#include "sharedutilities.h"
//**********************************************************************************************************************
-vector<string> SubSampleCommand::getValidParameters(){
- try {
- string Array[] = {"fasta", "group", "list","shared","rabund","persample", "name","sabund","size","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+vector<string> SubSampleCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
+ 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, "SubSampleCommand", "getValidParameters");
+ m->errorOut(e, "SubSampleCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SubSampleCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n";
+ helpString += "The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
+ helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
+ helpString += "The size parameter allows you indicate the size of your subsample.\n";
+ helpString += "The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n";
+ helpString += "persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n";
+ helpString += "The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n";
+ helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
+ helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+ helpString += "The sub.sample command outputs a .subsample file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getHelpString");
exit(1);
}
}
SubSampleCommand::SubSampleCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["list"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> SubSampleCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","list","shared","rabund", "sabund","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SubSampleCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta", "group", "list","shared","rabund","persample", "sabund","name","size","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();
else {
pickedGroups = true;
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
string temp = validParameter.validFile(parameters, "size", false); if (temp == "not found"){ temp = "0"; }
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void SubSampleCommand::help(){
- try {
- m->mothurOut("The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n");
- m->mothurOut("The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n");
- m->mothurOut("The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The size parameter allows you indicate the size of your subsample.\n");
- m->mothurOut("The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n");
- m->mothurOut("persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n");
- m->mothurOut("The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n");
- m->mothurOut("The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
- m->mothurOut("The sub.sample command outputs a .subsample file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-SubSampleCommand::~SubSampleCommand(){}
-
//**********************************************************************************************************************
int SubSampleCommand::execute(){
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