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|
//
// biomhdf5.cpp
// Mothur
//
// Created by Sarah Westcott on 10/26/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "biomhdf5.hpp"
/**************************************************************************************************/
BiomHDF5::BiomHDF5(string fname, string l) : Biom("Biological Observation Matrix 2.1.0"){
try {
label = l;
numOTUs = 0; numSamples = 0;
read(fname);
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "BiomHDF5");
exit(1);
}
}
/**************************************************************************************************/
BiomHDF5::BiomHDF5() : Biom("Biological Observation Matrix 2.1.0"){
try {
numOTUs = 0; numSamples = 0;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "BiomHDF5");
exit(1);
}
}
//**********************************************************************************************************************
#ifdef USE_HDF5
bool pathExists(hid_t id, const string& path) { return (H5Lexists( id, path.c_str(), H5P_DEFAULT ) > 0); }
#endif
/**************************************************************************************************/
void BiomHDF5::read(string fname){
try {
nnz = 0; maxLevel = 0;
otuNames.clear(); sampleNames.clear(); taxonomy.clear(); otuTaxonomies.clear();
#ifdef USE_HDF5
Picrust* picrust; vector<string> metadata;
H5::H5File file( fname.c_str(), H5F_ACC_RDONLY );
readAttributes(file); if (m->getControl_pressed()) { return; }
try {
//read otu names
if (pathExists(file.getId(), "observation/")) {
H5::Group group(file.openGroup("observation/"));
otuNames = readNames(file, group, "ids"); if (m->getControl_pressed()) { return; }
group.close();
}else {
m->mothurOut("[ERROR]: Missing /""observation/ids/"" needed for OTU names.\n");
m->setControl_pressed(true);
}
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: reading /""observation/ids/"" needed for OTU names.\n");
m->setControl_pressed(true);
}
try {
//read group names
if (pathExists(file.getId(), "sample/")) {
H5::Group group(file.openGroup("sample/"));
sampleNames = readNames(file, group, "ids"); if (m->getControl_pressed()) { return; }
group.close();
}else {
m->mothurOut("[ERROR]: Missing /""sample/ids/"" needed for group names.\n");
m->setControl_pressed(true);
}
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: reading /""sample/ids/"" needed for group names.\n");
m->setControl_pressed(true);
}
bool hasConsTaxonomy = false;
try {
//read otu taxonomies
if (pathExists(file.getId(), "observation/metadata/")) {
H5::Group group(file.openGroup("observation/metadata/"));
readTaxonomy(group, "taxonomy"); if (m->getControl_pressed()) { return; }
group.close();
if (otuTaxonomies.size() == otuNames.size()) { hasConsTaxonomy = true; }
}
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: reading /""observation/metadata/taxonomy"".\n");
hasConsTaxonomy = false;
m->setControl_pressed(true);
}
try {
//read otu abundances
if (pathExists(file.getId(), "observation/matrix/")) {
H5::Group group(file.openGroup("observation/matrix/"));
vector<string> datasets;
datasets.push_back("data"); datasets.push_back("indices"); datasets.push_back("indptr"); datasets.push_back("label");
label = readOTUAbundances(group, datasets); if (m->getControl_pressed()) { return; }
group.close();
}else {
m->mothurOut("[ERROR]: Missing /""observation/matrix/"" needed for OTU abundances.\n");
m->setControl_pressed(true);
}
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: reading /""observation/matrix/"" needed for OTU abundances.\n");
m->setControl_pressed(true);
}
bool error = false;
if (nnz != otudata.size()) { error = true; }
//create shared file
sort(sampleNames.begin(), sampleNames.end());
if (shared != nullptr) { delete shared; }
shared = new SharedRAbundVectors();
//create empty sharedrabundvectors so we can add otus below
for (int i = 0; i < sampleNames.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector();
temp->setGroup(sampleNames[i]);
shared->push_back(temp);
}
shared->setLabels(label);
if (matrixElementType == "float") {
if (sharedFloat != nullptr) { delete sharedFloat; }
sharedFloat = new SharedRAbundFloatVectors();
//creates new sharedRAbunds
for (int i = 0; i < sampleNames.size(); i++) {
SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(shared->getNumBins()); //sets all abunds to 0
temp->setLabel(label);
temp->setGroup(sampleNames[i]);
sharedFloat->push_back(temp);
}
sharedFloat->setLabels(label);
}
//for each otu
