//**********************************************************************************************************************
vector<string> RemoveRareCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
- CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);
- CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "atleast", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "atleast", "none","rabund",false,false,true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "atleast", "none","sabund",false,false,true); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "atleast", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "none", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnseqs);
+ CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pbygroup);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveRareCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveRareCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "rabund") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "sabund") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "rabund") { pattern = "[filename],pick,[extension]"; }
+ 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 == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
- string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
- string outputCountFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ 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);
util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}else if (countfile != "") {
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
if (ct.hasGroupInfo()) {
vector<string> namesGroups = ct.getNamesOfGroups();
SharedUtil util;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
+ variables["[extension]"] = m->getExtension(sabundfile);
+ string outputFileName = getOutputFileName("sabund", variables);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
+ variables["[extension]"] = m->getExtension(rabundfile);
+ string outputFileName = getOutputFileName("rabund", variables);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
m->setGroups(Groups);
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
- 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->currentBinLabels[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->currentBinLabels[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