#include "sharedutilities.h"
//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getValidParameters(){
+vector<string> MergeGroupsCommand::setParameters(){
try {
- string Array[] = {"shared","label","outputdir","design","groups","processors","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ 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, "MergeGroupsCommand", "getValidParameters");
+ m->errorOut(e, "MergeGroupsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-MergeGroupsCommand::MergeGroupsCommand(){
+string MergeGroupsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["shared"] = tempOutNames;
+ string helpString = "";
+ helpString += "The merge.groups command reads a shared or group file and a design file and merges the groups that are in the same grouping in the design file.\n";
+ helpString += "The merge.groups command outputs a .shared file. \n";
+ helpString += "The merge.groups command parameters are shared, group, groups, label and design. The design parameter is required.\n";
+ helpString += "The design parameter allows you to assign your groups to sets. It is required. \n";
+ helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your shared or group file 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 merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";
+ helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";
+ helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
+ m->errorOut(e, "MergeGroupsCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getRequiredParameters(){
- try {
- string Array[] = {"design", "shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getRequiredParameters");
- exit(1);
- }
+string MergeGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "shared") { pattern = "[filename],merge,[extension]"; }
+ else if (type == "group") { pattern = "[filename],merge,[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, "MergeGroupsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getRequiredFiles(){
+MergeGroupsCommand::MergeGroupsCommand(){
try {
- string Array[] = {};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getRequiredFiles");
+ m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
exit(1);
}
}
MergeGroupsCommand::MergeGroupsCommand(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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"groups","label","outputdir","shared","design","processors","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
}
//check for required parameters
designfile = validParameter.validFile(parameters, "design", true);
if (designfile == "not open") { abort = true; }
- else if (designfile == "not found") { designfile = ""; m->mothurOut("You must provide a design file."); m->mothurOutEndLine(); abort = true; }
+ else if (designfile == "not found") {
+ //if there is a current shared file, use it
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setDesignFile(designfile); }
- //make sure the user has already run the read.otu command
sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; m->mothurOut("You must provide a shared file."); m->mothurOutEndLine(); abort = true; }
+ if (sharedfile == "not open") { abort = true; sharedfile = ""; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; groupfile = ""; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->setGroups(Groups);
+
+ if ((sharedfile == "") && (groupfile == "")) {
+ //give priority to group, then shared
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
}
}
exit(1);
}
}
-
//**********************************************************************************************************************
-void MergeGroupsCommand::help(){
+int MergeGroupsCommand::execute(){
try {
- m->mothurOut("The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n");
- m->mothurOut("The merge.groups command outputs a .shared file. \n");
- m->mothurOut("The merge.groups command parameters are shared, groups, label and design. The design and shared parameter are required.\n");
- m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
- m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your shared 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 merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
- m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
- m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ designMap = new GroupMap(designfile);
+ designMap->readDesignMap();
+
+ if (groupfile != "") { processGroupFile(designMap); }
+ if (sharedfile != "") { processSharedFile(designMap); }
+
+ //reset groups parameter
+ m->clearGroups();
+ delete designMap;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0;}
+
+
+ //set shared file as new current sharedfile
+ string current = "";
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ 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();
+
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "help");
+ m->errorOut(e, "MergeGroupsCommand", "execute");
exit(1);
}
}
-
//**********************************************************************************************************************
-MergeGroupsCommand::~MergeGroupsCommand(){}
-
+int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+ try {
+
+ map<string, SharedRAbundVector> merged;
+ map<string, SharedRAbundVector>::iterator it;
+
+ for (int i = 0; i < thisLookUp.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ //what grouping does this group belong to
+ string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
+ if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
+
+ else {
+ //do we already have a member of this grouping?
+ it = merged.find(grouping);
+
+ if (it == merged.end()) { //nope, so create it
+ merged[grouping] = *thisLookUp[i];
+ merged[grouping].setGroup(grouping);
+ }else { //yes, merge it
+
+ for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
+ int abund = (it->second).getAbundance(j);
+ abund += thisLookUp[i]->getAbundance(j);
+
+ (it->second).set(j, abund, grouping);
+ }
+ }
+ }
+ }
+
+ //print new file
+ for (it = merged.begin(); it != merged.end(); it++) {
+ out << (it->second).getLabel() << '\t' << it->first << '\t';
+ (it->second).print(out);
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeGroupsCommand", "process");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-int MergeGroupsCommand::execute(){
+int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
try {
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" + m->getExtension(sharedfile);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ 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);
+ string outputFileName = getOutputFileName("shared", variables);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
- designMap = new GroupMap(designfile);
- designMap->readDesignMap();
-
InputData input(sharedfile, "sharedfile");
lookup = input.getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { out.close(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { out.close(); globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); m->clearGroups(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//get next line to process
lookup = input.getSharedRAbundVectors();
}
- if (m->control_pressed) { out.close(); globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); m->clearGroups(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
out.close();
- //reset groups parameter
- globaldata->Groups.clear();
- delete designMap;
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 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();
+
return 0;
+
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "execute");
+ m->errorOut(e, "MergeGroupsCommand", "processSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
-int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+int MergeGroupsCommand::processGroupFile(GroupMap*& designMap){
try {
- map<string, SharedRAbundVector> merged;
- map<string, SharedRAbundVector>::iterator it;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
+ outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
- for (int i = 0; i < thisLookUp.size(); i++) {
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ //read groupfile
+ GroupMap groupMap(groupfile);
+ groupMap.readMap();
+
+ //fill Groups - checks for "all" and for any typo groups
+ SharedUtil* util = new SharedUtil();
+ vector<string> nameGroups = groupMap.getNamesOfGroups();
+ util->setGroups(Groups, nameGroups);
+ delete util;
+
+ vector<string> namesOfSeqs = groupMap.getNamesSeqs();
+ bool error = false;
+
+ for (int i = 0; i < namesOfSeqs.size(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { break; }
- //what grouping does this group belong to
- string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
- if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
+ string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
- else {
- //do we already have a member of this grouping?
- it = merged.find(grouping);
+ //are you in a group the user wants
+ if (m->inUsersGroups(thisGroup, Groups)) {
+ string thisGrouping = designMap->getGroup(thisGroup);
- if (it == merged.end()) { //nope, so create it
- merged[grouping] = *thisLookUp[i];
- merged[grouping].setGroup(grouping);
- }else { //yes, merge it
-
- for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
- int abund = (it->second).getAbundance(j);
- abund += thisLookUp[i]->getAbundance(j);
-
- (it->second).set(j, abund, grouping);
- }
+ if (thisGrouping == "not found") { m->mothurOut("[ERROR]: " + namesOfSeqs[i] + " is from group " + thisGroup + " which is not in your design file, please correct."); m->mothurOutEndLine(); error = true; }
+ else {
+ out << namesOfSeqs[i] << '\t' << thisGrouping << endl;
}
}
}
- //print new file
- for (it = merged.begin(); it != merged.end(); it++) {
- out << (it->second).getLabel() << '\t' << it->first << '\t';
- (it->second).print(out);
- }
+ if (error) { m->control_pressed = true; }
+
+ out.close();
return 0;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "process");
+ m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
exit(1);
}
}
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