string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- convert(temp, abund);
+ m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, nIters);
+ m->mothurConvert(temp, nIters);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
if (m->control_pressed) { return 0; }
+ map<int, string> file2Group; //index in outputNames[i] -> group
for (int p = 0; p < inputFileNames.size(); p++) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
}
+ if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
}
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
- if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames); }
+ if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
}
//**********************************************************************************************************************
-vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
+vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
try {
vector<string> newFileNames;
//find different types of files
- map<string, vector<string> > typesFiles;
+ map<string, map<string, string> > typesFiles;
for (int i = 0; i < outputNames.size(); i++) {
string extension = m->getExtension(outputNames[i]);
string newLine = labels.substr(0, labels.find_first_of('\t'));
newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
-
- typesFiles[extension].push_back(outputNames[i]);
+
+ map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
+ if (itfind != typesFiles.end()) {
+ (itfind->second)[outputNames[i]] = file2Group[i];
+ }else {
+ map<string, string> temp;
+ temp[outputNames[i]] = file2Group[i];
+ typesFiles[extension] = temp;
+ }
string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
}
//for each type create a combo file
- for (map<string, vector<string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
+ map<int, int> lineToNumber;
+ for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
ofstream out;
string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
m->openOutputFileAppend(combineFileName, out);
newFileNames.push_back(combineFileName);
-
- vector<string> thisTypesFiles = it->second;
+ map<string, string> thisTypesFiles = it->second;
//open each type summary file
map<string, vector<string> > files; //maps file name to lines in file
int maxLines = 0;
- for (int i=0; i<thisTypesFiles.size(); i++) {
-
+ int numColumns = 0;
+ for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
+
+ string thisfilename = itFileNameGroup->first;
+ string group = itFileNameGroup->second;
+
ifstream temp;
- m->openInputFile(thisTypesFiles[i], temp);
+ m->openInputFile(thisfilename, temp);
//read through first line - labels
m->getline(temp); m->gobble(temp);
vector<string> thisFilesLines;
- string group = m->getRootName(thisTypesFiles[i]);
- group = group.substr(0, group.length()-1);
- group = group.substr(group.find_last_of('.')+1);
thisFilesLines.push_back(group);
+ int count = 1;
while (!temp.eof()){
string thisLine = m->getline(temp);
-
- thisFilesLines.push_back(thisLine);
+ string numSampled = thisLine.substr(0, thisLine.find_first_of('\t'));
+ int num = 0;
+ convert(numSampled, num);
+ numColumns = m->getNumChar(thisLine, '\t');
+ lineToNumber[count] = num;
+ count++;
+
+ thisFilesLines.push_back(thisLine);
m->gobble(temp);
}
- files[thisTypesFiles[i]] = thisFilesLines;
+ files[thisfilename] = thisFilesLines;
//save longest file for below
if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
temp.close();
- m->mothurRemove(thisTypesFiles[i]);
+ m->mothurRemove(thisfilename);
}
for (int k = 1; k < maxLines; k++) {
//grab data for each group
- for (int i=0; i<thisTypesFiles.size(); i++) {
-
- string output = "NA\t";
- if (k < files[thisTypesFiles[i]].size()) {
- string line = files[thisTypesFiles[i]][k];
- output = line.substr(0, line.find_first_of('\t'));
- output += '\t' + files[thisTypesFiles[i]][0] + '\t' + line.substr(line.find_first_of('\t'));
- }else{
- output += '\t' + files[thisTypesFiles[i]][0] + '\t';
- }
- out << output << endl;
+ for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
+
+ string thisfilename = itFileNameGroup->first;
+ map<int, int>::iterator itLine = lineToNumber.find(k);
+ if (itLine != lineToNumber.end()) {
+ string output = toString(itLine->second);
+ if (k < files[thisfilename].size()) {
+ string line = files[thisfilename][k];
+ output = line.substr(0, line.find_first_of('\t'));
+ output += '\t' + files[thisfilename][0] + '\t' + line.substr(line.find_first_of('\t'));
+ }else{
+ output += '\t' + files[thisfilename][0] + '\t';
+ for (int h = 0; h < numColumns; h++) {
+ output += "NA\t";
+ }
+ }
+ out << output << endl;
+ }else { m->mothurOut("[ERROR]: parsing results, cant find " + toString(k)); m->mothurOutEndLine(); }
}
}
projects / mothur.git / blobdiff