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mergegroupscommand.cpp
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mergegroupscommand.cpp
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/*
* mergegroupscommand.cpp
* mothur
*
* Created by westcott on 1/24/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "mergegroupscommand.h"
#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> MergeGroupsCommand::setParameters(){
try {
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", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MergeGroupsCommand::getHelpString(){
try {
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", "getHelpString");
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);
}
}
//**********************************************************************************************************************
MergeGroupsCommand::MergeGroupsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
exit(1);
}
}
//**********************************************************************************************************************
MergeGroupsCommand::MergeGroupsCommand(string option) {
try {
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check to make sure all parameters are valid for command
map<string,string>::iterator it;
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//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 changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("design");
//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["design"] = inputDir + it->second; }
}
it = parameters.find("shared");
//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["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") {
//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); }
sharedfile = validParameter.validFile(parameters, "shared", 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...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(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;
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "MergeGroupsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MergeGroupsCommand::execute(){
try {
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", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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::processSharedFile(GroupMap*& designMap){
try {
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);
InputData input(sharedfile, "sharedfile");
lookup = input.getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
//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]; } 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->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
}
lastLabel = 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(); 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(); 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;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "processSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
int MergeGroupsCommand::processGroupFile(GroupMap*& designMap){
try {
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);
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) { break; }
string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
//are you in a group the user wants
if (m->inUsersGroups(thisGroup, Groups)) {
string thisGrouping = designMap->getGroup(thisGroup);
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;
}
}
}
if (error) { m->control_pressed = true; }
out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
exit(1);
}
}
//**********************************************************************************************************************