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/*
* gendata.cpp
*
* Created on: Mar 8, 2012
* Author: mkooyman
*
*
* Copyright (C) 2009--2016 Various members of the GenABEL team. See
* the SVN commit logs for more details.
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
* MA 02110-1301, USA.
*
*/
#include <string>
#include <errno.h>
#include <limits>
#include "gendata.h"
#include "fvlib/FileVector.h"
#include "eigen_mematrix.h"
#include "eigen_mematrix.cpp"
#include "utilities.h"
void gendata::mldose_line_to_matrix(const int k,
const char *all_numbers,
const int amount_of_numbers){
int j = 0;
// Check if not a null pointer
if (!*all_numbers){
perror("Error while reading genetic data (expected pointer to char "
"but found a null pointer)");
exit(EXIT_FAILURE);
}
while (j < amount_of_numbers)
{
double result = 0;
// Skip whitespace
while (*all_numbers == ' ')
{
all_numbers++;
}
// check NaN (right now checks only first character)
// TODO: make catching of NaN more rigid
if (toupper(*all_numbers) == 'N')
{
result = std::numeric_limits<double>::quiet_NaN();
// Skip other characters of NaN
while ((toupper(*all_numbers) == 'A') |
(toupper(*all_numbers) == 'N'))
{
all_numbers++;
}
}
else
{
int sign = 0;
// set sign to -1 if negative: multiply by sign just before return
if (*all_numbers == '-')
{
all_numbers++;
sign = -1;
}
// Read digits before dot
while (*all_numbers <= '9' && *all_numbers >= '0')
{
result = result * 10 + (*all_numbers++ - '0');
}
// Read digit after dot
if (*all_numbers == '.')
{
double decimal_counter = 1.0;
all_numbers++;
while (*all_numbers <= '9' && *all_numbers >= '0')
{
decimal_counter *= 0.1;
result += (*all_numbers++ - '0') * decimal_counter;
}
}
// Correct for negative number
if (sign == -1)
{
result = sign * result;
}
}
G.put(result, k, j);
j++;
}
}
/**
* \brief Read the genetic data for all individuals for a given SNP
* and store in the array @data.
*
* Only one 'column' is extracted, so in case the number of genomic
* predictors is 2 (probability data) this function must be called
* twice.
*
* @param var Number of the SNP to read from the genetic data object
* @param data Pointer to an array in which the results will be
* returned.
*/
void gendata::get_var(const int var, double * data) const
{
if (DAG == NULL) // Read from text file
{
for (int i = 0; i < G.nrow; i++)
{
data[i] = G.get(i, var);
}
}
else if (DAG != NULL) // Read from fv file
{
// cout << "Data Type: " << dataTypeToString(DAG->getElementType())
// << endl;
double *tmpdata = new double[DAG->getNumObservations()];
DAG->readVariableAs((unsigned long int) var, tmpdata);
unsigned int j = 0;
for (unsigned int i = 0; i < DAG->getNumObservations(); i++)
{
if (!DAGmask[i])
{
// A dirty trick to get rid of conversion
// errors. Instead of casting float data to double we
// convert the data to string and then do strtod()
char tmpstr[1048576];
snprintf (tmpstr, sizeof(tmpstr), "%f", tmpdata[i]);
double val;
char *endptr;
errno = 0; // To distinguish success/failure
// after strtod()
val = strtod(tmpstr, &endptr);
if ((errno == ERANGE && (val == HUGE_VALF || val == HUGE_VALL))
|| (errno != 0 && val == 0)) {
perror("Error while reading genetic data (strtod)");
exit(EXIT_FAILURE);
}
if (endptr == tmpstr) {
cerr << "No digits were found while reading genetic data"
<< " (individual " << i + 1
<< ", position " << var + 1 << ")"
<< endl;
exit(EXIT_FAILURE);
}
/* If we got here, strtod() successfully parsed a number */
data[j++] = val;
}
}
delete[] tmpdata;
}
else
{
report_error("cannot get gendata");
}
}
/**
* Constructor. Initialises all variables to zero/NULL
*/
gendata::gendata() : nsnps(0), nids(0), ngpreds(0), DAG(NULL), DAGmask(NULL)
{
}
/**
* \brief Read genotype data from filevector files.
*
* @param filename File name of the filevector file (either .fvi or
* .fvd) that contains the genotype data.
* @param insnps The number of SNPs/genetic variants to read; usually
* inferred from the .info files.
* @param ingpreds The number of genomic predictors (1 for dosage
* data, 2 for probability data); usually given on the command line.
* @param npeople The total number of individuals to expect; usually
* inferred from the phenotype data (see phedata::nids_all).
* @param nmeasured The number of individuals with complete phenotype
* data; usually inferred from the phenotype data (see phedata::nids).
* @param allmeasured Array indicating which individuals have complete
* phenotype data (value: 1) and which haven't (0); usually inferred
* from the phenotype data (see phedata::allmeasured).
* @param idnames Array of strings containing the names of the
* individuals used in the analysis; usually inferred from the
* phenotype data (phedata::idnames).
