X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.cpp;h=73c1e5c76c48db67f0676ebb4a409aa0660b241d;hb=d945488119ad368b180537f36ed40298ff170f39;hp=b8bb7ad44462d64e661d1f9b640fbff87dc872d2;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp index b8bb7ad..73c1e5c 100644 --- a/subsamplecommand.cpp +++ b/subsamplecommand.cpp @@ -11,22 +11,61 @@ #include "sharedutilities.h" //********************************************************************************************************************** -vector SubSampleCommand::getValidParameters(){ - try { - string Array[] = {"fasta", "group", "list","shared","rabund", "name","sabund","size","groups","label","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); +vector SubSampleCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared); + CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize); + CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "SubSampleCommand", "getValidParameters"); + m->errorOut(e, "SubSampleCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SubSampleCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n"; + helpString += "The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n"; + helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n"; + helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n"; + helpString += "The size parameter allows you indicate the size of your subsample.\n"; + helpString += "The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n"; + helpString += "persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n"; + helpString += "The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n"; + helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n"; + helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n"; + helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"; + helpString += "The sub.sample command outputs a .subsample file.\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SubSampleCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** SubSampleCommand::SubSampleCommand(){ try { - abort = true; - //initialize outputTypes + abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["shared"] = tempOutNames; outputTypes["list"] = tempOutNames; @@ -42,43 +81,16 @@ SubSampleCommand::SubSampleCommand(){ } } //********************************************************************************************************************** -vector SubSampleCommand::getRequiredParameters(){ - try { - string Array[] = {"fasta","list","shared","rabund", "sabund","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SubSampleCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector SubSampleCommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SubSampleCommand", "getRequiredFiles"); - exit(1); - } -} -//********************************************************************************************************************** SubSampleCommand::SubSampleCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"fasta", "group", "list","shared","rabund", "sabund","name","size","groups","label","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -210,12 +222,17 @@ SubSampleCommand::SubSampleCommand(string option) { else { pickedGroups = true; m->splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->Groups = Groups; } string temp = validParameter.validFile(parameters, "size", false); if (temp == "not found"){ temp = "0"; } convert(temp, size); + temp = validParameter.validFile(parameters, "persample", false); if (temp == "not found"){ temp = "f"; } + persample = m->isTrue(temp); + + if (groupfile == "") { persample = false; } + if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; } if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) { @@ -238,41 +255,12 @@ SubSampleCommand::SubSampleCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void SubSampleCommand::help(){ - try { - m->mothurOut("The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n"); - m->mothurOut("The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n"); - m->mothurOut("The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n"); - m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n"); - m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n"); - m->mothurOut("The size parameter allows you indicate the size of your subsample.\n"); - m->mothurOut("The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files, 10% of number of seqs.\n"); - m->mothurOut("The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n"); - m->mothurOut("Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n"); - m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"); - m->mothurOut("The sub.sample command outputs a .subsample file.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); - - } - catch(exception& e) { - m->errorOut(e, "SubSampleCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -SubSampleCommand::~SubSampleCommand(){} - //********************************************************************************************************************** int SubSampleCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } if (sharedfile != "") { getSubSampleShared(); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } @@ -289,7 +277,44 @@ int SubSampleCommand::execute(){ if (fastafile != "") { getSubSampleFasta(); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } } - + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + + itTypes = outputTypes.find("shared"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); } + } + + itTypes = outputTypes.find("rabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); } + } + + itTypes = outputTypes.find("sabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); } + } + + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -331,80 +356,131 @@ int SubSampleCommand::getSubSampleFasta() { 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]); + int thisSize = names.size(); + if (persample) { + if (size == 0) { //user has not set size, set size = smallest samples size + size = groupMap->getNumSeqs(Groups[0]); + for (int i = 1; i < Groups.size(); i++) { + int thisSize = groupMap->getNumSeqs(Groups[i]); + + if (thisSize < size) { size = thisSize; } + } + }else { //make sure size is not too large + vector newGroups; + for (int i = 0; i < Groups.size(); i++) { + int thisSize = groupMap->getNumSeqs(Groups[i]); + + if (thisSize >= size) { newGroups.push_back(Groups[i]); } + else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); } + } + Groups = newGroups; + } + + m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine(); + }else { + 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 (total * 0.10); + size = int (names.size() * 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); + if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine(); + size = thisSize; } - 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; + if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); } + } - 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; } + if (persample) { + for (int i = 0; i < Groups.size(); i++) { + + //randomly select a subset of those names from this group to include in the subsample + 