in.close();
out.close();
+
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
// Initialize the matrices
size = row*col;
+//printf("size = %d\n.", size);
double matrix[row][col];
double pmatrix[size],pmatrix2[size],permuted[size];
double storage[row][9];
-
+//printf("here\n.", size);
for (i=0;i<row;i++){
for (j =0;j<9;j++){
storage[i][j]=0;
}
m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();
-
metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
m->mothurOutEndLine();
//**********************************************************************************************************************
vector<string> NormalizeSharedCommand::getValidParameters(){
try {
- string Array[] = {"groups","label","scale","outputdir","inputdir","norm"};
+ string Array[] = {"groups","label","method","outputdir","inputdir","norm"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","scale","outputdir","inputdir","norm"};
+ string AlignArray[] = {"groups","label","method","outputdir","inputdir","norm"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
eliminateZeroOTUS(thisLookUp);
for (int i = 0; i < thisLookUp.size(); i++) {
- out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
+ out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
thisLookUp[i]->print(out);
}
//open each groups summary file
string newLabel = "";
- ifstream* temp;
- map<string, ifstream*> filehandles;
+ map<string, vector<string> > files;
for (int i=0; i<outputNames.size(); i++) {
- temp = new ifstream;
- filehandles[outputNames[i]] = temp;
- m->openInputFile(outputNames[i], *(temp));
+ vector<string> thisFilesLines;
+
+ ifstream temp;
+ m->openInputFile(outputNames[i], temp);
//read through first line - labels
string tempLabel;
if (i == 0) { //we want to save the labels to output below
for (int j = 0; j < numCols+1; j++) {
- *(temp) >> tempLabel;
+ temp >> tempLabel;
if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
}else{ newLabel += tempLabel + '\t'; }
}
- }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } }
+ }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } }
+
+ m->gobble(temp);
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ string thisLine = "";
+ string tempLabel;
+
+ for (int j = 0; j < numCols+1; j++) {
+ temp >> tempLabel;
+
+ //save for later
+ if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
+ else{ thisLine += tempLabel + "\t"; }
+ }
+
+ thisLine += "\n";
+
+ thisFilesLines.push_back(thisLine);
+
+ m->gobble(temp);
+ }
+
+ files[outputNames[i]] = thisFilesLines;
- m->gobble(*(temp));
+ temp.close();
}
//output label line to new file
out << newLabel << endl;
//for each label
- for (int i = 0; i < numLines; i++) {
+ for (int k = 0; k < numLines; k++) {
//grab summary data for each group
for (int i=0; i<outputNames.size(); i++) {
- string tempLabel;
-
- for (int j = 0; j < numCols+1; j++) {
- *(filehandles[outputNames[i]]) >> tempLabel;
-
- //print to combined file
- if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; }
- else{ out << tempLabel << '\t'; }
- }
-
- out << endl;
- m->gobble(*(filehandles[outputNames[i]]));
+ out << files[outputNames[i]][k];
}
}
- //close each groups summary file
- for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); remove(outputNames[i].c_str()); }
outputNames.clear();
out.close();
//seach for filePos of each first name in the qfile and save in qfileFilePos
ifstream inQual;
m->openInputFile(qfilename, inQual);
-
+
string input;
while(!inQual.eof()){
input = m->getline(inQual);
}
inQual.close();
+
if (firstSeqNames.size() != 0) {
for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();