*/
void gendata::re_gendata(const string filename,
const unsigned int insnps,
const unsigned int ingpreds,
const unsigned int npeople,
const unsigned int nmeasured,
const unsigned short int * allmeasured,
const std::string * idnames)
{
nsnps = insnps;
ngpreds = ingpreds;
DAG = new FileVector(filename, 128, true);
DAGmask = new unsigned short int[DAG->getNumObservations()];
if (DAG->getNumObservations() != npeople)
report_error("dimension of fvf-data and phenotype data do not match\n");
if (DAG->getNumVariables() != insnps * ingpreds)
report_error("dimension of fvf-data and mlinfo data do not match\n");
long int j = -1;
for (unsigned int i = 0; i < npeople; i++)
{
if (allmeasured[i] == 0)
{
DAGmask[i] = 1;
}
else
{
DAGmask[i] = 0;
j++;
}
string DAGobsname = DAG->readObservationName(i).name;
if (DAGobsname.find("->") != string::npos)
{
DAGobsname = DAGobsname.substr(DAGobsname.find("->") + 2);
}
// if (allmeasured[i] && idnames[j] != DAGobsname)
// std::cerr << "names do not match for observation at phenofile "
// << "line (phe/geno) " << i+1 << "/+1 ("
// << idnames[i].c_str() << "/"
// << DAGobsname.c_str() << ")\n";
// fix thanks to Vadym Pinchuk
if (allmeasured[i] && idnames[j] != DAGobsname)
{
report_error("names do not match for observation at phenofile "
"line (phe/geno) %i/+1 (%s/%s)\n",
i + 1, idnames[j].c_str(), DAGobsname.c_str());
}
}
nids = j + 1;
// std::cout << "in INI: " << nids << " " << npeople << "\n";
if (nids != nmeasured)
report_error("nids != mneasured (%i != %i)\n", nids, nmeasured);
}
/**
* \brief Read genotype data from plain text files.
*
* @param fname File name of the filevector file (either .fvi or .fvd)
* that contains the genotype data.
* @param insnps The number of SNPs/genetic variants to read; usually
* inferred from the .info files.
* @param ingpreds The number of genomic predictors (1 for dosage
* data, 2 for probability data); usually given on the command line.
* @param npeople The total number of individuals to expect; usually
* inferred from the phenotype data (see phedata::nids_all).
* @param nmeasured The number of individuals with complete phenotype
* data; usually inferred from the phenotype data (see phedata::nids).
* @param allmeasured Array indicating which individuals have complete
* phenotype data (value: 1) and which haven't (0); usually inferred
* from the phenotype data (see phedata::allmeasured).
* @param skipd
* @param idnames Array of strings containing the names of the
* individuals used in the analysis; usually inferred from the
* phenotype data (phedata::idnames).
*/
void gendata::re_gendata(const char * fname,
const unsigned int insnps,
const unsigned int ingpreds,
const unsigned int npeople,
const unsigned int nmeasured,
const unsigned short int * allmeasured,
const int skipd,
const std::string * idnames)
{
nids = nmeasured;
nsnps = insnps;
ngpreds = ingpreds;
DAG = NULL;
// int nids_all = npeople;
G.reinit(nids, (nsnps * ngpreds));
std::ifstream infile;
infile.open(fname);
if (!infile)
{
std::cerr << "gendata: cannot open file " << fname << endl;
}
std::string tmpid, tmpstr;
int k = 0;
for (unsigned int i = 0; i < npeople; i++)
{
if (allmeasured[i] == 1)
{
if (skipd > 0)
{
// Read the genotype data and look for the signature
// arrow of MaCH/minimac. If found only use the part
// after the arrow as ID.
infile >> tmpstr;
size_t strpos = tmpstr.find("->");
if (strpos != string::npos)
{
tmpid = tmpstr.substr(strpos + 2, string::npos);
}
else
{
tmpid = tmpstr;
}
if (tmpid != idnames[k])
{
cerr << "phenotype file and dose or probability file "
<< "did not match at line " << i + 2 << " ("
<< tmpid << " != " << idnames[k] << ")" << endl;
infile.close();
exit(1);
}
}
for (int j = 1; j < skipd; j++)
{
infile >> tmpstr;
}
std::string all_numbers;
all_numbers.reserve(nsnps * ngpreds * 7);
std::getline(infile, all_numbers);
mldose_line_to_matrix(k, all_numbers.c_str(), nsnps * ngpreds);
k++;
}
else
{
for (int j = 0; j < skipd; j++)
{
infile >> tmpstr;
}
for (unsigned int j = 0; j < (nsnps * ngpreds); j++)
{
infile >> tmpstr;
}
}
}
infile.close();
}
// HERE NEED A NEW CONSTRUCTOR BASED ON DATABELBASECPP OBJECT
/**
* Destructor
*/
gendata::~gendata()
{
if (DAG != NULL)
{
delete DAG;
delete[] DAGmask;
}
// delete G;
}
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