X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;fp=otuhierarchycommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=2f99aa6091452933f6796f21aa043449bfce1dd4;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp deleted file mode 100644 index 2f99aa6..0000000 --- a/otuhierarchycommand.cpp +++ /dev/null @@ -1,363 +0,0 @@ -/* - * otuhierarchycommand.cpp - * Mothur - * - * Created by westcott on 1/19/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "otuhierarchycommand.h" - -//********************************************************************************************************************** -vector OtuHierarchyCommand::setParameters(){ - try { - CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput); - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); - 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, "OtuHierarchyCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string OtuHierarchyCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n"; - helpString += "The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n"; - helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n"; - helpString += "The otu.hierarchy command should be in the following format: \n"; - helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n"; - helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"; - helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\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, "OtuHierarchyCommand", "getHelpString"); - exit(1); - } -} - -//********************************************************************************************************************** -OtuHierarchyCommand::OtuHierarchyCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["otuheirarchy"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); - exit(1); - } -} -//********************************************************************************************************************** -OtuHierarchyCommand::OtuHierarchyCommand(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["otuheirarchy"] = 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 = ""; } - else { - string path; - 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; } - } - } - - listFile = validParameter.validFile(parameters, "list", true); - 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 if (listFile == "not open") { 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 = ""; - outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it - } - - //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") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; } - else { - m->splitAtDash(label, labels); - if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; } - } - - output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; } - - if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; } - } - - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int OtuHierarchyCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector) - vector lists = getListVectors(); - - if (m->control_pressed) { outputTypes.clear(); return 0; } - - //determine which is little and which is big, putting little first - if (lists.size() == 2) { - //if big is first swap them - if (lists[0].getNumBins() < lists[1].getNumBins()) { - reverse(lists.begin(), lists.end()); - } - }else{ - m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0; - } - - //map sequences to bin number in the "little" otu - map littleBins; - for (int i = 0; i < lists[0].getNumBins(); i++) { - - if (m->control_pressed) { return 0; } - - string names = lists[0].get(i); - - //parse bin - while (names.find_first_of(',') != -1) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); - littleBins[name] = i; - } - - //get last name - littleBins[names] = i; - } - - ofstream out; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy"; - m->openOutputFile(outputFileName, out); - - //go through each bin in "big" otu and output the bins in "little" otu which created it - for (int i = 0; i < lists[1].getNumBins(); i++) { - - if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; } - - string names = lists[1].get(i); - - //output column 1 - if (output == "name") { out << names << '\t'; } - else { out << i << '\t'; } - - map bins; //bin numbers in little that are in this bin in big - map::iterator it; - - //parse bin - while (names.find_first_of(',') != -1) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); - bins[littleBins[name]] = littleBins[name]; - } - - //get last name - bins[littleBins[names]] = littleBins[names]; - - string col2 = ""; - for (it = bins.begin(); it != bins.end(); it++) { - if (output == "name") { col2 += lists[0].get(it->first) + "\t"; } - else { col2 += toString(it->first) + "\t"; } - } - - //output column 2 - out << col2 << endl; - } - - out.close(); - - if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; } - - m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); - m->mothurOutEndLine(); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "execute"); - exit(1); - } -} - -//********************************************************************************************************************** -//returns a vector of listVectors where "little" vector is first -vector OtuHierarchyCommand::getListVectors() { - try { - - int pos; //to use in smart distancing, position of last read in file - int lastPos; - vector lists; - - //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; - - //open file - ifstream in; - m->openInputFile(listFile, in); - - //get first list vector in file - ListVector* list = NULL; - string lastLabel = ""; - if (!in.eof()) { - pos = in.tellg(); - lastPos = pos; - list = new ListVector(in); - m->gobble(in); - lastLabel = list->getLabel(); - } - - while ((list != NULL) && (userLabels.size() != 0)) { - - if (m->control_pressed) { in.close(); delete list; return lists; } - - //is this a listvector that we want? - if(labels.count(list->getLabel()) == 1){ - - //make copy of listvector - ListVector temp(*list); - lists.push_back(temp); - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - } - - //you have a label the user want that is smaller than this label and the last label has not already been processed - if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = list->getLabel(); - int savePos = in.tellg(); - - //get smart distance line - delete list; - in.seekg(lastPos); - if (!in.eof()) { - list = new ListVector(in); - }else { list = NULL; } - - //make copy of listvector - ListVector temp(*list); - lists.push_back(temp); - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - - //restore real lastlabel to save below - list->setLabel(saveLabel); - in.seekg(savePos); - } - - lastLabel = list->getLabel(); - lastPos = pos; - - //get next line - delete list; - if (!in.eof()) { - pos = in.tellg(); - list = new ListVector(in); - m->gobble(in); - }else { list = NULL; } - } - - if (m->control_pressed) { in.close(); return lists; } - - //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(); - } - } - - if (m->control_pressed) { in.close(); return lists; } - - //run last label if you need to - if (needToRun == true) { - if (list != NULL) { delete list; } - - in.seekg(lastPos); - if (!in.eof()) { - list = new ListVector(in); - - //make copy of listvector - ListVector temp(*list); - lists.push_back(temp); - - delete list; - } - } - - in.close(); - return lists; - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "getListVectors"); - exit(1); - } -} - -//********************************************************************************************************************** - - - - -