int SensSpecCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
+ int startTime = time(NULL);
+
+ //create list file with only unique names, saves time and memory by removing redundant names from list file that are not in the distance file.
+ string newListFile = preProcessList();
+ if (newListFile != "") { listFile = newListFile; }
+
setUpOutput();
outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }
+ //remove temp file if created
+ if (newListFile != "") { m->mothurRemove(newListFile); }
+
if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
-
+
+ m->mothurOut("It took " + toString(time(NULL) - startTime) + " to run sens.spec."); m->mothurOutEndLine();
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
exit(1);
}
}
+//***************************************************************************************************************
+bool SensSpecCommand::testFile(){
+ try{
+ ifstream fileHandle;
+ m->openInputFile(phylipfile, fileHandle);
+
+ bool square = false;
+ string numTest, name;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+ if(isalnum(d)){
+ square = true;
+ break;
+ }
+ if(d == '\n'){
+ square = false;
+ break;
+ }
+ }
+ fileHandle.close();
+
+ return square;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "testFile");
+ exit(1);
+ }
+}
//***************************************************************************************************************
int 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
- string origCutoff = "";
+ square = testFile();
+ string origCutoff = "";
bool getCutoff = 0;
if(cutoff == -1.00) { getCutoff = 1; }
- else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
+ else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
map<string, int> seqMap;
string seqList;
set<string> processedLabels;
set<string> userLabels = labels;
-
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(m->control_pressed){
else { trueNegatives++; }
}
}
+
+ if (square) { m->getline(phylipFile); } //get rest of line - redundant distances
+ m->gobble(phylipFile);
}
phylipFile.close();
exit(1);
}
}
+//***************************************************************************************************************
+
+string SensSpecCommand::preProcessList(){
+ try {
+ set<string> uniqueNames;
+ //get unique names from distance file
+ if (format == "phylip") {
+
+ ifstream phylipFile;
+ m->openInputFile(distFile, phylipFile);
+ string numTest;
+ int pNumSeqs;
+ phylipFile >> numTest; m->gobble(phylipFile);
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else {
+ m->mothurConvert(numTest, pNumSeqs);
+ }
+
+ string seqName;
+ for(int i=0;i<pNumSeqs;i++){
+ if (m->control_pressed) { return ""; }
+ phylipFile >> seqName; m->getline(phylipFile); m->gobble(phylipFile);
+ uniqueNames.insert(seqName);
+ }
+ phylipFile.close();
+ }else {
+ ifstream columnFile;
+ m->openInputFile(distFile, columnFile);
+ string seqNameA, seqNameB;
+ double distance;
+
+ while(columnFile){
+ if (m->control_pressed) { return ""; }
+ columnFile >> seqNameA >> seqNameB >> distance;
+ uniqueNames.insert(seqNameA); uniqueNames.insert(seqNameB);
+ m->gobble(columnFile);
+ }
+ columnFile.close();
+ }
+
+ //read list file, if numSeqs > unique names then remove redundant names
+ string newListFile = listFile + ".temp";
+ ofstream out;
+ m->openOutputFile(newListFile, out);
+ ifstream in;
+ m->openInputFile(listFile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(newListFile); return ""; }
+
+ //read in list vector
+ ListVector list(in);
+
+ //listfile is already unique
+ if (list.getNumSeqs() == uniqueNames.size()) { in.close(); out.close(); m->mothurRemove(newListFile); return ""; }
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+ vector<string> bnames;
+ m->splitAtComma(binnames, bnames);
+
+ string newNames = "";
+ for (int j = 0; j < bnames.size(); j++) {
+ string name = bnames[j];
+ //if that name is in the .accnos file, add it
+ if (uniqueNames.count(name) != 0) { newNames += name + ","; }
+ }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething) { return newListFile; }
+ else { m->mothurRemove(newListFile); }
+
+ return "";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "preProcessList");
+ exit(1);
+ }
+}
+
//***************************************************************************************************************
projects / mothur.git / blobdiff