*/
#include "otuhierarchycommand.h"
+#include "inputdata.h"
//**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(string option){
+vector<string> OtuHierarchyCommand::setParameters(){
try {
- abort = false;
+ CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n";
+ helpString += "The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n";
+ helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n";
+ helpString += "The otu.hierarchy command should be in the following format: \n";
+ helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
+ helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
+ helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "otuheirarchy") { pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"list","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
+
//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 = ""; }
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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; }
}
}
listFile = validParameter.validFile(parameters, "list", true);
- if (listFile == "not found") { mothurOut("list is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
- else if (listFile == "not open") { abort = true; }
+ if (listFile == "not found") {
+ listFile = m->getListFile();
+ if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (listFile == "not open") { abort = true; }
+ else { m->setListFile(listFile); }
//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 += hasPath(listFile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { mothurOut("label is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
+ if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(label, labels);
- if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; }
- }
+ m->splitAtDash(label, mylabels);
+ if (mylabels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
+
+ if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; }
}
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
exit(1);
}
}
//**********************************************************************************************************************
-void OtuHierarchyCommand::help(){
- try {
- mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
- mothurOut("The otu.hierarchy command parameters are list and label. Both parameters are required. \n");
- mothurOut("The otu.hierarchy command should be in the following format: \n");
- mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
- mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
- mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-OtuHierarchyCommand::~OtuHierarchyCommand(){}
-
-//**********************************************************************************************************************
-
int OtuHierarchyCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
- vector<ListVector> lists = getListVectors();
+ vector< vector<string> > lists = getListVectors();
+
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
//determine which is little and which is big, putting little first
- if (lists.size() == 2) {
+ if (lists.size() == 4) {
//if big is first swap them
- if (lists[0].getNumBins() < lists[1].getNumBins()) {
- reverse(lists.begin(), lists.end());
+ if (lists[0].size() < lists[2].size()) {
+ vector< vector<string> > tempLists;
+ tempLists.push_back(lists[2]);
+ tempLists.push_back(lists[3]);
+ tempLists.push_back(lists[0]);
+ tempLists.push_back(lists[1]);
+ lists = tempLists;
+ string tempLabel = list2Label;
+ list2Label = list1Label;
+ list1Label = tempLabel;
}
}else{
- mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); mothurOutEndLine(); return 0;
+ m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
}
//map sequences to bin number in the "little" otu
- map<string, int> littleBins;
- for (int i = 0; i < lists[0].getNumBins(); i++) {
- string names = lists[0].get(i);
-
- //parse bin
- 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());
- littleBins[name] = i;
- }
-
- //get last name
- littleBins[names] = i;
- }
+ map<string, int> littleBins;
+ vector<string> binLabels0 = lists[0];
+ for (int i = 0; i < lists[0].size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+ string bin = lists[1][i];
+ vector<string> names; m->splitAtComma(bin, names);
+ for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
+ }
ofstream out;
- string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
- openOutputFile(outputFileName, out);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+ variables["[distance1]"] = list1Label;
+ variables["[tag]"] = "-";
+ variables["[distance2]"] = list2Label;
+ string outputFileName = getOutputFileName("otuheirarchy",variables);
+ m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
- for (int i = 0; i < lists[1].getNumBins(); i++) {
+ vector<string> binLabels1 = lists[2];
+ for (int i = 0; i < lists[2].size(); i++) {
- string names = lists[1].get(i);
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ string binnames = lists[3][i];
+ vector<string> names; m->splitAtComma(binnames, names);
//output column 1
- out << names << '\t';
+ if (output == "name") { out << binnames << '\t'; }
+ else { out << binLabels1[i] << '\t'; }
map<int, int> bins; //bin numbers in little that are in this bin in big
map<int, int>::iterator it;
//parse bin
- 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());
- bins[littleBins[name]] = littleBins[name];
- }
-
- //get last name
- bins[littleBins[names]] = littleBins[names];
+ for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]]; }
string col2 = "";
for (it = bins.begin(); it != bins.end(); it++) {
- col2 += lists[0].get(it->first) + "\t";
+ if (output == "name") { col2 += lists[1][it->first] + "\t"; }
+ else { col2 += binLabels0[it->first] + "\t"; }
}
//output column 2
out.close();
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "execute");
+ m->errorOut(e, "OtuHierarchyCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
//returns a vector of listVectors where "little" vector is first
-vector<ListVector> OtuHierarchyCommand::getListVectors() {
+vector< vector<string> > OtuHierarchyCommand::getListVectors() { //return value [0] -> otulabelsFirstLabel [1] -> binsFirstLabel [2] -> otulabelsSecondLabel [3] -> binsSecondLabel
try {
-
- int pos; //to use in smart distancing, position of last read in file
- int lastPos;
- vector<ListVector> lists;
+ vector< vector<string> > lists;
+
+ int count = 0;
+ for (set<string>::iterator it = mylabels.begin(); it != mylabels.end(); it++) {
+ string realLabel;
+ vector< vector<string> > thisList = getListVector(*it, realLabel);
+
+ if (m->control_pressed) { return lists; }
+
+ for (int i = 0; i < thisList.size(); i++) { lists.push_back(thisList[i]); }
+
+ if (count == 0) { list1Label = realLabel; count++; }
+ else { list2Label = realLabel; }
+ }
+
+ return lists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<string> > OtuHierarchyCommand::getListVector(string label, string& realLabel){ //return value [0] -> otulabels [1] -> bins
+ try {
+ vector< vector<string> > myList;
+
+ InputData input(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<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
-
- //open file
- ifstream in;
- openInputFile(listFile, in);
-
- //get first list vector in file
- ListVector* list = NULL;
- string lastLabel = "";
- if (!in.eof()) {
- pos = in.tellg();
- lastPos = pos;
- list = new ListVector(in);
- gobble(in);
- lastLabel = list->getLabel();
- }
- while ((list != NULL) && (userLabels.size() != 0)) {
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return myList; }
- //is this a listvector that we want?
if(labels.count(list->getLabel()) == 1){
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
+ break;
}
-
- //you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
- int savePos = in.tellg();
- //get smart distance line
delete list;
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
- }else { list = NULL; }
+ list = input.getListVector(lastLabel);
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
+ userLabels.erase(list->getLabel());
+
//restore real lastlabel to save below
- list->setLabel(saveLabel);
- in.seekg(savePos);
+ //list->setLabel(saveLabel);
+ break;
}
lastLabel = list->getLabel();
- lastPos = pos;
- //get next line
+ //get next line to process
+ //prevent memory leak
delete list;
- if (!in.eof()) {
- pos = in.tellg();
- list = new ListVector(in);
- gobble(in);
- }else { list = NULL; }
+ list = input.getListVector();
}
-
+
+ if (m->control_pressed) { return myList; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- delete list;
- }
+ delete list;
+ list = input.getListVector(lastLabel);
}
-
- return lists;
+ //at this point the list vector has the right distance
+ myList.push_back(list->getLabels());
+ vector<string> bins;
+ for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { return myList; }
+ bins.push_back(list->get(i));
+ }
+ myList.push_back(bins);
+ realLabel = list->getLabel();
+
+ delete list;
+
+ return myList;
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ m->errorOut(e, "OtuHierarchyCommand", "getListVector");
exit(1);
}
}
projects / mothur.git / blobdiff