X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getotuscommand.cpp;h=3ca7f5d575db0a7e3a065ebcf371128698d5056b;hp=b39b4ab74ef178bb1a3dd2029549c69b2bda4be6;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17 diff --git a/getotuscommand.cpp b/getotuscommand.cpp index b39b4ab..3ca7f5d 100644 --- a/getotuscommand.cpp +++ b/getotuscommand.cpp @@ -15,13 +15,13 @@ //********************************************************************************************************************** vector GetOtusCommand::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); + 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); } @@ -53,7 +53,22 @@ string GetOtusCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string GetOtusCommand::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, "GetOtusCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** GetOtusCommand::GetOtusCommand(){ try { @@ -75,6 +90,7 @@ GetOtusCommand::GetOtusCommand(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 { vector myArray = setParameters(); @@ -133,7 +149,8 @@ GetOtusCommand::GetOtusCommand(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; } @@ -141,7 +158,7 @@ GetOtusCommand::GetOtusCommand(string option) { 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; } @@ -149,7 +166,7 @@ GetOtusCommand::GetOtusCommand(string option) { 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 = ""; } @@ -180,12 +197,14 @@ int GetOtusCommand::execute(){ groupMap->readMap(); //get groups you want to get - 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 gNamesOfGroups = groupMap->getNamesOfGroups(); + util->setGroups(Groups, gNamesOfGroups); + groupMap->setNamesOfGroups(gNamesOfGroups); delete util; if (m->control_pressed) { delete groupMap; return 0; } @@ -193,7 +212,7 @@ int GetOtusCommand::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(); @@ -225,26 +244,33 @@ int GetOtusCommand::execute(){ //********************************************************************************************************************** int GetOtusCommand::readListGroup(){ try { - string thisOutputDir = outputDir; + 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; } + + 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; + + 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); - - 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); @@ -256,7 +282,7 @@ int GetOtusCommand::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); @@ -290,7 +316,7 @@ int GetOtusCommand::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; @@ -341,6 +367,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream int numOtus = 0; //for each bin + vector binLabels = list->getLabels(); + vector newBinLabels; for (int i = 0; i < list->getNumBins(); i++) { if (m->control_pressed) { return 0; } @@ -374,7 +402,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream //if there are sequences from the groups we want in this bin add to new list, output to groupfile if (keepBin) { - newList.push_back(binnames); + newList.push_back(binnames); + newBinLabels.push_back(binLabels[i]); outGroup << groupFileOutput; numOtus++; } @@ -383,7 +412,9 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream //print new listvector if (newList.getNumBins() != 0) { wroteSomething = true; - newList.print(out); + newList.setLabels(newBinLabels); + newList.printHeaders(out); + newList.print(out); } m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine(); @@ -396,29 +427,5 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream } } //********************************************************************************************************************** -void GetOtusCommand::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, "GetOtusCommand", "readAccnos"); - exit(1); - } -} -//**********************************************************************************************************************