#include "getsharedotucommand.h"
-
//**********************************************************************************************************************
-vector<string> GetSharedOTUCommand::getValidParameters(){
+vector<string> GetSharedOTUCommand::setParameters(){
try {
- string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
+ CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
+ 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, "GetSharedOTUCommand", "getValidParameters");
+ m->errorOut(e, "GetSharedOTUCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetSharedOTUCommand::GetSharedOTUCommand(){
+string GetSharedOTUCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- outputTypes["sharedseqs"] = tempOutNames;
+ string helpString = "";
+ helpString += "The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required, unless you have valid current files.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
+ helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
+ helpString += "If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
+ helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n";
+ helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n";
+ helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
+ helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
+ helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
+ helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+ helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+ helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
+ helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetSharedOTUCommand::getRequiredParameters(){
- try {
- string Array[] = {"list","group"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> GetSharedOTUCommand::getRequiredFiles(){
+GetSharedOTUCommand::GetSharedOTUCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles");
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
exit(1);
}
}
GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
unique = true;
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[] = {"label","unique","shared","fasta","list","group","output","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 required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
+ else if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { format = "list"; }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
+ else if (groupfile == "not found") {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
output = validParameter.validFile(parameters, "output", false);
if (output == "not found") { output = ""; }
+ else if (output == "default") { output = ""; }
groups = validParameter.validFile(parameters, "unique", false);
if (groups == "not found") { groups = ""; }
else {
userGroups = "unique." + groups;
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
else {
userGroups = groups;
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
unique = false;
}
}
//**********************************************************************************************************************
-void GetSharedOTUCommand::help(){
- try {
- m->mothurOut("The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- m->mothurOut("The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n");
- m->mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n");
- m->mothurOut("If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n");
- m->mothurOut("If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n");
- m->mothurOut("The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n");
- m->mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n");
- m->mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n");
- m->mothurOut("The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n");
- m->mothurOut("The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
- m->mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
- m->mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n");
- m->mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetSharedOTUCommand::~GetSharedOTUCommand(){}
-
-//**********************************************************************************************************************
-
int GetSharedOTUCommand::execute(){
try {
if (m->control_pressed) { delete groupMap; return 0; }
- globaldata->gGroupmap = groupMap;
-
if (Groups.size() == 0) {
Groups = groupMap->namesOfGroups;
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
if (lastlist != NULL) { delete lastlist; }
projects / mothur.git / blobdiff