#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> RemoveRareCommand::getValidParameters(){
+vector<string> RemoveRareCommand::setParameters(){
try {
- string Array[] = {"rabund","sabund", "group", "list", "shared","bygroup","nseqs","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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 pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getValidParameters");
+ m->errorOut(e, "RemoveRareCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RemoveRareCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n";
+ helpString += "The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n";
+ helpString += "The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n";
+ helpString += "The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n";
+ helpString += "bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n";
+ helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";
+ helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";
+ helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> RemoveRareCommand::getRequiredParameters(){
- try {
- string Array[] = {"nseqs"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> RemoveRareCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"rabund","sabund", "group", "list", "shared", "bygroup", "nseqs","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for file parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
+ else { m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
+ else { m->setRabundFile(rabundfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
-
- if ((sabundfile == "") && (rabundfile == "") && (sharedfile == "") && (listfile == "")) { m->mothurOut("You must provide at least one of the following: rabund, sabund, shared or list."); m->mothurOutEndLine(); abort = true; }
+ else { m->setSharedFile(sharedfile); }
+
+ if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
string temp = validParameter.validFile(parameters, "nseqs", false);
if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
- else { convert(temp, nseqs); }
+ else { m->mothurConvert(temp, nseqs); }
temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }
byGroup = m->isTrue(temp);
}
//**********************************************************************************************************************
-void RemoveRareCommand::help(){
- try {
- m->mothurOut("The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n");
- m->mothurOut("The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.\n");
- m->mothurOut("The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n");
- m->mothurOut("The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n");
- m->mothurOut("bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n");
- m->mothurOut("The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n");
- m->mothurOut("The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n");
- m->mothurOut("Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int RemoveRareCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
if (listfile != "") { processList(); }
if (sharedfile != "") { processShared(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 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 rabund file as new current rabundfile
+ string current = "";
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
}
return 0;
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
SharedUtil util;
- util.setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> namesGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}
//for each bin
for (int i = 0; i < list->getNumBins(); i++) {
- if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); remove(outputGroupFileName.c_str()); } out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close(); m->mothurRemove(outputFileName); return 0; }
//parse out names that are in accnos file
string binnames = list->get(i);
//**********************************************************************************************************************
int RemoveRareCommand::processShared(){
try {
- globaldata->Groups = Groups;
+ m->setGroups(Groups);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processLookup(lookup, out);
}
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processLookup(lookup, out);
//restore real lastlabel to save below
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processLookup(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
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