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)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0)); + + if (subset.count(names[myrand]) == 0) { + + 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 (group == Groups[i]) { subset.insert(names[myrand]); break; } + } + } + } + } + }else { - //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)); + //randomly select a subset of those names to include in the subsample + for (int j = 0; j < size; j++) { + + if (m->control_pressed) { return 0; } - if (subset.count(names[myrand]) == 0) { + //get random sequence to add, making sure we have not already added it + bool done = false; + int myrand; + while (!done) { + myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0)); - 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 (subset.count(names[myrand]) == 0) { - if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups - if (m->inUsersGroups(group, Groups)) { + 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{ + }else{ //save everyone, group subset.insert(names[myrand]); break; - } - }else{ //save everyone, group - subset.insert(names[myrand]); break; - } + } + } } - } - } + } + } + + if (subset.size() == 0) { m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine(); 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); //read through fasta file outputting only the names on the subsample list ifstream in; @@ -573,14 +649,6 @@ int SubSampleCommand::readNames() { int SubSampleCommand::getSubSampleShared() { try { - string thisOutputDir = outputDir; - if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile); - - ofstream out; - m->openOutputFile(outputFileName, out); - outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); - InputData* input = new InputData(sharedfile, "sharedfile"); vector lookup = input->getSharedRAbundVectors(); string lastLabel = lookup[0]->getLabel(); @@ -596,9 +664,34 @@ int SubSampleCommand::getSubSampleShared() { if (thisSize < size) { size = thisSize; } } + }else { + m->Groups.clear(); + vector temp; + for (int i = 0; i < lookup.size(); i++) { + if (lookup[i]->getNumSeqs() < size) { + m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine(); + delete lookup[i]; + }else { + m->Groups.push_back(lookup[i]->getGroup()); + temp.push_back(lookup[i]); + } + } + lookup = temp; + Groups = m->Groups; } - m->mothurOut("Sampling " + toString(size) + " from " + toString(lookup[0]->getNumSeqs()) + "."); m->mothurOutEndLine(); + if (lookup.size() == 0) { m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; } + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); + + + m->mothurOut("Sampling " + toString(size) + " from each group."); 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))) { @@ -711,7 +804,7 @@ int SubSampleCommand::processShared(vector& thislookup, ofs 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 myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0)); int bin = order->get(myrand); @@ -794,37 +887,60 @@ int SubSampleCommand::getSubSampleList() { } //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); + if (persample) { + if (size == 0) { //user has not set size, set size = smallest samples size + size = groupMap->getNumSeqs(Groups[0]); + for (int i = 1; i < Groups.size(); i++) { + int thisSize = groupMap->getNumSeqs(Groups[i]); + + if (thisSize < size) { size = thisSize; } + } + }else { //make sure size is not too large + vector newGroups; + for (int i = 0; i < Groups.size(); i++) { + int thisSize = groupMap->getNumSeqs(Groups[i]); + + if (thisSize >= size) { newGroups.push_back(Groups[i]); } + else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); } + } + Groups = newGroups; } - m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine(); + m->mothurOut("Sampling " + toString(size) + " from each group."); 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; + 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(); } - - m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine(); } + //fill names for (int i = 0; i < list->getNumBins(); i++) { string binnames = list->get(i); @@ -872,22 +988,43 @@ int SubSampleCommand::getSubSampleList() { } 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 (persample) { + for (int i = 0; i < Groups.size(); i++) { - if (subset.count(names[myrand]) == 0) { subset.insert(names[myrand]); break; } + 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)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0)); + + if (subset.count(names[myrand]) == 0) { //you are not already added + if (groupMap->getGroup(names[myrand]) == Groups[i]) { subset.insert(names[myrand]); break; } + } + } + } } - } + }else{ + 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)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0)); + + if (subset.count(names[myrand]) == 0) { subset.insert(names[myrand]); break; } + } + } + } if (groupfile != "") { //write out new groupfile @@ -1009,7 +1146,7 @@ int SubSampleCommand::processList(ListVector*& list, ofstream& out, set& individual += binnames[j]; } } - if (subset.count(individual) != 0) { newNames += individual; } + if (subset.count(individual) != 0) { newNames += individual + ","; } //if there are names in this bin add to new list @@ -1037,15 +1174,6 @@ int SubSampleCommand::processList(ListVector*& list, ofstream& out, set& //********************************************************************************************************************** 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(); @@ -1056,10 +1184,18 @@ int SubSampleCommand::getSubSampleRabund() { if (size == 0) { //user has not set size, set size = 10% size = int((rabund->getNumSeqs()) * 0.10); - } + }else if (size > rabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping rabund file."); m->mothurOutEndLine(); delete input; delete rabund; return 0; } m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine(); + 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); + //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; } @@ -1168,7 +1304,7 @@ int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) { 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 myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0)); int bin = order->get(myrand); @@ -1194,15 +1330,7 @@ int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) { //********************************************************************************************************************** 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(); @@ -1213,10 +1341,20 @@ int SubSampleCommand::getSubSampleSabund() { if (size == 0) { //user has not set size, set size = 10% size = int((sabund->getNumSeqs()) * 0.10); - } + }else if (size > sabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping sabund file."); m->mothurOutEndLine(); delete input; delete sabund; return 0; } + m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine(); + 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); + + //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; } @@ -1328,7 +1466,7 @@ int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) { 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 myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0)); int bin = order->get(myrand);