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/*
* otuassociationcommand.cpp
* Mothur
*
* Created by westcott on 1/19/12.
* Copyright 2012 Schloss Lab. All rights reserved.
*
*/
#include "otuassociationcommand.h"
#include "linearalgebra.h"
//**********************************************************************************************************************
vector<string> OTUAssociationCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund);
CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
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,true); parameters.push_back(pmethod);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false; allLines = true;
vector<string> tempOutNames;
outputTypes["otucorr"] = tempOutNames;
vector<string> 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 += "If you provide a metadata file, mothur will calculate te correlation bewteen the metadata and the otus.\n";
helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method, cutoff 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 cutoff parameter allows you to set a pvalue at which the otu will be reported.\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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string OTUAssociationCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "otucorr") { pattern = "[filename],[distance],[tag],otu.corr"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
OTUAssociationCommand::OTUAssociationCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { inputFileName = sharedfile; current->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund");
if (relabundfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; current->setRelAbundFile(relabundfile); }
metadatafile = validParameter.validFile(parameters, "metadata");
if (metadatafile == "not open") { abort = true; metadatafile = ""; }
else if (metadatafile == "not found") { metadatafile = ""; }
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
pickedGroups = true;
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
if (outputdir == ""){ outputdir = util.hasPath(inputFileName); }
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
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 = current->getSharedFile();
if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
relabundfile = current->getRelAbundFile();
if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter.\n"); }
else {
m->mothurOut("You must provide either a shared or relabund file.\n"); abort = true;
}
}
}
if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may only use one of the following : shared or relabund file.\n"); abort = true; }
method = validParameter.valid(parameters, "method"); if (method == "not found"){ method = "pearson"; }
string temp = validParameter.valid(parameters, "cutoff");
if (temp == "not found") { temp = "10"; }
util.mothurConvert(temp, cutoff);
if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall.\n"); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand");
exit(1);
}
}
//**********************************************************************************************************************
int OTUAssociationCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (metadatafile != "") { readMetadata(); }
//function are identical just different datatypes
if (sharedfile != "") { processShared(); }
else if (relabundfile != "") { processRelabund(); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void OTUAssociationCommand::processShared(){
try {
InputData input(sharedfile, "sharedfile", Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
SharedRAbundVectors* lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
if (metadatafile != "") {
bool error = false;
if (metadata[0].size() != lookup->size()) { m->mothurOut("[ERROR]: You have selected to use " + toString(metadata[0].size()) + " data rows from the metadata file, but " + toString(lookup->size()) + " from the shared file.\n"); m->setControl_pressed(true); error=true; }
}
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
process(lookup); delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "processShared");
exit(1);
}
}
//**********************************************************************************************************************
void OTUAssociationCommand::process(SharedRAbundVectors*& lookup){
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputFileName));
variables["[distance]"] = lookup->getLabel();
variables["[tag]"] = method;
string outputFileName = getOutputFileName("otucorr",variables);
outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//column headings
if (metadatafile == "") { out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; }
else { out << "OTUA\tMetadata\t" << method << "Coef\tSignificance\n"; }
vector< vector<double> > xy; xy.resize(lookup->getNumBins());
vector<string> sampleNames = lookup->getNamesGroups();
for (int i = 0; i < lookup->getNumBins(); i++) {
vector<int> abunds = lookup->getOTU(i);
for (int j = 0; j < abunds.size(); j++) { xy[i].push_back(abunds[j]); }
}
LinearAlgebra linear;
vector<string> currentLabels = lookup->getOTUNames();
if (metadatafile == "") {//compare otus
for (int i = 0; i < xy.size(); i++) {
for (int k = 0; k < i; k++) {
if (m->getControl_pressed()) { out.close(); return; }
