#include "sensspeccommand.h"
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+ //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ 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, "SensSpecCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SensSpecCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sens.spec command....\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SensSpecCommand::SensSpecCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
+ exit(1);
+ }
+}
//***************************************************************************************************************
SensSpecCommand::SensSpecCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
string temp;
-
- //valid paramters for this command
- string AlignArray[] = {"list", "phylip", "column", "name", "hard", "label", "cutoff", "outputdir", "inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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["sensspec"] = 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; }
}
it = parameters.find("phylip");
//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["phylip"] = inputDir + it->second; }
}
it = parameters.find("column");
//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["column"] = inputDir + it->second; }
}
- it = parameters.find("name");
+ //it = parameters.find("name");
//user has given a template file
- if(it != parameters.end()){
- path = hasPath(it->second);
+ //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; }
- }
+ //if (path == "") { parameters["name"] = inputDir + it->second; }
+ //}
}
//check for required parameters
listFile = validParameter.validFile(parameters, "list", true);
- if (listFile == "not found") { m->mothurOut("list is a required parameter for the sens.spec command."); m->mothurOutEndLine(); 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("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (listFile == "not open") { abort = true; }
- distFile = validParameter.validFile(parameters, "column", true);
- format = "column";
- if(distFile == "not found") {
- distFile = validParameter.validFile(parameters, "phylip", true);
- format = "phylip";
- }
- if(distFile == "not found") { m->mothurOut("either column or phylip are required for the sens.spec command."); m->mothurOutEndLine(); abort = true; }
- else if (distFile == "not open") { abort = true; }
-
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not found") { phylipfile = ""; }
+ else if (phylipfile == "not open") { abort = true; }
+ else { distFile = phylipfile; format = "phylip"; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not found") { columnfile = ""; }
+ else if (columnfile == "not open") { abort = true; }
+ else { distFile = columnfile; format = "column"; }
+
+ if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { distFile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or column file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a sens.spec command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
+
+
//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...
temp = validParameter.validFile(parameters, "hard", false);
if (temp == "not found"){ hard = 0; }
- else if(!isTrue(temp)) { hard = 0; }
- else if(isTrue(temp)) { hard = 1; }
+ else if(!m->isTrue(temp)) { hard = 0; }
+ else if(m->isTrue(temp)) { hard = 1; }
// temp = validParameter.validFile(parameters, "name", true);
// if (temp == "not found") { nameFile = ""; }
// else { nameFile = temp; }
// cout << "name:\t" << nameFile << endl;
- temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = ""; }
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "-1.00"; }
convert(temp, cutoff);
- cout << "cutoff:\t" << cutoff << endl;
+// cout << cutoff << endl;
-// cutoff = 0.0349;
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, precision);
+// cout << precision << endl;
lineLabel = validParameter.validFile(parameters, "label", false); if (lineLabel == "not found") { lineLabel = ""; }
+ sensSpecFileName = listFile.substr(0,listFile.find_last_of('.')) + ".sensspec";
}
-
}
catch(exception& e) {
m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
exit(1);
}
}
-//**********************************************************************************************************************
-
-void SensSpecCommand::help(){
- try {
- m->mothurOut("The sens.spec command reads a fastaFile and creates .....\n");
-
-
-
- m->mothurOut("Example sens.spec(...).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
- m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "help");
