookup[i]->getNumSeqs(); + + if (thisSize < size) { size = thisSize; } + } + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(lookup[0]->getNumSeqs()) + "."); m->mothurOutEndLine(); + //as long as you are not at the end of the file or done wih the lines you want while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if (m->control_pressed) { out.close(); return 0; } - + if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } out.close(); return 0; } + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); processShared(lookup, out); - + processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); } 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); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); @@ -342,14 +629,14 @@ int SubSampleCommand::getSubSampleShared() { lastLabel = lookup[0]->getLabel(); //prevent memory leak for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } - + //get next line to process lookup = input->getSharedRAbundVectors(); } if (m->control_pressed) { out.close(); return 0; } - + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; @@ -362,7 +649,7 @@ int SubSampleCommand::getSubSampleShared() { 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]; } } @@ -374,11 +661,12 @@ int SubSampleCommand::getSubSampleShared() { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - + + delete input; out.close(); - + return 0; - + } catch(exception& e) { m->errorOut(e, "SubSampleCommand", "getSubSampleShared"); @@ -389,25 +677,14 @@ int SubSampleCommand::getSubSampleShared() { int SubSampleCommand::processShared(vector& thislookup, ofstream& out) { try { - if (pickedGroups) { eliminateZeroOTUS(thislookup); } - - if (size == 0) { //user has not set size, set size = smallest samples size - size = thislookup[0]->getNumSeqs(); - for (int i = 1; i < thislookup.size(); i++) { - int thisSize = thislookup[i]->getNumSeqs(); - - if (thisSize < size) { size = thisSize; } - } - } - int numBins = thislookup[0]->getNumBins(); for (int i = 0; i < thislookup.size(); i++) { int thisSize = thislookup[i]->getNumSeqs(); - + if (thisSize != size) { string thisgroup = thislookup[i]->getGroup(); - + OrderVector* order = new OrderVector(); for(int p=0;pgetAbundance(p);j++){ @@ -425,6 +702,9 @@ int SubSampleCommand::processShared(vector& thislookup, ofs for (int j = 0; j < size; j++) { + + if (m->control_pressed) { delete order; return 0; } + //get random number to sample from order between 0 and thisSize-1. int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1)); @@ -440,6 +720,8 @@ int SubSampleCommand::processShared(vector& thislookup, ofs //subsampling may have created some otus with no sequences in them eliminateZeroOTUS(thislookup); + if (m->control_pressed) { return 0; } + for (int i = 0; i < thislookup.size(); i++) { out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t'; thislookup[i]->print(out); @@ -449,11 +731,627 @@ int SubSampleCommand::processShared(vector& thislookup, ofs } catch(exception& e) { - m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS"); + m->errorOut(e, "SubSampleCommand", "processShared"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::getSubSampleList() { + try { + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); + + InputData* input = new InputData(listfile, "list"); + ListVector* list = input->getListVector(); + string lastLabel = list->getLabel(); + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + + ofstream outGroup; + GroupMap* groupMap; + if (groupfile != "") { + + groupMap = new GroupMap(groupfile); + groupMap->readMap(); + + //takes care of user setting groupNames that are invalid or setting groups=all + SharedUtil* util = new SharedUtil(); + util->setGroups(Groups, groupMap->namesOfGroups); + delete util; + + //create outputfiles + string groupOutputDir = outputDir; + if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); } + string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile); + + m->openOutputFile(groupOutputFileName, outGroup); + outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName); + + //file mismatch quit + if (list->getNumSeqs() != groupMap->getNumSeqs()) { + m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct."); + m->mothurOutEndLine(); + delete groupMap; + delete list; + delete input; + out.close(); + outGroup.close(); + return 0; + } + } + + //make sure that if your picked groups size is not too big + if (pickedGroups) { + int total = 0; + for(int i = 0; i < Groups.size(); i++) { + total += groupMap->getNumSeqs(Groups[i]); + } + + if (size == 0) { //user has not set size, set size = 10% samples size + size = int (total * 0.10); + } + + if (total < size) { + m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine(); + size = int (total * 0.10); + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine(); + }else{ + + if (size == 0) { //user has not set size, set size = 10% samples size + size = int (list->getNumSeqs() * 0.10); + } + + int thisSize = list->getNumSeqs(); + if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine(); + size = thisSize; + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine(); + } + + + for (int i = 0; i < list->getNumBins(); i++) { + string binnames = list->get(i); + + //parse names + string individual = ""; + int length = binnames.length(); + for(int j=0;jgetGroup(individual); + if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; } + + if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups + if (m->inUsersGroups(group, Groups)) { + names.push_back(individual); + } + }else{ + names.push_back(individual); + } + }else{ //save everyone, group + names.push_back(individual); + } + individual = ""; + } + else{ + individual += binnames[j]; + } + } + //save last name + if (groupfile != "") { //if there is a groupfile given fill in group info + string group = groupMap->getGroup(individual); + if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; } + + if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups + if (m->inUsersGroups(group, Groups)) { + names.push_back(individual); + } + }else{ + names.push_back(individual); + } + }else{ //save everyone, group + names.push_back(individual); + } + } + + random_shuffle(names.begin(), names.end()); + + //randomly select a subset of those names to include in the subsample + set subset; //dont want repeat sequence names added + for (int j = 0; j < size; j++) { + + if (m->control_pressed) { break; } + + //get random sequence to add, making sure we have not already added it + bool done = false; + int myrand; + while (!done) { + myrand = (int)((float)(rand()) / (RAND_MAX / (names.size()-1) + 1)); + + if (subset.count(names[myrand]) == 0) { subset.insert(names[myrand]); break; } + } + } + + if (groupfile != "") { + //write out new groupfile + for (set::iterator it = subset.begin(); it != subset.end(); it++) { + string group = groupMap->getGroup(*it); + if (group == "not found") { group = "NOTFOUND"; } + + outGroup << *it << '\t' << group << endl; + } + outGroup.close(); delete groupMap; + } + + + //as long as you are not at the end of the file or done wih the lines you want + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { delete list; delete input; out.close(); return 0; } + + if(allLines == 1 || labels.count(list->getLabel()) == 1){ + + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); + + processList(list, out, subset); + + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + } + + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + + delete list; + + list = input->getListVector(lastLabel); + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); + + processList(list, out, subset); + + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + + //restore real lastlabel to save below + list->setLabel(saveLabel); + } + + lastLabel = list->getLabel(); + + delete list; list = NULL; + + //get next line to process + list = input->getListVector(); + } + + + if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); return 0; } + + //output error messages about any remaining user labels + set::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) { + if (list != NULL) { delete list; } + + list = input->getListVector(lastLabel); + + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); + + processList(list, out, subset); + + delete list; list = NULL; + } + + out.close(); + if (list != NULL) { delete list; } + delete input; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getSubSampleList"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::processList(ListVector*& list, ofstream& out, set& subset) { + try { + + int numBins = list->getNumBins(); + + ListVector* temp = new ListVector(); + temp->setLabel(list->getLabel()); + + for (int i = 0; i < numBins; i++) { + + if (m->control_pressed) { break; } + + string binnames = list->get(i); + + //parse names + string individual = ""; + string newNames = ""; + int length = binnames.length(); + for(int j=0;jpush_back(newNames); + } + } + + delete list; + list = temp; + + if (m->control_pressed) { return 0; } + + list->print(out); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "processList"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::getSubSampleRabund() { + try { + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName); + + InputData* input = new InputData(rabundfile, "rabund"); + RAbundVector* rabund = input->getRAbundVector(); + string lastLabel = rabund->getLabel(); + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + + if (size == 0) { //user has not set size, set size = 10% + size = int((rabund->getNumSeqs()) * 0.10); + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine(); + + //as long as you are not at the end of the file or done wih the lines you want + while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { delete input; delete rabund; out.close(); return 0; } + + if(allLines == 1 || labels.count(rabund->getLabel()) == 1){ + + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + processRabund(rabund, out); + + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + } + + if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = rabund->getLabel(); + + delete rabund; + + rabund = input->getRAbundVector(lastLabel); + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + processRabund(rabund, out); + + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + + //restore real lastlabel to save below + rabund->setLabel(saveLabel); + } + + lastLabel = rabund->getLabel(); + + //prevent memory leak + delete rabund; rabund = NULL; + + //get next line to process + rabund = input->getRAbundVector(); + } + + + if (m->control_pressed) { out.close(); return 0; } + + //output error messages about any remaining user labels + set::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) { + if (rabund != NULL) { delete rabund; } + + rabund = input->getRAbundVector(lastLabel); + + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + processRabund(rabund, out); + + delete rabund; + } + + delete input; + out.