int count = 0;
for (int h = 0; h < indptr.size()-1; h++) {
int otuStart = indptr[h];
int otuEnd = indptr[h+1];
vector<int> otuAbunds; otuAbunds.resize(sampleNames.size(), 0); //initialze otus sample abundances to 0 - only non zero abunds are recorded
vector<float> otuFloatAbunds; otuFloatAbunds.resize(sampleNames.size(), 0); //initialze otus sample abundances to 0 - only non zero abunds are recorded
for (int i = otuStart; i < otuEnd; i++) {
otuAbunds[indices[i]] = (int)otudata[count];
otuFloatAbunds[indices[i]] = otudata[count];
count++;
}
shared->push_back(otuAbunds, otuNames[h]);
if (matrixElementType == "float") { sharedFloat->push_back(otuFloatAbunds, otuNames[h]); }
}
if (hasConsTaxonomy) {
if (shared->getNumBins() == otuTaxonomies.size()) {
for (int i = 0; i < otuTaxonomies.size(); i++) {
if (m->getControl_pressed()) { break; }
string thisOTUsTax = otuTaxonomies[i];
string newTax = util.addUnclassifieds(thisOTUsTax, maxLevel, false);
Taxonomy thisOTUsTaxonomy(otuNames[i], newTax, shared->getOTUTotal(i));
consTax.push_back(thisOTUsTaxonomy);
}
}
}
if (sampleNames.size() == taxonomy.size()) {
for (int i = 0; sampleNames.size(); i++) {
if (m->getControl_pressed()) { break; }
groupTaxonomies[sampleNames[i]] = taxonomy[i];
}
}
file.close();
#endif
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "read");
exit(1);
}
}
#ifdef USE_HDF5
//**********************************************************************************************************************
//Group = "observation/" or "sample/", datasetName = "ids"
vector<string> BiomHDF5::readNames( H5::H5File& file, H5::Group& group, string datasetname) {
try {
vector<string> items;
hsize_t numObjects = group.getNumObjs();
if (numObjects != 0) { //we have this group
H5::DataSet dataset = group.openDataSet(datasetname.c_str());
H5::DataType dataType(dataset.getDataType());
H5::DataSpace dataSpace = dataset.getSpace();
int rank = dataSpace.getSimpleExtentNdims(); //number of dimensions, should be 1
hsize_t dims[rank]; dataSpace.getSimpleExtentDims(dims); //size of each dimension
char **data = new char*[dims[0]];
H5::StrType str_type(H5::PredType::C_S1, H5T_VARIABLE);
dataset.read((void*)data, str_type);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + datasetname + " = "); }
for (int i = 0; i < dims[0]; i++) {
if (m->getDebug()) { m->mothurOut(toString(data[i]) + "\t"); }
items.push_back(data[i]);
delete[] data[i];
} if (m->getDebug()) { m->mothurOutEndLine(); }
delete[] data;
dataset.close();
}
return items;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readNames");
exit(1);
}
}
//**********************************************************************************************************************
//Group = "observation/metadata", datasetName = "taxonomy"
int BiomHDF5::readTaxonomy( H5::Group& group, string datasetName) {
try {
hsize_t numObjects = group.getNumObjs();
if (numObjects != 0) { //we have this group
H5::DataSet dataset = group.openDataSet(datasetName);
H5::DataType dataType(dataset.getDataType());
H5::DataSpace dataSpace = dataset.getSpace();
H5::StrType str_type(H5::PredType::C_S1, H5T_VARIABLE);
int rank = dataSpace.getSimpleExtentNdims(); //number of dimensions
hsize_t dims[rank]; dataSpace.getSimpleExtentDims(dims); //size of each dimension
if (dataset.getTypeClass() == H5T_STRING) {
int numberOfTaxonomies = dims[0];
if (rank == 2) { numberOfTaxonomies *= dims[1]; }
char **data = new char*[numberOfTaxonomies];
dataset.read((void*)data, dataType);
if (rank == 1) {
for (int i = 0; i < numberOfTaxonomies; i++) {
if (m->getDebug()) { m->mothurOut(toString(data[i]) + "\t"); }
taxonomy.push_back(data[i]);
delete[] data[i];
}
delete[] data;
}else if (rank == 2) {
string otuTaxonomy = ""; int count = 0;
for (int i = 0; i < numberOfTaxonomies; i++) {
otuTaxonomy += data[i]; otuTaxonomy += ";"; count++;
if (count == dims[1]) {
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + toString(otuTaxonomy) + "\n"); }
otuTaxonomies.push_back(otuTaxonomy);
if (count > maxLevel) { maxLevel = count; }
count = 0; otuTaxonomy = "";
}
}
}
}
dataset.close();
}
return numObjects;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readTaxonomy");
exit(1);
}
}
//**********************************************************************************************************************
//Group = "observation/matrix"
string BiomHDF5::readOTUAbundances( H5::Group& group, vector<string> datasets) {
try {
string thisLabel = "";