- exit(1);
- }
-}
-
-
-//***************************************************************************************************************
-
-SensSpecCommand::~SensSpecCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int SensSpecCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ setUpOutput();
+ outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
-// else if(format == "column") { processColumn(seqMap); }
-
-
-// string seqList;
-// map<string, int> seqMap;
+ else if(format == "column") { processColumn(); }
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
return 0;
void SensSpecCommand::processPhylip(){
try{
+ //probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
+
ifstream inputListFile;
- openInputFile(listFile, inputListFile);
-
+ m->openInputFile(listFile, inputListFile);
+
+ string origCutoff = "";
+ bool getCutoff = 0;
+ if(cutoff == -1.00) { getCutoff = 1; }
+ else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
+
string label;
int numOTUs;
}
seqMap[seqName] = i;
}
+ m->gobble(inputListFile);
+
+ int lNumSeqs = seqMap.size();
+ int pNumSeqs = 0;
+
+ ifstream phylipFile;
+ m->openInputFile(distFile, phylipFile);
+ phylipFile >> pNumSeqs;
+ if(pNumSeqs != lNumSeqs){ cout << "numSeq mismatch!" << endl; }
+
+ string seqName;
+ double distance;
+ vector<int> otuIndices(lNumSeqs, -1);
+
+ truePositives = 0;
+ falsePositives = 0;
+ trueNegatives = 0;
+ falseNegatives = 0;
+
+ if(getCutoff == 1){
+ if(label != "unique"){
+ origCutoff = label;
+ convert(label, cutoff);
+ if(hard == 0){ cutoff += (0.49 / double(precision)); }
+ }
+ else{
+ origCutoff = "unique";
+ cutoff = 0.0000;
+ }
+ }
+
+ cout << label << endl;
+
+ for(int i=0;i<lNumSeqs;i++){
+ phylipFile >> seqName;
+ otuIndices[i] = seqMap[seqName];
+
+ for(int j=0;j<i;j++){
+ phylipFile >> distance;
+
+ if(distance <= cutoff){
+ if(otuIndices[i] == otuIndices[j]) { truePositives++; }
+ else { falseNegatives++; }
+ }
+ else{
+ if(otuIndices[i] == otuIndices[j]) { falsePositives++; }
+ else { trueNegatives++; }
+ }
+ }
+ }
+ phylipFile.close();
+
+ outputStatistics(label, origCutoff);
}
inputListFile.close();
-
- int lNumSeqs = seqMap.size();
- int pNumSeqs = 0;
- ifstream phylipFile;
- openInputFile(distFile, phylipFile);
- phylipFile >> pNumSeqs;
- if(pNumSeqs != lNumSeqs){ cout << "numSeq mismatch!" << endl; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "processPhylip");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+void SensSpecCommand::processColumn(){
+ try{
+ ifstream inputListFile;
+ m->openInputFile(listFile, inputListFile);
- string seqName;
- double distance;
- vector<int> otuIndices(lNumSeqs, -1);
-
- truePositives = 0;
- falsePositives = 0;
- trueNegatives = 0;
- falseNegatives = 0;
+ string origCutoff = "";
+ bool getCutoff = 0;
+ if(cutoff == -1.00) { getCutoff = 1; }
+ else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
+ set<string> seqPairSet;
- for(int i=0;i<lNumSeqs;i++){
- phylipFile >> seqName;
- otuIndices[i] = seqMap[seqName];
+ string label, seqList;
+ int numOTUs;
+ int numSeqs;
+
+ while(inputListFile){
+ numSeqs = 0;
- for(int j=0;j<i;j++){
- phylipFile >> distance;
- if(distance <= cutoff){
- if(otuIndices[i] == otuIndices[j]){
- truePositives++;
+ inputListFile >> label >> numOTUs;
+ for(int i=0;i<numOTUs;i++){
+
+ vector<string> seqNameVector;
+
+ inputListFile >> seqList;
+ int seqListLength = seqList.length();
+ string seqName = "";
+ for(int j=0;j<seqListLength;j++){
+
+ if(seqList[j] == ','){
+ seqNameVector.push_back(seqName);
+ seqName = "";
}
else{
- falseNegatives++;
+ seqName += seqList[j];
}
}
+ seqNameVector.push_back(seqName);
+
+ numSeqs += seqNameVector.size();
+
+ int numSeqsInOTU = seqNameVector.size();
+ for(int j=0;j<numSeqsInOTU;j++){
+ string seqPairString = "";
+ for(int k=0;k<j;k++){
+ if(seqNameVector[j] < seqNameVector[k]) { seqPairString = seqNameVector[j] + '\t' + seqNameVector[k]; }
+ else { seqPairString = seqNameVector[k] + '\t' + seqNameVector[j]; }
+ seqPairSet.insert(seqPairString);
+ }
+ }
+ }
+ m->gobble(inputListFile);
+
+ int numDists = (numSeqs * (numSeqs-1) / 2);
+
+ ifstream columnFile;
+ m->openInputFile(distFile, columnFile);
+ string seqNameA, seqNameB, seqPairString;
+ double distance;
+
+ truePositives = 0;
+ falsePositives = 0;
+ trueNegatives = numDists;
+ falseNegatives = 0;
+
+ if(getCutoff == 1){
+ if(label != "unique"){
+ origCutoff = label;
+ convert(label, cutoff);
+ if(hard == 0){ cutoff += (0.49 / double(precision)); }
+ }
else{
- if(otuIndices[i] == otuIndices[j]){
- falsePositives++;
+ origCutoff = "unique";
