groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else {
- //read in group map info.
- groupMap = new GroupMap(groupfile);
- int error = groupMap->readMap();
- if (error == 1) { delete groupMap; abort = true; }
- }
-
+
sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found"){ sorted = ""; }
if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
m->mothurOut(sorted + " is not a valid option for the sorted parameter. The only options are: name, bin, size and group. I will not sort."); m->mothurOutEndLine();
readMatrix->read(nameMap);
- if (m->control_pressed) { delete readMatrix; delete groupMap; return 0; }
+ if (m->control_pressed) { delete readMatrix; return 0; }
//get matrix
if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
// via the index of a sequence in the distance matrix
seqVec = vector<SeqMap>(globaldata->gListVector->size());
for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
- if (m->control_pressed) { delete readMatrix; delete groupMap; return 0; }
+ if (m->control_pressed) { delete readMatrix; return 0; }
seqVec[currentCell->row][currentCell->column] = currentCell->dist;
}
delete matrix;
delete readMatrix;
+ delete nameMap;
- if (m->control_pressed) { delete groupMap; return 0; }
+ if (m->control_pressed) { return 0; }
}else {
//process file and set up indexes
if (format == "column") { formatMatrix = new FormatColumnMatrix(distFile); }
formatMatrix->read(nameMap);
- if (m->control_pressed) { delete formatMatrix; delete groupMap; return 0; }
+ if (m->control_pressed) { delete formatMatrix; return 0; }
//get matrix
if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
rowPositions = formatMatrix->getRowPositions();
delete formatMatrix;
+ delete nameMap;
//openfile for getMap to use
openInputFile(distFile, inRow);
- if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); delete groupMap; return 0; }
+ if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); return 0; }
}
}
} else { m->mothurOut("error, no listvector."); m->mothurOutEndLine(); }
- fasta = new FastaMap();
-
- //read fastafile
- fasta->readFastaFile(fastafile);
-
+
if (m->control_pressed) {
if (large) { inRow.close(); remove(distFile.c_str()); }
- delete fasta; return 0;
+ return 0;
}
- //if user gave a namesfile then use it
- if (namefile != "") { readNamesFile(); }
-
//set format to list so input can get listvector
globaldata->setFormat("list");
if (m->control_pressed) {
if (large) { inRow.close(); remove(distFile.c_str()); }
- delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
}
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
if (large) { inRow.close(); remove(distFile.c_str()); }
- if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
}
processedLabels.insert(list->getLabel());
if (m->control_pressed) {
if (large) { inRow.close(); remove(distFile.c_str()); }
- if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
}
processedLabels.insert(list->getLabel());
if (m->control_pressed) {
if (large) { inRow.close(); remove(distFile.c_str()); }
- if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- delete fasta; delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
}
}
globaldata->gListVector = NULL;
delete input; globaldata->ginput = NULL;
delete read;
+
+ if (groupfile != "") {
+ //read in group map info.
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; m->mothurOut("Error reading your groupfile. Proceeding without groupfile."); m->mothurOutEndLine(); groupfile = ""; }
+ }
+
+ //read fastafile
+ fasta = new FastaMap();
+ fasta->readFastaFile(fastafile);
+
+ //if user gave a namesfile then use it
+ if (namefile != "") { readNamesFile(); }
+
+ //output create and output the .rep.fasta files
+ map<string, string>::iterator itNameFile;
+ for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) {
+ processNames(itNameFile->first, itNameFile->second);
+ }
+
delete fasta;
if (groupfile != "") {
delete groupMap; globaldata->gGroupmap = NULL;
}
}
//**********************************************************************************************************************
-string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, int& binsize) {
+string GetOTURepCommand::findRep(int bin, ListVector* thisList) {
try{
vector<string> names;
map<string, string> groups;
//parse names into vector
string binnames = thisList->get(bin);
splitAtComma(binnames, names);
- binsize = names.size();
-
- //if you have a groupfile
- if (groupfile != "") {
- //find the groups that are in this bin
- for (size_t i = 0; i < names.size(); i++) {
