X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuassociationcommand.cpp;fp=otuassociationcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=0d41e63f3526bc9af4e3933d5f3337d62ebd0f2a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp deleted file mode 100644 index 0d41e63..0000000 --- a/otuassociationcommand.cpp +++ /dev/null @@ -1,461 +0,0 @@ -/* - * otuassociationcommand.cpp - * Mothur - * - * Created by westcott on 1/19/12. - * Copyright 2012 Schloss Lab. All rights reserved. - * - */ - -#include "otuassociationcommand.h" -#include "linearalgebra.h" - -//********************************************************************************************************************** -vector OTUAssociationCommand::setParameters(){ - try { - CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared); - CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod); - 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, "OTUAssociationCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string OTUAssociationCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n"; - helpString += "The otu.association command parameters are shared, relabund, groups, method and label. The shared or relabund parameter is required.\n"; - helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n"; - helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n"; - helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n"; - helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n"; - helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n"; - helpString += "The otu.association command outputs a .otu.corr file.\n"; - helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -OTUAssociationCommand::OTUAssociationCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["otu.corr"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand"); - exit(1); - } -} -//********************************************************************************************************************** -OTUAssociationCommand::OTUAssociationCommand(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 { - 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; } - } - - vector tempOutNames; - outputTypes["otu.corr"] = 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("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; } - } - - 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; } - } - } - - - //check for required parameters - sharedfile = validParameter.validFile(parameters, "shared", true); - if (sharedfile == "not open") { abort = true; } - else if (sharedfile == "not found") { sharedfile = ""; } - else { inputFileName = 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; m->setRelAbundFile(relabundfile); } - - groups = validParameter.validFile(parameters, "groups", false); - if (groups == "not found") { groups = ""; pickedGroups = false; } - else { - pickedGroups = true; - m->splitAtDash(groups, Groups); - } - m->setGroups(Groups); - - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputFileName); } - - label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; } - else { - if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } - else { allLines = 1; } - } - - if ((relabundfile == "") && (sharedfile == "")) { - //is there are current file available for any of these? - //give priority to shared, then relabund - //if there is a current shared file, use it - sharedfile = m->getSharedFile(); - if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } - else { - relabundfile = m->getRelAbundFile(); - if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); } - else { - m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true; - } - } - } - - - if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may only use one of the following : shared or relabund file."); m->mothurOutEndLine(); abort = true; } - - method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; } - - if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; } - - } - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int OTUAssociationCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - //function are identical just different datatypes - if (sharedfile != "") { processShared(); } - else if (relabundfile != "") { processRelabund(); } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - 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, "OTUAssociationCommand", "execute"); - exit(1); - } -} -//********************************************************************************************************************** -int OTUAssociationCommand::processShared(){ - try { - InputData* input = new InputData(sharedfile, "sharedfile"); - 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) { delete input; return 0; } - - if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - process(lookup); - } - - 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); - - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - - //restore real lastlabel to save below - lookup[0]->setLabel(saveLabel); - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - process(lookup); - } - - lastLabel = lookup[0]->getLabel(); - - //get next line to process - //prevent memory leak - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - lookup = input->getSharedRAbundVectors(); - } - - - if (m->control_pressed) { delete input; 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(); - process(lookup); - } - - delete input; - - return 0; - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "processShared"); - exit(1); - } -} -//********************************************************************************************************************** -int OTUAssociationCommand::process(vector& lookup){ - try { - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr"; - outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); - - ofstream out; - m->openOutputFile(outputFileName, out); - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - - //column headings - out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; - - vector< vector > xy; xy.resize(lookup[0]->getNumBins()); - for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } } - - LinearAlgebra linear; - for (int i = 0; i < xy.size(); i++) { - - for (int k = 0; k < i; k++) { - - if (m->control_pressed) { out.close(); return 0; } - - double coef = 0.0; - double sig = 0.0; - if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); } - else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); } - else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); } - else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - - out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; - } - } - - out.close(); - - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "process"); - exit(1); - } -} -//********************************************************************************************************************** -int OTUAssociationCommand::processRelabund(){ - try { - InputData* input = new InputData(relabundfile, "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) { delete input; return 0; } - - if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - process(lookup); - } - - 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); - - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - - //restore real lastlabel to save below - lookup[0]->setLabel(saveLabel); - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - process(lookup); - } - - lastLabel = lookup[0]->getLabel(); - - //get next line to process - //prevent memory leak - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - lookup = input->getSharedRAbundFloatVectors(); - } - - - if (m->control_pressed) { delete input; 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(); - process(lookup); - } - - delete input; - - return 0; - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "processRelabund"); - exit(1); - } -} -//********************************************************************************************************************** -int OTUAssociationCommand::process(vector& lookup){ - try { - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr"; - outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); - - ofstream out; - m->openOutputFile(outputFileName, out); - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - - //column headings - out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; - - vector< vector > xy; xy.resize(lookup[0]->getNumBins()); - for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } } - - LinearAlgebra linear; - for (int i = 0; i < xy.size(); i++) { - - for (int k = 0; k < i; k++) { - - if (m->control_pressed) { out.close(); return 0; } - - double coef = 0.0; - double sig = 0.0; - if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); } - else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); } - else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); } - else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - - out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; - } - } - - out.close(); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "OTUAssociationCommand", "process"); - exit(1); - } -} -/*****************************************************************/ - - - - - - - -