hsize_t numObjects = group.getNumObjs();
if (numObjects == 0) { return thisLabel; }
for (int h = 0; h < datasets.size(); h++) {
H5std_string datasetName = datasets[h];
if (pathExists(group.getId(), datasetName)) {
H5::DataSet dataset = group.openDataSet(datasetName);
H5::DataSpace dataSpace = dataset.getSpace();
if (dataset.getTypeClass() == H5T_INTEGER) {
int rank = dataSpace.getSimpleExtentNdims(); //number of dimensions, should be 1
hsize_t dims[rank]; dataSpace.getSimpleExtentDims(dims); //size of each dimension
matrixElementType = "int";
if (rank == 1) {
int* data = new int[dims[0]];
H5::DataSpace data_mspace(rank, dims);
dataset.read(data, H5::PredType::NATIVE_INT, data_mspace, dataSpace);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + datasetName + " = "); }
for (int i = 0; i < dims[0]; i++) {
if (m->getDebug()) { m->mothurOut(toString(data[i]) + "\t"); }
if (datasetName == "data") { otudata.push_back(data[i]); }
else if (datasetName == "indices") { indices.push_back(data[i]); }
else if (datasetName == "indptr") { indptr.push_back(data[i]); }
} if (m->getDebug()) { m->mothurOutEndLine(); }
delete[] data;
}
}else if (dataset.getTypeClass() == H5T_FLOAT) {
int rank = dataSpace.getSimpleExtentNdims(); //number of dimensions, should be 1
hsize_t dims[rank]; dataSpace.getSimpleExtentDims(dims); //size of each dimension
matrixElementType = "float";
if (rank == 1) {
float* data = new float[dims[0]];
H5::DataSpace data_mspace(rank, dims);
dataset.read(data, H5::PredType::NATIVE_FLOAT, data_mspace, dataSpace);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + datasetName + " = "); }
for (int i = 0; i < dims[0]; i++) {
if (m->getDebug()) { m->mothurOut(toString(data[i]) + "\t"); }
if (datasetName == "data") { otudata.push_back(data[i]); }
else if (datasetName == "indices") { indices.push_back((int)data[i]); }
else if (datasetName == "indptr") { indptr.push_back((int)data[i]); }
} if (m->getDebug()) { m->mothurOutEndLine(); }
delete[] data;
}
}else if (dataset.getTypeClass() == H5T_STRING) {
H5::StrType strdatatype(H5::PredType::C_S1, H5T_VARIABLE);
H5std_string value;
dataset.read(value, strdatatype);
thisLabel = value;
}
dataset.close();
}
}
return thisLabel;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readOTUAbundances");
exit(1);
}
}
//**********************************************************************************************************************
//read attribute of group
string BiomHDF5::readStringAttributes(H5::Group& fileAttributes, string name) {
try {
H5::Attribute attribute(fileAttributes.openAttribute(name));
H5std_string attributeName; attribute.getName(attributeName);
H5::DataType attributeType(attribute.getDataType());
string attributeValue = "";
// Read the Attribute Data. Depends on the kind of data
if (attributeType.getClass() == H5T_STRING) {
H5std_string value; attribute.read(attributeType, value);
attributeValue = value;
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + attributeName + " = " + value + "\n"); }
}
attribute.close();
return attributeValue;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readStringAttributes");
exit(1);
}
}
//**********************************************************************************************************************
//read attribute of group
void BiomHDF5::readIntAttributes(H5::Group& fileAttributes, string name) {
try {
H5::Attribute attribute(fileAttributes.openAttribute(name));
H5std_string attributeName; attribute.getName(attributeName);
H5::DataType attributeType(attribute.getDataType());
H5::DataSpace attDataSpace = attribute.getSpace();
int rank = attDataSpace.getSimpleExtentNdims(); //number of dimensions
hsize_t dims[rank]; attDataSpace.getSimpleExtentDims(dims); //size of each dimension
// Read the Attribute Data. Depends on the kind of data
if (attributeType.getClass() == H5T_INTEGER) {
if (attDataSpace.isSimple()) {
if (rank == 0) {
hsize_t data = 0;
attribute.read(attributeType, &data);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + attributeName + " = " + toString(data) + "\n"); }
if (attributeName == "nnz") { nnz = data; }
}else if (rank == 1) {
hsize_t data[dims[0]];
attribute.read(attributeType, data);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + attributeName + " = "); }
for (int i = 0; i < dims[0]; i++) {
if (m->getDebug()) { m->mothurOut(toString(data[i]) + "\t"); }
if (attributeName == "nnz") { nnz = data[i]; }
} if (m->getDebug()) { m->mothurOutEndLine(); }