- string groupName = groupMap->getGroup(names[i]);
- if (groupName == "not found") {
- m->mothurOut(names[i] + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- groupError = true;
- } else {
- groups[groupName] = groupName;
- }
- }
-
- //turn the groups into a string
- for (groupIt = groups.begin(); groupIt != groups.end(); groupIt++) {
- group += groupIt->first + "-";
- }
- //rip off last dash
- group = group.substr(0, group.length()-1);
- }else{ group = ""; }
// if only 1 sequence in bin or processing the "unique" label, then
// the first sequence of the OTU is the representative one
//create output file
if (outputDir == "") { outputDir += hasPath(listfile); }
- string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.fasta";
- openOutputFile(outputFileName, out);
- vector<repStruct> reps;
- outputNames.push_back(outputFileName);
-
+
ofstream newNamesOutput;
string outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
openOutputFile(outputNamesFile, newNamesOutput);
outputNames.push_back(outputNamesFile);
+ outputNameFiles[outputNamesFile] = processList->getLabel();
//for each bin in the list vector
for (int i = 0; i < processList->size(); i++) {
- string groups;
- int binsize;
-
- if (m->control_pressed) { out.close(); newNamesOutput.close(); return 0; }
-
- nameRep = findRep(i, groups, processList, binsize);
+ nameRep = findRep(i, processList);
if (m->control_pressed) { out.close(); newNamesOutput.close(); return 0; }
//output to new names file
newNamesOutput << nameRep << '\t' << processList->get(i) << endl;
+ }
+
+ newNamesOutput.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOTURepCommand::processNames(string filename, string label) {
+ try{
+
+ //create output file
+ if (outputDir == "") { outputDir += hasPath(listfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + label + ".rep.fasta";
+ openOutputFile(outputFileName, out);
+ vector<repStruct> reps;
+ outputNames.push_back(outputFileName);
+
+ ifstream in;
+ openInputFile(filename, in);
+
+ int i = 0;
+ while (!in.eof()) {
+ string rep, binnames;
+ in >> rep >> binnames; gobble(in);
+
+ vector<string> names;
+ splitAtComma(binnames, names);
+ int binsize = names.size();
+
+ //if you have a groupfile
+ string group = "";
+ if (groupfile != "") {
+ map<string, string> groups;
+ map<string, string>::iterator groupIt;
+
+ //find the groups that are in this bin
+ for (size_t i = 0; i < names.size(); i++) {
+ string groupName = groupMap->getGroup(names[i]);
+ if (groupName == "not found") {
+ m->mothurOut(names[i] + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ groupError = true;
+ } else {
+ groups[groupName] = groupName;
+ }
+ }
+
+ //turn the groups into a string
+ for (groupIt = groups.begin(); groupIt != groups.end(); groupIt++) {
+ group += groupIt->first + "-";
+ }
+ //rip off last dash
+ group = group.substr(0, group.length()-1);
+ }else{ group = ""; }
+
//print out name and sequence for that bin
- sequence = fasta->getSequence(nameRep);
+ string sequence = fasta->getSequence(rep);
if (sequence != "not found") {
if (sorted == "") { //print them out
- nameRep = nameRep + "|" + toString(i+1);
- nameRep = nameRep + "|" + toString(binsize);
+ rep = rep + "|" + toString(i+1);
+ rep = rep + "|" + toString(binsize);
if (groupfile != "") {
- nameRep = nameRep + "|" + groups;
+ rep = rep + "|" + group;
}
- out << ">" << nameRep << endl;
+ out << ">" << rep << endl;
out << sequence << endl;
}else { //save them
- repStruct newRep(nameRep, i+1, binsize, groups);
+ repStruct newRep(rep, i+1, binsize, group);
reps.push_back(newRep);
}
}else {
- m->mothurOut(nameRep + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- remove(outputNamesFile.c_str());
- return 1;
+ m->mothurOut(rep + " is missing from your fasta or name file, ignoring. Please correct."); m->mothurOutEndLine();
}
+ i++;
}
+
if (sorted != "") { //then sort them and print them
if (sorted == "name") { sort(reps.begin(), reps.end(), compareName); }
else if (sorted == "bin") { sort(reps.begin(), reps.end(), compareBin); }
out << sequence << endl;
}
}
-
+
out.close();
- newNamesOutput.close();
+
return 0;
}
catch(exception& e) {
- m->errorOut(e, "GetOTURepCommand", "process");
+ m->errorOut(e, "GetOTURepCommand", "processNames");
exit(1);
}
}
-
//**********************************************************************************************************************
SeqMap GetOTURepCommand::getMap(int row) {
try {
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