+ cutoff = 0.0000;
+ }
+ }
+
+ cout << label << endl;
+
+ while(columnFile){
+ columnFile >> seqNameA >> seqNameB >> distance;
+ if(seqNameA < seqNameB) { seqPairString = seqNameA + '\t' + seqNameB; }
+ else { seqPairString = seqNameB + '\t' + seqNameA; }
+
+ set<string>::iterator it = seqPairSet.find(seqPairString);
+
+ if(distance <= cutoff){
+ if(it != seqPairSet.end()){
+ truePositives++;
+ seqPairSet.erase(it);
}
else{
- trueNegatives++;
+ falseNegatives++;
}
+ trueNegatives--;
}
+ else if(it != seqPairSet.end()){
+ falsePositives++;
+ trueNegatives--;
+ seqPairSet.erase(it);
+ }
+
+ m->gobble(columnFile);
}
+ falsePositives += seqPairSet.size();
+
+ outputStatistics(label, origCutoff);
}
- phylipFile.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "processColumn");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+void SensSpecCommand::setUpOutput(){
+ try{
+ ofstream sensSpecFile;
+ m->openOutputFile(sensSpecFileName, sensSpecFile);
- cout << "truePositives:\t" << truePositives << endl;
- cout << "trueNegatives:\t" << trueNegatives << endl;
- cout << "falsePositives:\t" << falsePositives << endl;
- cout << "falseNegatives:\t" << falseNegatives << endl;
+ sensSpecFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
+
+ sensSpecFile.close();
}
catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "processPhylip");
+ m->errorOut(e, "SensSpecCommand", "setUpOutput");
exit(1);
}
}
//***************************************************************************************************************
-//void SensSpecCommand::processColumn(map<string, int> seqMap){
-//
-// truePositives = 0;
-// falsePositives = 0;
-// trueNegatives = numDists;
-// falseNegatives = 0;
-//
-// ifstream columnFile;
-// openInputFile(distFile, columnFile);
-//
-// string seqNameA, seqNameB, oldSeqNameA;
-// int otuA, otuB, oldOTUA;
-// double distance;
-//
-// while(columnFile){
-// columnFile >> seqNameA >> seqNameB >> distance;
-//
-// if(seqNameA == oldSeqNameA) { otuA = oldOTUA; }
-// else { otuA = seqMap[seqNameA]; oldOTUA = otuA; }
-//
-// otuB = seqMap[seqNameB];
-//
-// if(distance <= cutoff){
-// if(otuA == otuB){
-// truePositives++;
-// }
-// else{
-// falseNegatives++;
-// }
-// trueNegatives--;
-// }
-// else{
-// if(otuA == otuB){
-// falsePositives++;
-// trueNegatives--;
-// }
-// }
-//
-// gobble(columnFile);
-// }
-// columnFile.close();
-//
-// cout << "truePositives:\t" << truePositives << endl;
-// cout << "trueNegatives:\t" << trueNegatives << endl;
-// cout << "falsePositives:\t" << falsePositives << endl;
-// cout << "falseNegatives:\t" << falseNegatives << endl;
-//}
+void SensSpecCommand::outputStatistics(string label, string cutoff){
+ try{
+ double tp = (double) truePositives;
+ double fp = (double) falsePositives;
+ double tn = (double) trueNegatives;
+ double fn = (double) falseNegatives;
+
+ double p = tp + fn;
+ double n = fp + tn;
+ double pPrime = tp + fp;
+ double nPrime = tn + fn;
+
+ double sensitivity = tp / p;
+ double specificity = tn / n;
+ double positivePredictiveValue = tp / pPrime;
+ double negativePredictiveValue = tn / nPrime;
+ double falseDiscoveryRate = fp / pPrime;
+
+ double accuracy = (tp + tn) / (p + n);
+ double matthewsCorrCoef = (tp * tn - fp * fn) / sqrt(p * n * pPrime * nPrime); if(p == 0 || n == 0){ matthewsCorrCoef = 0; }
+ double f1Score = 2.0 * tp / (p + pPrime);
+
+
+ if(p == 0) { sensitivity = 0; matthewsCorrCoef = 0; }
+ if(n == 0) { specificity = 0; matthewsCorrCoef = 0; }
+ if(p + n == 0) { accuracy = 0; }
+ if(p + pPrime == 0) { f1Score = 0; }
+ if(pPrime == 0) { positivePredictiveValue = 0; falseDiscoveryRate = 0; matthewsCorrCoef = 0; }
+ if(nPrime == 0) { negativePredictiveValue = 0; matthewsCorrCoef = 0; }
+
+ ofstream sensSpecFile;
+ m->openOutputFileAppend(sensSpecFileName, sensSpecFile);
+
+ sensSpecFile << label << '\t' << cutoff << '\t';
+ sensSpecFile << truePositives << '\t' << trueNegatives << '\t' << falsePositives << '\t' << falseNegatives << '\t';
+ sensSpecFile << setprecision(4);
+ sensSpecFile << sensitivity << '\t' << specificity << '\t' << positivePredictiveValue << '\t' << negativePredictiveValue << '\t';
+ sensSpecFile << falseDiscoveryRate << '\t' << accuracy << '\t' << matthewsCorrCoef << '\t' << f1Score << endl;
+
+ sensSpecFile.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "outputStatistics");
+ exit(1);
+ }
+}
//***************************************************************************************************************
+
+
+
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