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.\n"); m->setControl_pressed(true); }
if (sig < cutoff) { out << currentLabels[i] << '\t' << currentLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
for (int i = 0; i < xy.size(); i++) {
for (int k = 0; k < metadata.size(); k++) {
if (m->getControl_pressed()) { out.close(); return; }
double coef = 0.0;
double sig = 0.0;
if (method == "spearman") { coef = linear.calcSpearman(xy[i], metadata[k], sig); }
else if (method == "pearson") { coef = linear.calcPearson(xy[i], metadata[k], sig); }
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall.\n"); m->setControl_pressed(true); }
if (sig < cutoff) { out << currentLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}
out.close();
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
void OTUAssociationCommand::processRelabund(){
try {
InputData input(relabundfile, "relabund", Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
SharedRAbundFloatVectors* lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
if (metadatafile != "") {
bool error = false;
if (metadata[0].size() != lookup->size()) { m->mothurOut("[ERROR]: You have selected to use " + toString(metadata[0].size()) + " data rows from the metadata file, but " + toString(lookup->size()) + " from the relabund file.\n"); m->setControl_pressed(true); error=true;}
}
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
process(lookup); delete lookup;
lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
}
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "processRelabund");
exit(1);
}
}
//**********************************************************************************************************************
void OTUAssociationCommand::process(SharedRAbundFloatVectors*& lookup){
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputFileName));
variables["[distance]"] = lookup->getLabel();
variables["[tag]"] = method;
string outputFileName = getOutputFileName("otucorr",variables);
outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//column headings
if (metadatafile == "") { out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; }
else { out << "OTUA\tMetadata\t" << method << "Coef\tSignificance\n"; }
vector< vector<double> > xy; xy.resize(lookup->getNumBins());
vector<string> sampleNames = lookup->getNamesGroups();
for (int i = 0; i < lookup->getNumBins(); i++) {
for (int j = 0; j < sampleNames.size(); j++) { xy[i].push_back(lookup->get(i, sampleNames[j])); }
}
LinearAlgebra linear;
vector<string> currentLabels = lookup->getOTUNames();
if (metadatafile == "") {//compare otus
for (int i = 0; i < xy.size(); i++) {
for (int k = 0; k < i; k++) {
if (m->getControl_pressed()) { out.close(); return; }
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.\n"); m->setControl_pressed(true); }
if (sig < cutoff) { out << currentLabels[i] << '\t' << currentLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
for (int i = 0; i < xy.size(); i++) {
for (int k = 0; k < metadata.size(); k++) {
if (m->getControl_pressed()) { out.close(); return; }
double coef = 0.0;
double sig = 0.0;
if (method == "spearman") { coef = linear.calcSpearman(xy[i], metadata[k], sig); }
else if (method == "pearson") { coef = linear.calcPearson(xy[i], metadata[k], sig); }
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall.\n"); m->setControl_pressed(true); }
if (sig < cutoff) { out << currentLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}
out.close();
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "process");
exit(1);
}
}
/*****************************************************************/
void OTUAssociationCommand::readMetadata(){
try {
ifstream in; util.openInputFile(metadatafile, in);
string headerLine = util.getline(in); gobble(in);
metadataLabels = util.splitWhiteSpace(headerLine);
metadataLabels.erase(metadataLabels.begin());
int count = metadataLabels.size();
SharedRAbundFloatVectors* metadataLookup = new SharedRAbundFloatVectors();
metadataLookup->setLabels("1");
//read rest of file
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); return; }
string group = "";
in >> group; gobble(in);
if (m->getDebug()) { m->mothurOut("[DEBUG]: metadata group = " + group + "\n"); }
SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
tempLookup->setLabel("1");
tempLookup->setGroup(group);
for (int i = 0; i < count; i++) {
float temp = 0.0;
in >> temp;
if (m->getDebug()) { m->mothurOut("[DEBUG]: metadata value = " + toString(temp) + "\n"); }
tempLookup->push_back(temp);
}
if (Groups.size() == 0) { metadataLookup->push_back(tempLookup); }
else if (util.inUsersGroups(group, Groups)) { metadataLookup->push_back(tempLookup); }
gobble(in);
}
in.close();
metadataLookup->setOTUNames(metadataLabels);
metadataLookup->eliminateZeroOTUS();
metadata.resize(metadataLookup->getNumBins());
vector<string> sampleNames = metadataLookup->getNamesGroups();
for (int i = 0; i < metadataLookup->getNumBins(); i++) {
for (int j = 0; j < sampleNames.size(); j++) { metadata[i].push_back(metadataLookup->get(i, sampleNames[j])); }
}
delete metadataLookup;
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "readMetadata");
exit(1);
}
}
/*****************************************************************/
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