#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\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "getHelpString");
exit(1);
}
}
RemoveRareCommand::RemoveRareCommand(){
try {
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; calledHelp = false;
allLines = 1;
if(option == "help") { help(); 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();
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; }
+ 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"; }
}
//**********************************************************************************************************************
-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 {
//**********************************************************************************************************************
int RemoveRareCommand::processShared(){
try {
- globaldata->Groups = Groups;
+ m->Groups = Groups;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
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