X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeotuscommand.cpp;h=16fd8dce8bab96b030a57effd81d218e122628a5;hp=347bb0870f3fde2ab71c86c5b67918fad4a4904c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18 diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp index 347bb08..16fd8dc 100644 --- a/removeotuscommand.cpp +++ b/removeotuscommand.cpp @@ -11,55 +11,78 @@ #include "inputdata.h" #include "sharedutilities.h" - //********************************************************************************************************************** -vector RemoveOtusCommand::getValidParameters(){ +vector RemoveOtusCommand::setParameters(){ try { - string Array[] = { "group", "accnos","label", "groups","list","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,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", "getValidParameters"); + m->errorOut(e, "RemoveOtusCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -RemoveOtusCommand::RemoveOtusCommand(){ +string RemoveOtusCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["group"] = tempOutNames; - outputTypes["list"] = tempOutNames; + 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", "RemoveOtusCommand"); + m->errorOut(e, "RemoveOtusCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector RemoveOtusCommand::getRequiredParameters(){ - try { - string Array[] = {"group","label", "list"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "getRequiredParameters"); - exit(1); - } +string RemoveOtusCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; } + else if (type == "list") { pattern = "[filename],[tag],pick,[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, "RemoveOtusCommand", "getOutputPattern"); + exit(1); + } } -//********************************************************************************************************************** -vector RemoveOtusCommand::getRequiredFiles(){ +///********************************************************************************************************************** +RemoveOtusCommand::RemoveOtusCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["list"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "getRequiredFiles"); + m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand"); exit(1); } } + //********************************************************************************************************************** RemoveOtusCommand::RemoveOtusCommand(string option) { try { @@ -67,11 +90,10 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { //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 Array[] = { "group", "accnos","label", "groups", "list","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -127,15 +149,24 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { //check for required parameters accnosfile = validParameter.validFile(parameters, "accnos", true); if (accnosfile == "not open") { abort = true; } - else if (accnosfile == "not found") { accnosfile = ""; } + 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->mothurOut("You must provide a group file."); m->mothurOutEndLine(); 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->mothurOut("You must provide a list file."); m->mothurOutEndLine(); 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 = ""; } @@ -144,7 +175,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { } label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; m->mothurOut("You must provide a label to process."); m->mothurOutEndLine(); abort = true; } + 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; } } @@ -157,27 +188,6 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { } //********************************************************************************************************************** -void RemoveOtusCommand::help(){ - try { - m->mothurOut("The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n"); - m->mothurOut("It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n"); - m->mothurOut("The remove.otus command parameters are accnos, group, list, label and groups. The group, list and label parameters are required.\n"); - m->mothurOut("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"); - m->mothurOut("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"); - m->mothurOut("The label parameter allows you to specify which distance you want to process.\n"); - m->mothurOut("The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n"); - m->mothurOut("Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n"); - m->mothurOut("or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int RemoveOtusCommand::execute(){ try { @@ -187,12 +197,13 @@ int RemoveOtusCommand::execute(){ groupMap->readMap(); //get groups you want to remove - if (accnosfile != "") { readAccnos(); } + if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); } //make sure groups are valid //takes care of user setting groupNames that are invalid or setting groups=all SharedUtil* util = new SharedUtil(); - util->setGroups(Groups, groupMap->namesOfGroups); + vector allGroups = groupMap->getNamesOfGroups(); + util->setGroups(Groups, allGroups); delete util; if (m->control_pressed) { delete groupMap; return 0; } @@ -200,13 +211,25 @@ int RemoveOtusCommand::execute(){ //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++) { remove(outputNames[i].c_str()); } return 0; } + 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; @@ -222,14 +245,20 @@ 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); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[tag]"] = label; + variables["[extension]"] = m->getExtension(listfile); + string outputFileName = getOutputFileName("list", variables); 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); + variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string outputGroupFileName = getOutputFileName("group", variables); ofstream outGroup; m->openOutputFile(outputGroupFileName, outGroup); @@ -238,6 +267,9 @@ int RemoveOtusCommand::readListGroup(){ 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; @@ -248,7 +280,7 @@ int RemoveOtusCommand::readListGroup(){ //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(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str());return 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); @@ -282,7 +314,7 @@ int RemoveOtusCommand::readListGroup(){ } - if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str()); return 0; } + 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; @@ -396,30 +428,6 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr } } //********************************************************************************************************************** -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); - } -} -//**********************************************************************************************************************