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getSubSampleRabund"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) { + try { + + int numBins = rabund->getNumBins(); + int thisSize = rabund->getNumSeqs(); + + if (thisSize != size) { + + OrderVector* order = new OrderVector(); + for(int p=0;pget(p);j++){ + order->push_back(p); + } + } + random_shuffle(order->begin(), order->end()); + + RAbundVector* temp = new RAbundVector(numBins); + temp->setLabel(rabund->getLabel()); + + delete rabund; + rabund = temp; + + for (int j = 0; j < size; j++) { + + if (m->control_pressed) { delete order; return 0; } + + //get random number to sample from order between 0 and thisSize-1. + int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1)); + + int bin = order->get(myrand); + + int abund = rabund->get(bin); + rabund->set(bin, (abund+1)); + } + + delete order; + } + + if (m->control_pressed) { return 0; } + + rabund->print(out); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "processRabund"); + exit(1); + } +} +//********************************************************************************************************************** +int SubSampleCommand::getSubSampleSabund() { + try { + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName); + + InputData* input = new InputData(sabundfile, "sabund"); + SAbundVector* sabund = input->getSAbundVector(); + string lastLabel = sabund->getLabel(); + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + + if (size == 0) { //user has not set size, set size = 10% + size = int((sabund->getNumSeqs()) * 0.10); + } + + m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine(); + + //as long as you are not at the end of the file or done wih the lines you want + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { delete input; delete sabund; out.close(); return 0; } + + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ + + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + + processSabund(sabund, out); + + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + } + + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + + delete sabund; + + sabund = input->getSAbundVector(lastLabel); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + + processSabund(sabund, out); + + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + + //restore real lastlabel to save below + sabund->setLabel(saveLabel); + } + + lastLabel = sabund->getLabel(); + + //prevent memory leak + delete sabund; sabund = NULL; + + //get next line to process + sabund = input->getSAbundVector(); + } + + + if (m->control_pressed) { out.close(); return 0; } + + //output error messages about any remaining user labels + set::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) { + if (sabund != NULL) { delete sabund; } + + sabund = input->getSAbundVector(lastLabel); + + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + + processSabund(sabund, out); + + delete sabund; + } + + delete input; + out.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getSubSampleSabund"); exit(1); } } //********************************************************************************************************************** +int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) { + try { + + RAbundVector* rabund = new RAbundVector(); + *rabund = sabund->getRAbundVector(); + + int numBins = rabund->getNumBins(); + int thisSize = rabund->getNumSeqs(); + + if (thisSize != size) { + + OrderVector* order = new OrderVector(); + for(int p=0;pget(p);j++){ + order->push_back(p); + } + } + random_shuffle(order->begin(), order->end()); + + RAbundVector* temp = new RAbundVector(numBins); + temp->setLabel(rabund->getLabel()); + + delete rabund; + rabund = temp; + + for (int j = 0; j < size; j++) { + + if (m->control_pressed) { delete order; return 0; } + + //get random number to sample from order between 0 and thisSize-1. + int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1)); + + int bin = order->get(myrand); + + int abund = rabund->get(bin); + rabund->set(bin, (abund+1)); + } + + delete order; + } + + if (m->control_pressed) { return 0; } + + delete sabund; + sabund = new SAbundVector(); + *sabund = rabund->getSAbundVector(); + delete rabund; + + sabund->print(out); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "processSabund"); + exit(1); + } +} +//********************************************************************************************************************** int SubSampleCommand::eliminateZeroOTUS(vector& thislookup) { try {