if (attributeName == "shape") {
if (dims[0] == 2) { numOTUs = data[0]; numSamples = data[1]; }
}
}
}
}
attribute.close();
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readIntAttributes");
exit(1);
}
}
//**********************************************************************************************************************
//Process attribute of group or dataset
void BiomHDF5::readAttributes(H5::H5File& file) {
try {
H5::Group fileAttributes(file.openGroup( "/" ));
//read table id
tableID = readStringAttributes(fileAttributes, "id");
//read table type
tableType = readStringAttributes(fileAttributes, "type");
//read format-url
formatURL = readStringAttributes(fileAttributes, "format-url");
//read shape
readIntAttributes(fileAttributes, "shape");
//read number non zero
readIntAttributes(fileAttributes, "nnz");
fileAttributes.close();
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "readAttributes");
exit(1);
}
}
//**********************************************************************************************************************
//print required dataset attributes
void BiomHDF5::printRequiredFileAttributes(H5::Group& fileAttributes, int numBins, int numSamples) {
try {
H5::DataSpace attr_dataspace = H5::DataSpace(H5S_SCALAR); // Create new dataspace for attribute
H5::StrType strdatatype(H5::PredType::C_S1, H5T_VARIABLE);
H5std_string idValue(tableID);
H5::Attribute idAttribute = fileAttributes.createAttribute("id", strdatatype, attr_dataspace);
idAttribute.write(strdatatype, idValue);
H5std_string typeValue(tableType);
H5::Attribute typeAttribute = fileAttributes.createAttribute("type", strdatatype, attr_dataspace);
typeAttribute.write(strdatatype, typeValue);
H5std_string formatUrl(formatURL);
H5::Attribute urlAttribute = fileAttributes.createAttribute("format-url", strdatatype, attr_dataspace);
urlAttribute.write(strdatatype, formatUrl);
H5std_string generatedByValue(mothurVersion);
H5::Attribute generatedByAttribute = fileAttributes.createAttribute("generated-by", strdatatype, attr_dataspace);
generatedByAttribute.write(strdatatype, generatedByValue);
time_t rawtime; struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
string dateString = asctime (timeinfo);
int pos = dateString.find('\n');
if (pos != string::npos) { dateString = dateString.substr(0, pos);}
H5std_string dataValue(dateString);
H5::Attribute dateAttribute = fileAttributes.createAttribute("creation-date", strdatatype, attr_dataspace);
dateAttribute.write(strdatatype, dataValue);
hsize_t dims[1]; dims[0] = 2;
H5::DataSpace dataspace( 1, dims );
hsize_t data[2]; data[0] = 2; data[1] = 1;
H5::Attribute formatVersionAttribute = fileAttributes.createAttribute("format-version", H5::PredType::NATIVE_INT, dataspace);
formatVersionAttribute.write(H5::PredType::NATIVE_INT, data);
data[0] = numBins; data[1] = numSamples;
H5::Attribute shapeAttribute = fileAttributes.createAttribute("shape", H5::PredType::NATIVE_INT, dataspace);
shapeAttribute.write(H5::PredType::NATIVE_INT, data);
hsize_t nnzValue = nnz;
H5::Attribute nnzAttribute = fileAttributes.createAttribute("nnz", H5::PredType::NATIVE_INT, attr_dataspace);
nnzAttribute.write(H5::PredType::NATIVE_INT, &nnzValue);
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printRequiredAttributes");
exit(1);
}
}
//**********************************************************************************************************************
//print otuNames
//"observation/ids" -> otuLabels - "GG_OTU_1", "GG_OTU_2", "GG_OTU_3", "GG_OTU_4", "GG_OTU_5
//"sample/ids" -> group names - "Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6"
void BiomHDF5::printNames(H5::Group& group, vector<string> names, string datasetname) {
try {
hsize_t dimsf[1]; dimsf[0] = names.size();
H5::DataSpace dataspace( 1, dimsf );
H5::StrType datatype(H5::PredType::C_S1, H5T_VARIABLE);
//fill data with names
char* data[dimsf[0]];
for (int i = 0; i < names.size(); i++) { data[i] = (char*) names[i].c_str(); }
const H5std_string DATASET_NAME( datasetname.c_str() );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, datatype, dataspace );
dataset.write( data, datatype );
dataset.close();
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printNames");
exit(1);
}
}
//**********************************************************************************************************************
//"observation/metadata/taxonomy" -> taxonomy info - otu classifications
void BiomHDF5::printOTUTaxonomy(H5::Group& group, string datasetname) {
try {
int maxLevel = consTax[0].getNumLevels();
hsize_t dimsf[2]; dimsf[0] = consTax.size(); dimsf[1] = maxLevel;
H5::DataSpace dataspace(2, dimsf); //2D array, (numOtus x vector<taxonomy>)
H5::StrType datatype(H5::PredType::C_S1, H5T_VARIABLE);
const H5std_string DATASET_NAME( datasetname.c_str() );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, datatype, dataspace );
vector<char*> cPara;
for (int i = 0; i < consTax.size(); i++) {
if (m->getControl_pressed()) { break; }
vector<string> thisOtusTaxonomy = consTax[i].getSimpleTaxons();
for (int j = 0; j < maxLevel; j++) { cPara.push_back(util.mothurConvert(thisOtusTaxonomy[j])); }
}
char** data; data = new char*[cPara.size()];
for (int i = 0; i < cPara.size(); i++) {
data[i] = cPara[i];
}
dataset.write(data, datatype);
dataset.close();
//free memory
for(int i = 0; i < cPara.size(); i++) { delete cPara[i]; }
delete[] data;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printOTUTaxonomy");
exit(1);
}
}
//**************************************************************************************************************
//"observation/matrix/data" -> otu abundances for each non zero abundnace entry - 1, 5, 1, 2, 3, 1, 1, 4, 2, 2, 1, 1, 1, 1, 1
//"observation/matrix/indices" -> index of group - maps into samples/ids 2, 0, 1, 3, 4, 5, 2, 3, 5, 0, 1, 2, 5, 1, 2
//"observation/matrix/indptr" -> maps non zero abundance to OTU - 0, 1, 6, 9, 13, 15 - 0 start of OTU1s indexes, 1 start of OTU2s indexes, ... 15 start of OTU5s indexes
/*
label group numOtus GG_OTU_1 GG_OTU_2 GG_OTU_3 GG_OTU_4 GG_OTU_5
userLabel Sample1 0 5 0 2 0
userLabel Sample2 0 1 0 2 1
userLabel Sample3 1 0 1 1 1
userLabel Sample4 0 2 4 0 0
userLabel Sample5 0 3 0 0 0
userLabel Sample6 0 1 2 1 0
*/
//group = "observation/matrix/";
void BiomHDF5::printOTUAbundances(H5::Group& group, int numBins, int numSamples, string label, bool useRelabund=false) {
try {
int otusStartIndex = 0;
vector<int> indptr, indices, abunds;
vector<float> abundsFloat;
//fill indices, indptr and data vectors
for (int i = 0; i < numBins; i++) {
if (m->getControl_pressed()) { return; }
vector<int> thisOtusAbundances; vector<float> thisOtusFloatAbundances; float zero = 0.0;
if (useRelabund) { thisOtusFloatAbundances = sharedFloat->getOTU(i); }
else { thisOtusAbundances = shared->getOTU(i); }
indptr.push_back(otusStartIndex);
for (int j = 0; j < numSamples; j++) {
if (useRelabund) {
if (util.isEqual(thisOtusFloatAbundances[j], zero)) {} //skip zero values
else {
otusStartIndex++; //update number of non zero values for this OTU - use to create indptr values
indices.push_back(j); //index to sample providing this abund
abundsFloat.push_back(thisOtusFloatAbundances[j]); //save this samples OTU abundance
}
}else {
if (thisOtusAbundances[j] == 0) {} //skip zero values
else {
otusStartIndex++; //update number of non zero values for this OTU - use to create indptr values
indices.push_back(j); //index to sample providing this abund
abunds.push_back(thisOtusAbundances[j]); //save this samples OTU abundance
}
}
}
}
// dataset dimensions
hsize_t dimsf[1]; dimsf[0] = nnz;
H5::DataSpace dataspace( 1, dimsf ); //dataspace 1 x nnz
int data[nnz];
for (int i = 0; i < nnz; i++) { data[i] = indices[i]; } //fill data with indices
const H5std_string DATASET_NAME( "indices" );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, H5::PredType::NATIVE_INT, dataspace );
dataset.write( data, H5::PredType::NATIVE_INT );
dataset.close();
//create data dataset - type depends on whether or not we are using the relabund values
if (useRelabund) { //print float
float dataFloat[nnz];
for (int i = 0; i < nnz; i++) { dataFloat[i] = abundsFloat[i]; } //fill data with abunds
const H5std_string DATASET_NAME( "data" );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, H5::PredType::NATIVE_FLOAT, dataspace );
dataset.write( dataFloat, H5::PredType::NATIVE_FLOAT );
dataset.close();
}else { //print shared
for (int i = 0; i < nnz; i++) { data[i] = abunds[i]; } //fill data with abunds
const H5std_string DATASET_NAME( "data" );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, H5::PredType::NATIVE_INT, dataspace );
dataset.write( data, H5::PredType::NATIVE_INT );
dataset.close();
}
//create indptr dataset
dimsf[0] = numBins+1;
H5::DataSpace dataspaceIndptr(1, dimsf); //dataspace 1 x numBins
int dataIndptr[numBins+1];
for (int i = 0; i < numBins; i++) { dataIndptr[i] = indptr[i]; } //fill data with indptr
dataIndptr[numBins] = nnz;
