else if (type == "sabund") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
- else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
//**********************************************************************************************************************
int RemoveRareCommand::processList(){
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- map<string, string> variables;
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
- variables["[extension]"] = m->getExtension(listfile);
- string outputFileName = getOutputFileName("list", variables);
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
- variables["[extension]"] = m->getExtension(groupfile);
- string outputGroupFileName = getOutputFileName("group", variables);
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
- variables["[extension]"] = m->getExtension(countfile);
- string outputCountFileName = getOutputFileName("count", variables);
-
- ofstream out, outGroup;
- m->openOutputFile(outputFileName, out);
-
- bool wroteSomething = false;
-
+
//you must provide a label because the names in the listfile need to be consistent
string thisLabel = "";
if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
list = input.getListVector(lastLabel);
}
}
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ variables["[tag]"] = list->getLabel();
+ string outputFileName = getOutputFileName("list", variables);
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputGroupFileName = getOutputFileName("group", variables);
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputCountFileName = getOutputFileName("count", variables);
+
+ ofstream out, outGroup;
+ m->openOutputFile(outputFileName, out);
+
+ bool wroteSomething = false;
+
//if groupfile is given then use it
GroupMap* groupMap;
util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}else if (countfile != "") {
- ct.readTable(countfile);
+ ct.readTable(countfile, true, false);
if (ct.hasGroupInfo()) {
vector<string> namesGroups = ct.getNamesOfGroups();
SharedUtil util;
}
- if (list != NULL) {
+ if (list != NULL) {
+
+ vector<string> binLabels = list->getLabels();
+ vector<string> newLabels;
+
//make a new list vector
ListVector newList;
newList.setLabel(list->getLabel());
if (binsize > nseqs) { //keep bin
newList.push_back(saveBinNames);
+ newLabels.push_back(binLabels[i]);
if (groupfile != "") { for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; } }
else if (countfile != "") { for(int k = 0; k < newGroupFile.size(); k++) { ct.remove(newGroupFile[k]); } }
}else { if (countfile != "") { for(int k = 0; k < names.size(); k++) { ct.remove(names[k]); } } }
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
- newList.print(out);
+ newList.setLabels(newLabels);
+ newList.printHeaders(out);
+ newList.print(out);
}
}
try {
m->setGroups(Groups);
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- map<string, string> variables;
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
- variables["[extension]"] = m->getExtension(sharedfile);
- string outputFileName = getOutputFileName("shared", variables);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } out.close(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
+ processLookup(lookup);
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
+ processLookup(lookup);
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
lookup = input.getSharedRAbundVectors();
}
- if (m->control_pressed) { out.close(); return 0; }
+ if (m->control_pressed) { return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- processLookup(lookup, out);
+ processLookup(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
}
}
//**********************************************************************************************************************
-int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup, ofstream& out){
+int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup){
try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
vector<SharedRAbundVector> newRabunds; newRabunds.resize(lookup.size());
+ vector<string> headers;
for (int i = 0; i < lookup.size(); i++) {
newRabunds[i].setGroup(lookup[i]->getGroup());
newRabunds[i].setLabel(lookup[i]->getLabel());
for (int i = 0; i < lookup[0]->getNumBins(); i++) {
bool allZero = true;
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
//for each group
for (int j = 0; j < lookup.size(); j++) {
//eliminates zero otus
if (allZero) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
+ else { headers.push_back(m->currentSharedBinLabels[i]); }
}
}else {
//for each otu
for (int i = 0; i < lookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
int totalAbund = 0;
//get total otu abundance
//eliminates otus below rare cutoff
if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
+ else { headers.push_back(m->currentSharedBinLabels[i]); }
}
}
//do we have any otus above the rare cutoff
- if (newRabunds[0].getNumBins() != 0) {
+ if (newRabunds[0].getNumBins() != 0) {
+ out << "label\tGroup\tnumOtus\t";
+ for (int j = 0; j < headers.size(); j++) { out << headers[j] << '\t'; }
+ out << endl;
for (int j = 0; j < newRabunds.size(); j++) {
out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';
newRabunds[j].print(out);
}
}
+ out.close();
+
return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff