X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;fp=otuhierarchycommand.cpp;h=2f99aa6091452933f6796f21aa043449bfce1dd4;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp new file mode 100644 index 0000000..2f99aa6 --- /dev/null +++ b/otuhierarchycommand.cpp @@ -0,0 +1,363 @@ +/* + * 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); + } +} + +//********************************************************************************************************************** + + + + +