const H5std_string DATASET_NAME_INDPTR( "indptr" );
H5::DataSet datasetIndptr = group.createDataSet( DATASET_NAME_INDPTR, H5::PredType::NATIVE_INT, dataspaceIndptr );
datasetIndptr.write(dataIndptr, H5::PredType::NATIVE_INT);
datasetIndptr.close();
//create label dataset to store shared label
H5::DataSpace attr_dataspace = H5::DataSpace(H5S_SCALAR); // Create new dataspace for attribute
H5::StrType strdatatype(H5::PredType::C_S1, H5T_VARIABLE);
const H5std_string DATASET_NAME_LABEL( "label" );
H5::DataSet labelDataset = group.createDataSet( DATASET_NAME_LABEL, strdatatype, attr_dataspace );
labelDataset.write(label, strdatatype);
labelDataset.close();
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printOTUAbundances");
exit(1);
}
}
#endif
//**********************************************************************************************************************
void BiomHDF5::printShared(string outputFileName, vector<string> sampleMetadata, Picrust* picrust) {
try {
//set required datasets - groupname -> datasetname
//"observation/ids" -> otuLabels - "GG_OTU_1", "GG_OTU_2", "GG_OTU_3", "GG_OTU_4", "GG_OTU_5
//"observation/matrix/data" -> otu abundances for each non zero abundnace entry - 1, 5, 1, 2, 3, 1, 1, 4, 2, 2, 1, 1, 1, 1, 1
//"observation/matrix/indices" -> index of group - maps into samples/ids 2, 0, 1, 3, 4, 5, 2, 3, 5, 0, 1, 2, 5, 1, 2
//"observation/matrix/indptr" -> maps non zero abundance to OTU - 0, 1, 6, 9, 13, 15 - 0 start of OTU1s indexes, 1 start of OTU2s indexes, ... 15 start of OTU5s indexes
/*
label group numOtus GG_OTU_1 GG_OTU_2 GG_OTU_3 GG_OTU_4 GG_OTU_5
userLabel Sample1 5 0 5 0 2 0
userLabel Sample2 5 0 1 0 2 1
userLabel Sample3 5 1 0 1 1 1
userLabel Sample4 5 0 2 4 0 0
userLabel Sample5 5 0 3 0 0 0
userLabel Sample6 5 0 1 2 1 0
*/
//"observation/metadata/taxonomy" -> taxonomy info - otu classifications
//"sample/ids" -> group names - "Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6"
//"sample/metadata/" -> group metadata (optional)
//run this first because if picrust alters the shared vector we will need to use the updated info
//taxMetadata[0] = taxonomy for otu0
vector< vector<string> > taxMetadata = getMetaData(picrust);
//find number of non zero otus
nnz = 0;
for (int j = 0; j < shared->getNumBins(); j++) {
vector<int> thisOTU = shared->getOTU(j);
for (int i = 0; i < thisOTU.size(); i++) {
if (thisOTU[i] != 0) { nnz++; }
}
}
#ifdef USE_HDF5
H5::H5File file(outputFileName.c_str(), H5F_ACC_TRUNC );
try {
//print required file attributes
H5::Group fileAttributes(file.openGroup( "/" ));
printRequiredFileAttributes(fileAttributes, shared->getNumBins(), shared->size()); //id, type, format-url, format-version, generated-by, creation-date, shape, nnz
fileAttributes.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print H5 required file attributes.\n");
m->setControl_pressed(true);
}
try {
//print otuLabels called "observation/ids" in biom file
H5::Group observationGroup( file.createGroup( "observation" ));
printNames(observationGroup, shared->getOTUNames(), "ids");
observationGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otuLabels in 'observation/ids' group.\n");
m->setControl_pressed(true);
}
try {
//print group names called "sample/ids" in biom file
H5::Group sampleGroup( file.createGroup( "sample" ));
printNames(sampleGroup, shared->getNamesGroups(), "ids");
if (sampleMetadata.size() != 0) {
printNames(sampleGroup, sampleMetadata, "metadata");
}
sampleGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print sample names or sample metadata.\n");
m->setControl_pressed(true);
}
try {
//print otuAbundances called "observation/matrix/" (data, indicies, indptr) in biom file
H5::Group matrixGroup( file.createGroup( "observation/matrix/" ));
printOTUAbundances(matrixGroup, shared->getNumBins(), shared->size(), shared->getLabel());
matrixGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otu abundances in 'observation/matrix/' group.\n");
m->setControl_pressed(true);
}
if (consTax.size() != 0) {
try {
//print otuTaxonomies called "observation/metadata/taxonomy" in the biom file
H5::Group taxonomyGroup( file.createGroup( "observation/metadata/" ));
printOTUTaxonomy(taxonomyGroup, "taxonomy");
taxonomyGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otu consensus taxonomies in 'observation/metadata/' group.\n");
m->setControl_pressed(true);
}
}
file.close();
#endif
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printShared");
