int MergeGroupsCommand::processGroupFile(DesignMap*& designMap){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[extension]"] = m->getExtension(groupfile);
string outputFileName = getOutputFileName("group", variables);
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
//read groupfile
GroupMap groupMap(groupfile);
groupMap.readMap();
//fill Groups - checks for "all" and for any typo groups
SharedUtil* util = new SharedUtil();
vector<string> nameGroups = groupMap.getNamesOfGroups();
util->setGroups(Groups, nameGroups);
delete util;
vector<string> namesOfSeqs = groupMap.getNamesSeqs();
bool error = false;
for (int i = 0; i < namesOfSeqs.size(); i++) {
if (m->control_pressed) { break; }
string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
//are you in a group the user wants
if (m->inUsersGroups(thisGroup, Groups)) {
string thisGrouping = designMap->get(thisGroup);
if (thisGrouping == "not found") { m->mothurOut("[ERROR]: " + namesOfSeqs[i] + " is from group " + thisGroup + " which is not in your design file, please correct."); m->mothurOutEndLine(); error = true; }
else {
out << namesOfSeqs[i] << '\t' << thisGrouping << endl;
}
}
}
if (error) { m->control_pressed = true; }
out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
exit(1);
}
}
int RenameSeqsCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
GroupMap groupMap(groupfile);
groupMap.readMap();
//prepare filenames and open files
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastaFile); }
string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
map<string, string> variables;
variables["[filename]"] = outFastaFile;
variables["[extension]"] = m->getExtension(fastaFile);
outFastaFile = getOutputFileName("fasta", variables);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
ofstream outFasta;
m->openOutputFile(outFastaFile, outFasta);
ifstream in;
m->openInputFile(fastaFile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
Sequence seq(in); m->gobble(in);
string group = groupMap.getGroup(seq.getName());
if (group == "not found") { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = seq.getName() + "_" + group;
seq.setName(newName);
seq.printSequence(outFasta);
}
}
in.close();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
bool notDone = true;
if (nameFile != "") {
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(nameFile); }
string outNameFile = thisOutputDir + m->getRootName(m->getSimpleName(nameFile));
variables["[filename]"] = outNameFile;
variables["[extension]"] = m->getExtension(nameFile);
outNameFile = getOutputFileName("group", variables);
outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile);
ofstream outName;
m->openOutputFile(outNameFile, outName);
map<string, vector<string> > nameMap;
m->readNames(nameFile, nameMap);
//process name file changing names
for (map<string, vector<string> >::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
for (int i = 0; i < (it->second).size()-1; i++) {
if (m->control_pressed) { break; }
string group = groupMap.getGroup((it->second)[i]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[i] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[i] + "_" + group;
groupMap.renameSeq((it->second)[i], newName); //change in group file
(it->second)[i] = newName; //change in namefile
}
if (i == 0) { outName << (it->second)[i] << '\t' << (it->second)[i] << ','; }
else { outName << (it->second)[i] << ','; }
}
//print last one
if ((it->second).size() == 1) {
string group = groupMap.getGroup((it->second)[0]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[0] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[0] + "_" + group;
groupMap.renameSeq((it->second)[0], newName); //change in group file
(it->second)[0] = newName; //change in namefile
outName << (it->second)[0] << '\t' << (it->second)[0] << endl;
}
}
else {
string group = groupMap.getGroup((it->second)[(it->second).size()-1]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[(it->second).size()-1] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[(it->second).size()-1] + "_" + group;
groupMap.renameSeq((it->second)[(it->second).size()-1], newName); //change in group file
(it->second)[(it->second).size()-1] = newName; //change in namefile
outName << (it->second)[(it->second).size()-1] << endl;
}
}
}
notDone = false;
outName.close();
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (notDone) {
vector<string> seqs = groupMap.getNamesSeqs();
for (int i = 0; i < seqs.size(); i++) {
if (m->control_pressed) { break; }
string group = groupMap.getGroup(seqs[i]);
string newName = seqs[i] + "_" + group;
groupMap.renameSeq(seqs[i], newName);
}
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
string outGroupFile = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[filename]"] = outGroupFile;
variables["[extension]"] = m->getExtension(groupfile);
outGroupFile = getOutputFileName("group", variables);
outputNames.push_back(outGroupFile); outputTypes["group"].push_back(outGroupFile);
ofstream outGroup;
m->openOutputFile(outGroupFile, outGroup);
groupMap.print(outGroup);
outGroup.close();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "execute");
exit(1);
}
}