X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.cpp;fp=removeotuscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=25ed99eacbbd3c6dcbcad18daf5fef44ec13b746;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp deleted file mode 100644 index 25ed99e..0000000 --- a/removeotuscommand.cpp +++ /dev/null @@ -1,436 +0,0 @@ -/* - * 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); - } -} -//********************************************************************************************************************** - - -