X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.cpp;fp=removeotuscommand.cpp;h=25ed99eacbbd3c6dcbcad18daf5fef44ec13b746;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp new file mode 100644 index 0000000..25ed99e --- /dev/null +++ b/removeotuscommand.cpp @@ -0,0 +1,436 @@ +/* + * removeotuscommand.cpp + * Mothur + * + * Created by westcott on 11/12/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "removeotuscommand.h" +#include "inputdata.h" +#include "sharedutilities.h" + +//********************************************************************************************************************** +vector RemoveOtusCommand::setParameters(){ + try { + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string RemoveOtusCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n"; + helpString += "It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n"; + helpString += "The remove.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n"; + helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n"; + helpString += "The label parameter allows you to specify which distance you want to process.\n"; + helpString += "The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n"; + helpString += "Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n"; + helpString += "or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "getHelpString"); + exit(1); + } +} + +///********************************************************************************************************************** +RemoveOtusCommand::RemoveOtusCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand"); + exit(1); + } +} + +//********************************************************************************************************************** +RemoveOtusCommand::RemoveOtusCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["list"] = 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("accnos"); + //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["accnos"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //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["list"] = 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 + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { abort = true; } + else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + 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("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setGroupFile(groupfile); } + + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { abort = true; } + else if (listfile == "not found") { + listfile = m->getListFile(); + if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setListFile(listfile); } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + } + + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; } + + if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; } + } + + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int RemoveOtusCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + groupMap = new GroupMap(groupfile); + groupMap->readMap(); + + //get groups you want to remove + if (accnosfile != "") { readAccnos(); } + + //make sure groups are valid + //takes care of user setting groupNames that are invalid or setting groups=all + SharedUtil* util = new SharedUtil(); + vector allGroups = groupMap->getNamesOfGroups(); + util->setGroups(Groups, allGroups); + delete util; + + if (m->control_pressed) { delete groupMap; return 0; } + + //read through the list file keeping any otus that contain any sequence from the groups selected + readListGroup(); + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if (outputNames.size() != 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(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + } + + return 0; + } + + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +int RemoveOtusCommand::readListGroup(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label + m->getExtension(listfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + + string GroupOutputDir = outputDir; + if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); } + string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label + m->getExtension(groupfile); + + ofstream outGroup; + m->openOutputFile(outputGroupFileName, outGroup); + + InputData* input = new InputData(listfile, "list"); + ListVector* list = input->getListVector(); + string lastLabel = list->getLabel(); + + //using first label seen if none is provided + if (label == "") { label = lastLabel; } + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set labels; labels.insert(label); + set processedLabels; + set userLabels = labels; + + bool wroteSomething = false; + + //as long as you are not at the end of the file or done wih the lines you want + while((list != NULL) && (userLabels.size() != 0)) { + + if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; } + + if(labels.count(list->getLabel()) == 1){ + processList(list, groupMap, out, outGroup, wroteSomething); + + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + } + + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + + delete list; + + list = input->getListVector(lastLabel); + + processList(list, groupMap, out, outGroup, wroteSomething); + + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + + //restore real lastlabel to save below + list->setLabel(saveLabel); + } + + lastLabel = list->getLabel(); + + delete list; list = NULL; + + //get next line to process + list = input->getListVector(); + } + + + if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; } + + //output error messages about any remaining user labels + set::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) { + if (list != NULL) { delete list; } + + list = input->getListVector(lastLabel); + + processList(list, groupMap, out, outGroup, wroteSomething); + + delete list; list = NULL; + } + + out.close(); + outGroup.close(); + + if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file ONLY contains otus containing sequences from the groups you wish to remove."); m->mothurOutEndLine(); } + outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); + outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "readList"); + exit(1); + } +} +//********************************************************************************************************************** +int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup, bool& wroteSomething){ + try { + + //make a new list vector + ListVector newList; + newList.setLabel(list->getLabel()); + + int numOtus = 0; + //for each bin + for (int i = 0; i < list->getNumBins(); i++) { + if (m->control_pressed) { return 0; } + + //parse out names that are in accnos file + string binnames = list->get(i); + + bool removeBin = false; + string groupFileOutput = ""; + + //parse names + string individual = ""; + int length = binnames.length(); + for(int j=0;jgetGroup(individual); + if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; } + + if (m->inUsersGroups(group, Groups)) { removeBin = true; break; } + groupFileOutput += individual + "\t" + group + "\n"; + individual = ""; + + } + else{ individual += binnames[j]; } + } + + if (!removeBin) { + //get last name + string group = groupMap->getGroup(individual); + if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; } + + if (m->inUsersGroups(group, Groups)) { removeBin = true; } + groupFileOutput += individual + "\t" + group + "\n"; + + if (!removeBin) { + //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile + newList.push_back(binnames); + outGroup << groupFileOutput; + }else { + numOtus++; + } + }else { + numOtus++; + } + + } + + //print new listvector + if (newList.getNumBins() != 0) { + wroteSomething = true; + newList.print(out); + } + + m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "processList"); + exit(1); + } +} +//********************************************************************************************************************** +void RemoveOtusCommand::readAccnos(){ + try { + Groups.clear(); + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + + while(!in.eof()){ + in >> name; + + Groups.push_back(name); + + m->gobble(in); + } + in.close(); + + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "readAccnos"); + exit(1); + } +} +//********************************************************************************************************************** + + +