X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parselistscommand.cpp;h=cfd1b6b9705ccb131e050ce132547192892d12ea;hp=9955a19f677dd96cccf7b9f4171e0f7d28b9deac;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3 diff --git a/parselistscommand.cpp b/parselistscommand.cpp index 9955a19..cfd1b6b 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -9,19 +9,85 @@ #include "parselistscommand.h" +//********************************************************************************************************************** +vector ParseListCommand::setParameters(){ + try { + 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); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ParseListCommand::getHelpString(){ + try { + string helpString = ""; + 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"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string ParseListCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[group],[distance],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; + setParameters(); + vector tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "ParseListCommand"); + exit(1); + } +} //********************************************************************************************************************** ParseListCommand::ParseListCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; allLines = 1; //allow user to run help - if(option == "help") { help(); abort = true; } + 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[] = {"list","group", "label", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -33,7 +99,11 @@ ParseListCommand::ParseListCommand(string option) { for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - + + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + //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 = ""; } @@ -42,7 +112,7 @@ ParseListCommand::ParseListCommand(string option) { it = parameters.find("list"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -50,40 +120,75 @@ ParseListCommand::ParseListCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } + + 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); if (listfile == "not open") { abort = true; } - else if (listfile == "not found") { listfile = ""; } + 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("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); + abort = true; + + } + }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 = ""; } - else { + 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, false); + 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... label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; allLines = 1; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } } @@ -95,67 +200,29 @@ ParseListCommand::ParseListCommand(string option) { } } //********************************************************************************************************************** -void ParseListCommand::help(){ - try { - m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n"); - m->mothurOut("The parse.list command parameters are list, group and label.\n"); - m->mothurOut("The list and group parameters are required.\n"); - m->mothurOut("The label parameter is used to read specific labels in your input you want to use.\n"); - m->mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n"); - m->mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.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, "ParseListCommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** -ParseListCommand::~ParseListCommand(){} -//********************************************************************************************************************** int ParseListCommand::execute(){ try { - if (abort == true) { return 0; } - - //set fileroot - string fileroot = outputDir + getRootName(getSimpleName(listfile)); - vector outputNames; - - //fill filehandles with neccessary ofstreams - int i; - ofstream* temp; - for (i=0; inamesOfGroups.size(); i++) { - temp = new ofstream; - filehandles[groupMap->namesOfGroups[i]] = temp; - - string filename = fileroot + groupMap->namesOfGroups[i] + ".list"; - outputNames.push_back(filename); - openOutputFile(filename, *temp); - } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. 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; - for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; + delete list; if (groupfile != "") { delete groupMap; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if (m->control_pressed) { - delete input; delete list; delete groupMap; - for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + delete list; if (groupfile != "") { delete groupMap; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -168,11 +235,10 @@ int ParseListCommand::execute(){ userLabels.erase(list->getLabel()); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + 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); @@ -188,14 +254,13 @@ 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; - for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; + if (groupfile != "") { delete groupMap; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; } //output error messages about any remaining user labels @@ -213,16 +278,15 @@ int ParseListCommand::execute(){ } if (m->control_pressed) { - delete input; delete groupMap; - for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; + if (groupfile != "") { delete groupMap; } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; } //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); @@ -230,20 +294,20 @@ int ParseListCommand::execute(){ delete list; } - for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { - (*(filehandles[it3->first])).close(); - delete it3->second; - } - - - delete groupMap; - delete input; + if (groupfile != "") { delete groupMap; } if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -259,8 +323,33 @@ int ParseListCommand::execute(){ /**********************************************************************************************************************/ int ParseListCommand::parse(ListVector* thisList) { try { + map filehandles; + map::iterator it3; + + //set fileroot + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[distance]"] = thisList->getLabel(); + + //fill filehandles with neccessary ofstreams + ofstream* temp; + vector gGroups; + if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); } + else { gGroups = ct.getNamesOfGroups(); } + + for (int i=0; iopenOutputFile(filename, *temp); + outputNames.push_back(filename); outputTypes["list"].push_back(filename); + } + map groupVector; + map groupLabels; map::iterator itGroup; map groupNumBins; @@ -268,43 +357,72 @@ int ParseListCommand::parse(ListVector* thisList) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { groupNumBins[it3->first] = 0; groupVector[it3->first] = ""; + groupLabels[it3->first] = "label\tnumOtus\t"; } - + vector binLabels = thisList->getLabels(); for (int i = 0; i < thisList->getNumBins(); i++) { - if (m->control_pressed) { return 0; } + if (m->control_pressed) { break; } map groupBins; string bin = list->get(i); vector names; - splitAtComma(bin, names); //parses bin into individual sequence names + m->splitAtComma(bin, names); //parses bin into individual sequence names //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 for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) { - groupVector[itGroup->first] += itGroup->second + '\t'; + groupVector[itGroup->first] += itGroup->second + '\t'; + groupLabels[itGroup->first] += binLabels[i] + '\t'; } } + if (m->control_pressed) { + for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { + (*(filehandles[it3->first])).close(); + delete it3->second; + } + return 0; + } + //end list vector for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { + (*(filehandles[it3->first])) << groupLabels[it3->first] << endl; (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group + (*(filehandles[it3->first])).close(); + delete it3->second; } return 0;