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ArffDataset.cpp
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ArffDataset.cpp
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/*
* ArffDataset.cpp - Bill White
* see ArffDataset.h and http://www.cs.waikato.ac.nz/ml/weka/arff.html
*/
#include <string>
#include <iostream>
#include <fstream>
#include <cstring>
#include <string>
#include <sstream>
#include <boost/lexical_cast.hpp>
#include "Dataset.h"
#include "DatasetInstance.h"
#include "StringUtils.h"
#include "ArffDataset.h"
#include "Insilico.h"
using namespace std;
using namespace insilico;
using namespace boost;
ArffDataset::ArffDataset() {
::Dataset();
missingAttributeValuesToCheck.push_back("?");
missingClassValuesToCheck.push_back("?");
}
bool ArffDataset::LoadSnps(string filename) {
snpsFilename = filename;
ifstream dataStream(snpsFilename.c_str());
if (!dataStream.is_open()) {
cerr << "ERROR: Could not open dataset: " << snpsFilename << endl;
return false;
}
cout << Timestamp() << "ArffDataset: Reading lines from " << snpsFilename
<< endl;
string line;
int firstSpace = -1, secondSpace = -1;
string attributeName = "";
int attributeIndex = 0;
int numericsIndex = 0;
string attributeType = "";
string classTypeString = "";
unsigned int lineNumber = 0;
double minPheno = 0.0, maxPheno = 0.0;
while (getline(dataStream, line)) {
++lineNumber;
string trimmedLine = trim(line);
// skip blank lines
if (trimmedLine.size() < 1) {
continue;
}
// check the first character of the line
switch (trimmedLine.at(0)) {
case '%':
// skip comment lines
continue;
case '@':
// relation, attribute or data
firstSpace = trimmedLine.find(" ");
string keyword = to_upper(trimmedLine.substr(1, firstSpace - 1));
// cout << "keyword => " << keyword << endl;
if (keyword == "RELATION") {
relationName = keyword;
}
if (keyword == "ATTRIBUTE") {
secondSpace = trimmedLine.find(" ", firstSpace + 1);
attributeName = trimmedLine.substr(firstSpace + 1,
secondSpace - firstSpace - 1);
// cout << "DEBUG attribute name: [" << attributeName << "]" << endl;
if (to_upper(attributeName) == "CLASS") {
classColumn = attributeIndex;
cout << Timestamp() << "Class column detect: " << classColumn << endl;
classTypeString = to_upper(trimmedLine.substr(secondSpace + 1));
if (classTypeString == "NUMERIC") {
hasContinuousPhenotypes = true;
cout << Timestamp() << "Detected continuous phenotype" << endl;
} else {
hasContinuousPhenotypes = false;
cout << Timestamp() << "Detected case-control phenotype" << endl;
}
} else {
attributeNames.push_back(attributeName);
attributeType = to_upper(trimmedLine.substr(secondSpace + 1));
if (attributeType == "STRING") {
cerr << "ERROR: STRING attributes are not yet supported" << endl;
return false;
attributeTypes.push_back(ARFF_STRING_TYPE);
}
if (attributeType == "DATE") {
cerr << "ERROR: DATE attributes are not yet supported" << endl;
return false;
attributeTypes.push_back(ARFF_DATE_TYPE);
}
if (attributeType == "NUMERIC") {
attributeTypes.push_back(ARFF_NUMERIC_TYPE);
numericsMask[attributeName] = numericsIndex;
numericsNames.push_back(attributeName);
++numericsIndex;
} else {
// must be nominal type - add nominal values to map
attributeTypes.push_back(ARFF_NOMINAL_TYPE);
vector<string> tokens;
split(tokens, trimmedLine, "{");
vector<string>::const_iterator it = tokens.end() - 1;
string nominalsListWithCurly = *it;
string nominalsList = trim(
nominalsListWithCurly.substr(0,
nominalsListWithCurly.size() - 1));
vector<string> nominals;
split(nominals, nominalsList, ",");
// GENETICS CHECK HERE for plink recodeA encoding
if (nominals.size() != 3) {
cerr << "ERROR: This dataset is currently unsupported. SNP data "
<< "must be encoded with {0, 1, 2} for {homozygous1, "
<< "heterzygote, homozygous2} respectively. The following "
<< "attributes were read successfully" << endl;