exit(1);
}
}
//**********************************************************************************************************************
void BiomHDF5::printFloat(string outputFileName, vector<string> sampleMetadata, Picrust* picrust) {
try {
//set required datasets - groupname -> datasetname
//"observation/ids" -> otuLabels - "GG_OTU_1", "GG_OTU_2", "GG_OTU_3", "GG_OTU_4", "GG_OTU_5
//"observation/matrix/data" -> otu abundances for each non zero abundnace entry - 1, 5, 1, 2, 3, 1, 1, 4, 2, 2, 1, 1, 1, 1, 1
//"observation/matrix/indices" -> index of group - maps into samples/ids 2, 0, 1, 3, 4, 5, 2, 3, 5, 0, 1, 2, 5, 1, 2
//"observation/matrix/indptr" -> maps non zero abundance to OTU - 0, 1, 6, 9, 13, 15 - 0 start of OTU1s indexes, 1 start of OTU2s indexes, ... 15 start of OTU5s indexes
/*
label group numOtus GG_OTU_1 GG_OTU_2 GG_OTU_3 GG_OTU_4 GG_OTU_5
userLabel Sample1 5 0 5 0 2 0
userLabel Sample2 5 0 1 0 2 1
userLabel Sample3 5 1 0 1 1 1
userLabel Sample4 5 0 2 4 0 0
userLabel Sample5 5 0 3 0 0 0
userLabel Sample6 5 0 1 2 1 0
*/
//"observation/metadata/taxonomy" -> taxonomy info - otu classifications
//"sample/ids" -> group names - "Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6"
//"sample/metadata/" -> group metadata (optional)
//run this first because if picrust alters the shared vector we will need to use the updated info
//taxMetadata[0] = taxonomy for otu0
vector< vector<string> > taxMetadata = getMetaData(picrust);
//find number of non zero otus
nnz = 0; float zero = 0.0;
for (int j = 0; j < sharedFloat->getNumBins(); j++) {
vector<float> thisOTU = sharedFloat->getOTU(j);
for (int i = 0; i < thisOTU.size(); i++) {
if (util.isEqual(thisOTU[i], zero)) { nnz++; }
}
}
#ifdef USE_HDF5
H5::H5File file(outputFileName.c_str(), H5F_ACC_TRUNC );
try {
//print required file attributes
H5::Group fileAttributes(file.openGroup( "/" ));
printRequiredFileAttributes(fileAttributes, sharedFloat->getNumBins(), sharedFloat->size()); //id, type, format-url, format-version, generated-by, creation-date, shape, nnz
fileAttributes.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print H5 required file attributes.\n");
m->setControl_pressed(true);
}
try {
//print otuLabels called "observation/ids" in biom file
H5::Group observationGroup( file.createGroup( "observation" ));
printNames(observationGroup, sharedFloat->getOTUNames(), "ids");
observationGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otuLabels in 'observation/ids' group.\n");
m->setControl_pressed(true);
}
try {
//print group names called "sample/ids" in biom file
H5::Group sampleGroup( file.createGroup( "sample" ));
printNames(sampleGroup, sharedFloat->getNamesGroups(), "ids");
if (sampleMetadata.size() != 0) {
printNames(sampleGroup, sampleMetadata, "metadata");
}
sampleGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print sample names or sample metadata.\n");
m->setControl_pressed(true);
}
try {
//print otuAbundances called "observation/matrix/" (data, indicies, indptr) in biom file
H5::Group matrixGroup( file.createGroup( "observation/matrix/" ));
printOTUAbundances(matrixGroup, sharedFloat->getNumBins(), sharedFloat->size(), sharedFloat->getLabel());
matrixGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otu abundances in 'observation/matrix/' group.\n");
m->setControl_pressed(true);
}
if (consTax.size() != 0) {
try {
//print otuTaxonomies called "observation/metadata/taxonomy" in the biom file
H5::Group taxonomyGroup( file.createGroup( "observation/metadata/" ));
printOTUTaxonomy(taxonomyGroup, "taxonomy");
taxonomyGroup.close();
}catch(H5::Exception& e){ //do nothing taxonomy info does not exist
m->mothurOut("[ERROR]: Unable to print otu consensus taxonomies in 'observation/metadata/' group.\n");
m->setControl_pressed(true);
}
}
file.close();
#endif
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "printFloat");
exit(1);
}
}
//**********************************************************************************************************************
void BiomHDF5::print(string outputFileName, vector<string> sampleMetadata, Picrust* picrust) {
try {
if (matrixElementType == "int") {
printShared(outputFileName, sampleMetadata, picrust);
}else {
printFloat(outputFileName, sampleMetadata, picrust);
}
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "print");
exit(1);
}
}
//**********************************************************************************************************************
