+++ /dev/null
-/*
- * 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",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,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);
- }
-}
-//**********************************************************************************************************************
-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); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" + m->getExtension(sharedfile);
- 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); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "merge" + m->getExtension(groupfile);
- 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);
- }
-}
-//**********************************************************************************************************************
-
-
-
projects / mothur.git / blobdiff