PrintNominalsMapping();
return false;
}
// GENETICS CHECK HERE
if ((nominals[0] == "0") && (nominals[1] == "1")
&& (nominals[2] == "2")) {
nominalValues[attributeName] = nominals;
attributesMask[attributeName] = attributeIndex;
} else {
cerr << "ERROR: This dataset is currently unsupported. SNP data "
<< "must be encoded with {0, 1, 2} for {homozygous1, "
<< "heterzygote, homozygous2} respectively. The following "
<< "attributes were read successfully" << endl;
PrintNominalsMapping();
return false;
} // end genetics check
} // end nominal
} // end class or attribute
++attributeIndex;
} // keyword = attribute
// the rest of the file is instances
if (keyword == "DATA") {
int numAttributes = attributesMask.size();
if (numAttributes) {
hasGenotypes = true;
levelCounts.resize(numAttributes);
levelCountsByClass.resize(numAttributes);
attributeLevelsSeen.resize(numAttributes);
attributeAlleleCounts.resize(numAttributes);
attributeMinorAllele.resize(numAttributes);
genotypeCounts.resize(numAttributes);
attributeMutationTypes.resize(numAttributes);
} else {
hasGenotypes = false;
}
int numNumerics = numericsMask.size();
if (numNumerics) {
hasNumerics = true;
} else {
hasNumerics = false;
}
lineNumber = 0;
bool makeLineIntoInstance = true;
unsigned int instanceIndex = 0;
int numericsAdded = 0;
while (getline(dataStream, line)) {
++lineNumber;
string trimmedLine = trim(line);
// skip blank lines in the data section (usually end of file)
if (!trimmedLine.size()) {
continue;
}
// only load matching IDs, line numbers for non-plink files
ostringstream ssLineNum;
ssLineNum << zeroPadNumber(lineNumber, 8);
string ID = ssLineNum.str() + ssLineNum.str();
// filter out IDs
if (!IsLoadableInstanceID(ID)) {
cout << Timestamp() << "WARNING: " << "Dataset instance ID [" << ID
<< "] skipped. "
<< "Not found in list of loadable IDs. Numerics and/or "
<< "phenotype file(s) matching filtered out this ID" << endl;
continue;
}
vector<string> attributesStringVector;
split(attributesStringVector, trimmedLine, ",");
vector<AttributeLevel> attributeVector;
vector<NumericLevel> numericsVector;
unsigned int attrIdx = 0;
unsigned int vectorIdx = 0;
makeLineIntoInstance = true;
vector<string>::const_iterator it = attributesStringVector.begin();
ClassLevel discreteClassLevel = MISSING_DISCRETE_CLASS_VALUE;
NumericLevel numericClassLevel = MISSING_NUMERIC_CLASS_VALUE;
for (; it != attributesStringVector.end(); ++it, ++vectorIdx) {
string thisAttr = *it;
if (vectorIdx == classColumn) {
discreteClassLevel = MISSING_DISCRETE_CLASS_VALUE;
numericClassLevel = MISSING_NUMERIC_CLASS_VALUE;
if (hasContinuousPhenotypes) {
if (thisAttr != "-9") {
numericClassLevel = lexical_cast<NumericLevel>(thisAttr);
if (lineNumber == 1) {
minPheno = maxPheno = numericClassLevel;
} else {
if (numericClassLevel < minPheno) {
minPheno = numericClassLevel;
}
if (numericClassLevel > maxPheno) {
maxPheno = numericClassLevel;
}
}
} else {
if (!hasAlternatePhenotypes) {
cout << Timestamp() << "Instance ID " << ID
<< " filtered out by missing value" << endl;
continue;
}
}
} else {
if (thisAttr != "-9") {
discreteClassLevel = lexical_cast<ClassLevel>(thisAttr);
} else {
if (!hasAlternatePhenotypes) {
cout << Timestamp() << "Instance ID " << ID
<< " filtered out by missing value" << endl;
continue;
}
}
}
} else {
if (attributeTypes[attrIdx] == ARFF_NUMERIC_TYPE) {
if (thisAttr == "?") {
numericsVector.push_back(MISSING_NUMERIC_VALUE);
missingNumericValues[ID].push_back(attrIdx);
} else {
double thisNumericValue = lexical_cast<NumericLevel>(
thisAttr);
numericsVector.push_back(thisNumericValue);
}
++numericsAdded;
} else {
if (attributeTypes[attrIdx] == ARFF_NOMINAL_TYPE) {
AttributeLevel thisAttrLevel = MISSING_ATTRIBUTE_VALUE;
if (thisAttr == "?") {
missingValues[ID].push_back(attrIdx);
} else {
thisAttrLevel = lexical_cast<AttributeLevel>(thisAttr);
