//**********************************************************************************************************************
vector<string> SubSampleCommand::getValidParameters(){
try {
- string Array[] = {"groups","label","outputdir","inputdir"};
+ string Array[] = {"fasta", "group", "list","shared","rabund", "name","sabund","size","groups","label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
//**********************************************************************************************************************
vector<string> SubSampleCommand::getRequiredParameters(){
try {
- vector<string> myArray;
+ string Array[] = {"fasta","list","shared","rabund", "sabund","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
catch(exception& e) {
//**********************************************************************************************************************
vector<string> SubSampleCommand::getRequiredFiles(){
try {
- string Array[] = {"shared","list","rabund","sabund","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray;
return myArray;
}
catch(exception& e) {
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ string Array[] = {"fasta", "group", "list","shared","rabund", "sabund","name","size","groups","label","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ map<string,string>::iterator it;
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
}
- //make sure the user has already run the read.otu command
- if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the sub.sample command."); m->mothurOutEndLine(); abort = true; }
-
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { rabundfile = ""; abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
else { allLines = 1; }
}
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
globaldata->Groups = Groups;
}
+ string temp = validParameter.validFile(parameters, "size", false); if (temp == "not found"){ temp = "0"; }
+ convert(temp, size);
+
+ if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
+
+ if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
+ m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
+
+ if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
+ m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
+
+ if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
+ m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
+
}
}
void SubSampleCommand::help(){
try {
- m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
- m->mothurOut("The get.relabund command parameters are groups, scale and label. No parameters are required.\n");
+ 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 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 scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
- m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\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 get.relabund command outputs a .relabund file.\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");
}
//**********************************************************************************************************************
-SubSampleCommand::~SubSampleCommand(){
-}
+SubSampleCommand::~SubSampleCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "subsample" + m->getExtension(globaldata->inputFileName);
- ofstream out;
- m->openOutputFile(outputFileName, out);
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- string format = globaldata->getFormat();
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
-
- if (format == "sharedfile") {
- lookup = input->getSharedRAbundVectors();
- outputTypes["shared"].push_back(outputFileName);
- getSubSampleShared(lookup, out);
- }else if (format == "list") {
- list = globaldata->glist;
- outputTypes["list"].push_back(outputFileName);
- //getSubSamplesList();
- }else if (format == "rabund") {
- rabund = globaldata->rabund;
- outputTypes["rabund"].push_back(outputFileName);
- //getSubSamplesRabund();
-
- }else if (format == "sabund") {
- sabund = globaldata->sabund;
- outputTypes["sabund"].push_back(outputFileName);
- //getSubSamplesSabund();
- }
-
- out.close();
-
- //reset groups parameter
- delete input; globaldata->ginput = NULL;
- delete read;
-
- if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
-
+ if (sharedfile != "") { getSubSampleShared(); }
+ //if (listfile != "") { getSubSampleList(); }
+ //if (rabund != "") { getSubSampleRabund(); }
+ //if (sabundfile != "") { getSubSampleSabund(); }
+ //if (fastafile != "") { getSubSampleFasta(); }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName);
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
}
//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleShared(vector<SharedRAbundVector*>& thislookup, ofstream& filename) {
+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<SharedRAbundVector*> 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<string> processedLabels;
set<string> userLabels = labels;
- string lastLabel = lookup[0]->getLabel();
//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) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- //process lookup
-
-
+ processShared(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- //process lookup
+ processShared(lookup, out);
+
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- //process lookup
-
-
+ processShared(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- //reset groups parameter
- globaldata->Groups.clear();
+ out.close();
return 0;
exit(1);
}
}
-
-
+//**********************************************************************************************************************
+int SubSampleCommand::processShared(vector<SharedRAbundVector*>& 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;p<numBins;p++){
+ for(int j=0;j<thislookup[i]->getAbundance(p);j++){
+ order->push_back(p);
+ }
+ }
+ random_shuffle(order->begin(), order->end());
+
+ SharedRAbundVector* temp = new SharedRAbundVector(numBins);
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+
+ delete thislookup[i];
+ thislookup[i] = temp;
+
+
+ for (int j = 0; j < size; j++) {
+ //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 = thislookup[i]->getAbundance(bin);
+ thislookup[i]->set(bin, (abund+1), thisgroup);
+ }
+ delete order;
+ }
+ }
+
+ //subsampling may have created some otus with no sequences in them
+ eliminateZeroOTUS(thislookup);
+
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
try {
//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++) {
}
}
}
-
+
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
+ thislookup.clear();
+
thislookup = newLookup;
return 0;
-
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
//**********************************************************************************************************************
+
projects / mothur.git / blobdiff