X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=b49af32a76c1cbb2d65ab2a5bf32555a171c5de7;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=bc87211e0bde9a4581119a91592683e34262d006;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp index bc87211..b49af32 100644 --- a/otuhierarchycommand.cpp +++ b/otuhierarchycommand.cpp @@ -10,15 +10,63 @@ #include "otuhierarchycommand.h" //********************************************************************************************************************** -OtuHierarchyCommand::OtuHierarchyCommand(string option){ +vector OtuHierarchyCommand::getValidParameters(){ try { - abort = false; + string Array[] = {"list","label","output","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +OtuHierarchyCommand::OtuHierarchyCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["otuheirarchy"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector OtuHierarchyCommand::getRequiredParameters(){ + try { + string Array[] = {"list","label"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector OtuHierarchyCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +OtuHierarchyCommand::OtuHierarchyCommand(string option) { + try { + abort = false; calledHelp = false; + //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"list","label","outputdir","inputdir"}; + string Array[] = {"list","label","output","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -32,6 +80,10 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){ 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 = ""; } @@ -40,35 +92,39 @@ OtuHierarchyCommand::OtuHierarchyCommand(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; } } } listFile = validParameter.validFile(parameters, "list", true); - if (listFile == "not found") { mothurOut("list is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; } + if (listFile == "not found") { m->mothurOut("list is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; } else if (listFile == "not open") { abort = true; } //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 += hasPath(listFile); //if user entered a file with a path then preserve it + 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") { mothurOut("label is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; } + if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(label, labels); - if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; } - } + 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) { - errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); + m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); exit(1); } } @@ -76,16 +132,17 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){ void OtuHierarchyCommand::help(){ try { - mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n"); - mothurOut("The otu.hierarchy command parameters are list and label. Both parameters are required. \n"); - mothurOut("The otu.hierarchy command should be in the following format: \n"); - mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n"); - mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"); - mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); + m->mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n"); + m->mothurOut("The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n"); + m->mothurOut("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"); + m->mothurOut("The otu.hierarchy command should be in the following format: \n"); + m->mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n"); + m->mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"); + m->mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); } catch(exception& e) { - errorOut(e, "OtuHierarchyCommand", "help"); + m->errorOut(e, "OtuHierarchyCommand", "help"); exit(1); } } @@ -99,11 +156,13 @@ OtuHierarchyCommand::~OtuHierarchyCommand(){} int OtuHierarchyCommand::execute(){ try { - if (abort == true) { return 0; } + 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 @@ -111,12 +170,15 @@ int OtuHierarchyCommand::execute(){ reverse(lists.begin(), lists.end()); } }else{ - mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); mothurOutEndLine(); return 0; + 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 @@ -131,16 +193,19 @@ int OtuHierarchyCommand::execute(){ } ofstream out; - string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy"; - openOutputFile(outputFileName, 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(); remove(outputFileName.c_str()); return 0; } + string names = lists[1].get(i); //output column 1 - out << names << '\t'; + 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; @@ -157,7 +222,8 @@ int OtuHierarchyCommand::execute(){ string col2 = ""; for (it = bins.begin(); it != bins.end(); it++) { - col2 += lists[0].get(it->first) + "\t"; + if (output == "name") { col2 += lists[0].get(it->first) + "\t"; } + else { col2 += toString(it->first) + "\t"; } } //output column 2 @@ -166,10 +232,17 @@ int OtuHierarchyCommand::execute(){ out.close(); + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); 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) { - errorOut(e, "OtuHierarchyCommand", "execute"); + m->errorOut(e, "OtuHierarchyCommand", "execute"); exit(1); } } @@ -189,7 +262,7 @@ vector OtuHierarchyCommand::getListVectors() { //open file ifstream in; - openInputFile(listFile, in); + m->openInputFile(listFile, in); //get first list vector in file ListVector* list = NULL; @@ -198,11 +271,13 @@ vector OtuHierarchyCommand::getListVectors() { pos = in.tellg(); lastPos = pos; list = new ListVector(in); - gobble(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){ @@ -216,7 +291,7 @@ vector OtuHierarchyCommand::getListVectors() { } //you have a label the user want that is smaller than this label and the last label has not already been processed - 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(); int savePos = in.tellg(); @@ -247,25 +322,27 @@ vector OtuHierarchyCommand::getListVectors() { if (!in.eof()) { pos = in.tellg(); list = new ListVector(in); - gobble(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++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + 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; } @@ -282,11 +359,11 @@ vector OtuHierarchyCommand::getListVectors() { } } - + in.close(); return lists; } catch(exception& e) { - errorOut(e, "OtuHierarchyCommand", "getListVectors"); + m->errorOut(e, "OtuHierarchyCommand", "getListVectors"); exit(1); } }