X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=5a568f3511d38f56601362d860a9643e702c9a1b;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=bb096d8646873f74c42bd8970b9eef9693a3252e;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index bb096d8..5a568f3 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -12,11 +12,12 @@ //********************************************************************************************************************** vector ParseListCommand::setParameters(){ try { - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); - 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 plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist); + CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "CountGroup", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none","",false,false,true); parameters.push_back(pgroup); + 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); } @@ -31,9 +32,11 @@ vector ParseListCommand::setParameters(){ string ParseListCommand::getHelpString(){ try { string helpString = ""; - helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n"; - helpString += "The parse.list command parameters are list, group and label.\n"; - helpString += "The list and group parameters are required.\n"; + helpString += "The parse.list command reads a list and group or count file and generates a list file for each group in the group or count file. \n"; + helpString += "The parse.list command parameters are list, group, count and label.\n"; + helpString += "The list and group or count parameters are required.\n"; + helpString += "If a count file is provided, mothur assumes the list file contains only unique names.\n"; + helpString += "If a group file is provided, mothur assumes the list file contains all names.\n"; helpString += "The label parameter is used to read specific labels in your input you want to use.\n"; helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n"; helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n"; @@ -46,6 +49,21 @@ string ParseListCommand::getHelpString(){ } } //********************************************************************************************************************** +string ParseListCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[group],list"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** ParseListCommand::ParseListCommand(){ try { abort = true; calledHelp = true; @@ -106,11 +124,18 @@ ParseListCommand::ParseListCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = inputDir + it->second; } } + + it = parameters.find("count"); + //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["count"] = inputDir + it->second; } + } } - //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 = ""; } + //check for required parameters listfile = validParameter.validFile(parameters, "list", true); @@ -124,28 +149,39 @@ ParseListCommand::ParseListCommand(string option) { } }else { m->setListFile(listfile); } + + //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 = m->hasPath(listfile); } - groupfile = validParameter.validFile(parameters, "group", true); - if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { - groupfile = m->getListFile(); - if (groupfile != "") { - m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); - groupMap = new GroupMap(groupfile); - - int error = groupMap->readMap(); - if (error == 1) { abort = true; } - }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); abort = true; } - }else { - m->setGroupFile(groupfile); + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not found") { groupfile = ""; groupMap = NULL; } + else if (groupfile == "not open") { abort = true; groupfile = ""; groupMap = NULL; } + else { + m->setGroupFile(groupfile); groupMap = new GroupMap(groupfile); int error = groupMap->readMap(); if (error == 1) { abort = true; } - } - - //do you have all files needed - if ((listfile == "") || (groupfile == "")) { m->mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); m->mothurOutEndLine(); abort = true; } + } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not found") { countfile = ""; } + else if (countfile == "not open") { abort = true; countfile = ""; } + else { + m->setCountTableFile(countfile); + ct.readTable(countfile, true); + if (!ct.hasGroupInfo()) { + abort = true; + m->mothurOut("[ERROR]: The parse.list command requires group info to be present in your countfile, quitting."); m->mothurOutEndLine(); + } + + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + }else if ((groupfile == "") && (countfile == "")) { + m->mothurOut("[ERROR]: you must provide one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -170,17 +206,22 @@ int ParseListCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } //set fileroot - string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile)); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); //fill filehandles with neccessary ofstreams int i; ofstream* temp; - vector gGroups = groupMap->getNamesOfGroups(); + vector gGroups; + if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); } + else { gGroups = ct.getNamesOfGroups(); } + for (i=0; iopenOutputFile(filename, *temp); } @@ -189,13 +230,12 @@ int ParseListCommand::execute(){ set processedLabels; set userLabels = labels; - input = new InputData(listfile, "list"); - list = input->getListVector(); + InputData input(listfile, "list"); + list = input.getListVector(); string lastLabel = list->getLabel(); if (m->control_pressed) { - delete input; delete list; delete groupMap; - vector gGroups = groupMap->getNamesOfGroups(); + delete list; if (groupfile != "") { delete groupMap; } for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; @@ -204,7 +244,7 @@ int ParseListCommand::execute(){ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if (m->control_pressed) { - delete input; delete list; delete groupMap; + delete list; if (groupfile != "") { delete groupMap; } for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; @@ -222,8 +262,7 @@ int ParseListCommand::execute(){ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); - delete list; - list = input->getListVector(lastLabel); //get new list vector to process + list = input.getListVector(lastLabel); //get new list vector to process m->mothurOut(list->getLabel()); m->mothurOutEndLine(); parse(list); @@ -239,11 +278,11 @@ int ParseListCommand::execute(){ lastLabel = list->getLabel(); delete list; - list = input->getListVector(); //get new list vector to process + list = input.getListVector(); //get new list vector to process } if (m->control_pressed) { - delete input; delete groupMap; + if (groupfile != "") { delete groupMap; } for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; @@ -264,7 +303,7 @@ int ParseListCommand::execute(){ } if (m->control_pressed) { - delete input; delete groupMap; + if (groupfile != "") { delete groupMap; } for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; @@ -273,7 +312,7 @@ int ParseListCommand::execute(){ //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } - list = input->getListVector(lastLabel); //get new list vector to process + list = input.getListVector(lastLabel); //get new list vector to process m->mothurOut(list->getLabel()); m->mothurOutEndLine(); parse(list); @@ -286,9 +325,7 @@ int ParseListCommand::execute(){ delete it3->second; } - - delete groupMap; - delete input; + if (groupfile != "") { delete groupMap; } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); @@ -340,17 +377,33 @@ int ParseListCommand::parse(ListVector* thisList) { //parse bin into list of sequences in each group for (int j = 0; j < names.size(); j++) { - string group = groupMap->getGroup(names[j]); + if (groupfile != "") { + string group = groupMap->getGroup(names[j]); - if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); } + if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); } - itGroup = groupBins.find(group); - if(itGroup == groupBins.end()) { - groupBins[group] = names[j]; //add first name - groupNumBins[group]++; - }else{ //add another name - groupBins[group] = groupBins[group] + "," + names[j]; - } + itGroup = groupBins.find(group); + if(itGroup == groupBins.end()) { + groupBins[group] = names[j]; //add first name + groupNumBins[group]++; + }else{ //add another name + groupBins[group] = groupBins[group] + "," + names[j]; + } + }else{ + vector thisSeqsGroups = ct.getGroups(names[j]); + + for (int k = 0; k < thisSeqsGroups.size(); k++) { + string group = thisSeqsGroups[k]; + itGroup = groupBins.find(group); + if(itGroup == groupBins.end()) { + groupBins[group] = names[j]; //add first name + groupNumBins[group]++; + }else{ //add another name + groupBins[group] = groupBins[group] + "," + names[j]; + } + + } + } } //print parsed bin info to files