X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listotulabelscommand.cpp;fp=listotulabelscommand.cpp;h=becfae3ff949f0a3f8bba42604459f8e4267dc65;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=0000000000000000000000000000000000000000;hpb=4522aebe2246c5f47875d5c8cc505f1b615bfc7e;p=mothur.git diff --git a/listotulabelscommand.cpp b/listotulabelscommand.cpp new file mode 100644 index 0000000..becfae3 --- /dev/null +++ b/listotulabelscommand.cpp @@ -0,0 +1,387 @@ +// +// listotucommand.cpp +// Mothur +// +// Created by Sarah Westcott on 5/15/12. +// Copyright (c) 2012 Schloss Lab. All rights reserved. +// + +#include "listotulabelscommand.h" +#include "inputdata.h" + +//********************************************************************************************************************** +vector ListOtuLabelsCommand::setParameters(){ + try { + CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files. + 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, "ListOtuLabelsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ListOtuLabelsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The list.labels lists otu labels from shared or relabund file. The results can be used by the get.labels to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n"; + helpString += "The list.labels parameters are: shared, relabund, label and groups.\n"; + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n"; + helpString += "The list.labels commmand should be in the following format: \n"; + helpString += "list.otulabels(shared=yourSharedFile, groups=yourGroup1-yourGroup2)\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +ListOtuLabelsCommand::ListOtuLabelsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["otulabels"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "ListOtuLabelsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +ListOtuLabelsCommand::ListOtuLabelsCommand(string option) { + try { + abort = false; calledHelp = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + //valid paramters for this command + 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; } + } + + + //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 { + + //edit file types below to include only the types you added as parameters + + string path; + it = parameters.find("relabund"); + //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["relabund"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //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["shared"] = inputDir + it->second; } + } + } + + vector tempOutNames; + outputTypes["otulabels"] = tempOutNames; + + //check for parameters + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); } + + relabundfile = validParameter.validFile(parameters, "relabund", true); + if (relabundfile == "not open") { abort = true; } + else if (relabundfile == "not found") { relabundfile = ""; } + else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); } + + if ((relabundfile == "") && (sharedfile == "")) { + //is there are current file available for either of these? + //give priority to shared, then relabund + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + relabundfile = m->getRelAbundFile(); + if (relabundfile != "") { inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine(); + 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 = m->hasPath(inputFileName); //if user entered a file with a path then preserve it + } + + string groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { m->splitAtDash(groups, Groups); } + m->setGroups(Groups); + + string label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + } + + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "ListOtuLabelsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int ListOtuLabelsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + InputData input(inputFileName, format); + + if (format == "relabund") { + vector lookup = input.getSharedRAbundFloatVectors(); + string lastLabel = lookup[0]->getLabel(); + + //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; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundFloatVectors(lastLabel); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //get next line to process + lookup = input.getSharedRAbundFloatVectors(); + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //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(); + } + } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundFloatVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + }else { + + vector lookup = input.getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + + //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; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(lastLabel); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //get next line to process + lookup = input.getSharedRAbundVectors(); + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //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(); + } + } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + createList(lookup); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //output files created by command + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** + +int ListOtuLabelsCommand::createList(vector& lookup){ + try { + + string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels"; + outputNames.push_back(outputFileName); outputTypes["otulabels"].push_back(outputFileName); + ofstream out; + m->openOutputFile(outputFileName, out); + + for (int i = 0; i < m->currentBinLabels.size(); i++) { out << m->currentBinLabels[i] << endl; } + + out.close(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "createTable"); + exit(1); + } +} + +//********************************************************************************************************************** + +int ListOtuLabelsCommand::createList(vector& lookup){ + try { + + string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels"; + outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName); + ofstream out; + m->openOutputFile(outputFileName, out); + + for (int i = 0; i < m->currentBinLabels.size(); i++) { out << m->currentBinLabels[i] << endl; } + + out.close(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "ListOtuLabelsCommand", "createTable"); + exit(1); + } +} + +//********************************************************************************************************************** +