vector< vector<string> > BiomHDF5::getMetaData(Picrust* picrust, bool useRelabund){
try {
vector< vector<string> > metadata;
if (consTax.size() == 0) {
if (!useRelabund) {
for (int i = 0; i < shared->getNumBins(); i++) { vector<string> temp; temp.push_back("null"); metadata.push_back(temp); } }
else {
for (int i = 0; i < sharedFloat->getNumBins(); i++) { vector<string> temp; temp.push_back("null"); metadata.push_back(temp); }
}
}
else {
if (!useRelabund) {
if (shared == nullptr) { m->setControl_pressed(true); return metadata; }
}else {
if (sharedFloat == nullptr) { m->setControl_pressed(true); return metadata; }
}
//should the labels be Otu001 or PhyloType001
vector<string> otuNames;
if (!useRelabund) { otuNames = shared->getOTUNames(); }
else { otuNames = sharedFloat->getOTUNames(); }
string firstBin = otuNames[0];
string binTag = "Otu";
if ((firstBin.find("Otu")) == string::npos) { binTag = "PhyloType"; }
map<string, string> labelTaxMap;
string snumBins = toString(otuNames.size());
for (int i = 0; i < consTax.size(); i++) {
if (m->getControl_pressed()) { return metadata; }
string thisOtuLabel = consTax[i].getName();
//if there is a bin label use it otherwise make one
if (util.isContainingOnlyDigits(thisOtuLabel)) {
string binLabel = binTag;
string sbinNumber = thisOtuLabel;
if (sbinNumber.length() < snumBins.length()) {
int diff = snumBins.length() - sbinNumber.length();
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
binLabel = util.getSimpleLabel(binLabel);
labelTaxMap[binLabel] = consTax[i].getConsTaxString();
}else {
map<string, string>::iterator it = labelTaxMap.find(util.getSimpleLabel(thisOtuLabel));
if (it == labelTaxMap.end()) {
labelTaxMap[util.getSimpleLabel(thisOtuLabel)] = consTax[i].getConsTaxString();
}else {
m->mothurOut("[ERROR]: Cannot add OTULabel " + thisOtuLabel + " because it's simple label " + util.getSimpleLabel(consTax[i].getName()) + " has already been added and will result in downstream errors. Have you mixed mothur labels and non mothur labels? To make the files work well together and backwards compatible mothur treats 1, OTU01, OTU001, OTU0001 all the same. We do this by removing any non numeric characters and leading zeros. For eaxample: Otu000018 and OtuMY18 both map to 18.\n"); m->setControl_pressed(true);
}
}
}
//sanity check for file issues - do you have the same number of bins in the shared and constaxonomy file
if (!useRelabund) {
if (shared->getNumBins() != labelTaxMap.size()) {
m->mothurOut("[ERROR]: Your constaxonomy file contains " + toString(labelTaxMap.size()) + " otus and your shared file contain " + toString(shared->getNumBins()) + " otus, cannot continue.\n"); m->setControl_pressed(true); return metadata;
}
}else {
if (sharedFloat->getNumBins() != labelTaxMap.size()) {
m->mothurOut("[ERROR]: Your constaxonomy file contains " + toString(labelTaxMap.size()) + " otus and your shared file contain " + toString(sharedFloat->getNumBins()) + " otus, cannot continue.\n"); m->setControl_pressed(true); return metadata;
}
}
//merges OTUs classified to same gg otuid, sets otulabels to gg otuids, averages confidence scores of merged otus. overwritting of otulabels is fine because constaxonomy only allows for one label to be processed. If this assumption changes, could cause bug.
if (picrust != nullptr) {
if (!useRelabund) { picrust->setGGOTUIDs(labelTaxMap, shared); }
else { picrust->setGGOTUIDs(labelTaxMap, sharedFloat); }
}
//{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}
//traverse the binLabels forming the metadata strings and saving them
//make sure to sanity check
map<string, string>::iterator it;
vector<string> currentLabels; int numBins = 0;
if (!useRelabund) { currentLabels = shared->getOTUNames(); numBins = shared->getNumBins(); }
else { currentLabels = sharedFloat->getOTUNames(); numBins = sharedFloat->getNumBins();
}
for (int i = 0; i < numBins; i++) {
if (m->getControl_pressed()) { return metadata; }
it = labelTaxMap.find(util.getSimpleLabel(currentLabels[i]));
if (it == labelTaxMap.end()) { m->mothurOut("[ERROR]: can't find taxonomy information for " + currentLabels[i] + ".\n"); m->setControl_pressed(true); }
else {
vector<string> scores;
vector<string> taxonomies = util.parseTax(it->second, scores);
metadata.push_back(taxonomies);
}
}
}
return metadata;
}
catch(exception& e) {
m->errorOut(e, "BiomHDF5", "getMetadata");
exit(1);
}
}
/**************************************************************************************************/
|