attributeLevelsSeen[attrIdx].insert(thisAttr);
}
attributeVector.push_back(thisAttrLevel);
++attrIdx;
} else {
cout << Timestamp() << "Unrecognized attribute type!" << endl;
return false;
}
}
}
}
// create an instance from the vector of attribute and class values
if (makeLineIntoInstance) {
DatasetInstance * newInst = 0;
if ((int) attributeVector.size() != numAttributes) {
cerr << "ERROR: Number of attributes parsed on line "
<< lineNumber << ": " << attributesStringVector.size()
<< " is not equal to the number of attributes "
<< " read from the data file header: " << numAttributes
<< endl;
return false;
}
if ((int) numericsVector.size() != numNumerics) {
cerr << "ERROR: Number of numerics parsed on line " << lineNumber
<< ": " << numericsVector.size()
<< " is not equal to the number of attributes "
<< " read from the data file header: " << numNumerics << endl;
return false;
}
newInst = new DatasetInstance(this);
if (newInst) {
if (hasContinuousPhenotypes) {
newInst->SetPredictedValueTau(numericClassLevel);
} else {
newInst->SetClass(discreteClassLevel);
classIndexes[discreteClassLevel].push_back(instanceIndex);
}
if (hasGenotypes) {
newInst->LoadInstanceFromVector(attributeVector);
}
if (hasNumerics) {
for (int i = 0; i < (int) numericsVector.size(); ++i) {
newInst->AddNumeric(numericsVector[i]);
}
}
instances.push_back(newInst);
instanceIds.push_back(ID);
// instanceIdsToLoad.push_back(ID);
instancesMask[ID] = instanceIndex;
} else {
cerr << "ERROR: loading ARFF @data section. "
<< "Could not create dataset instance for line number "
<< lineNumber << endl;
return false;
}
++instanceIndex;
} // make new instance
// happy lights
if ((lineNumber - 1) && ((lineNumber % 100) == 0)) {
cout << Timestamp() << lineNumber << endl;
}
} // while reading file lines
} // keyword = data
break;
} // end switch
} // end while
cout << Timestamp() << lineNumber << " lines read" << endl;
dataStream.close();
cout << Timestamp() << "There are " << NumInstances()
<< " instances in the data set" << endl;
cout << Timestamp() << "There are " << instancesMask.size()
<< " instances in the instance mask" << endl;
if (instancesMask.size() == 0) {
cerr << "ERROR: no instances in the instance mask" << endl;
return false;
}
if (hasContinuousPhenotypes) {
continuousPhenotypeMinMax = make_pair(minPheno, maxPheno);
cout << Timestamp() << "Continuous phenotypes." << endl;
} else {
cout << Timestamp() << "There are " << classIndexes.size()
<< " classes in the data set" << endl;
}
if (hasNumerics) {
// find the min and max values for each numeric attribute
// used in diff/distance calculation metrics
vector<NumericLevel> numericColumn;
for (unsigned int i = 0; i < NumNumerics(); ++i) {
GetNumericValues(i, numericColumn);
double minElement = *numericColumn.begin();
double maxElement = *numericColumn.begin();
for (vector<NumericLevel>::const_iterator it = numericColumn.begin();
it != numericColumn.end(); ++it) {
if ((*it != MISSING_NUMERIC_VALUE) && (*it < minElement)) {
minElement = *it;
}
if ((*it != MISSING_NUMERIC_VALUE) && (*it > maxElement)) {
maxElement = *it;
}
}
numericsMinMax.push_back(make_pair(minElement, maxElement));
}
}
if (hasGenotypes) {
UpdateAllLevelCounts();
CreateDummyAlleles();
}
return true;
}
ArffAttributeType ArffDataset::GetTypeOf(unsigned int columnIndex) {
if (columnIndex < attributeTypes.size()) {
return attributeTypes[columnIndex];
} else
return (ARFF_ERROR_TYPE);
}
void ArffDataset::PrintNominalsMapping() {
cout << Timestamp() << "Nominals and their accepted values:" << endl;
map<string, vector<string> >::const_iterator mit = nominalValues.begin();
for (; mit != nominalValues.end(); ++mit) {
cout << (*mit).first << ":";
vector<string>::const_iterator it = (*mit).second.begin();
for (; it != (*mit).second.end(); ++it) {
cout << " " << *it;
}
cout << endl;
}
}