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// [[Rcpp::depends(BH)]]
#include <Rcpp.h>
using namespace Rcpp;
#include <cstdlib>
#include <vector>
#include <map>
#include <string>
#include <climits>
#include <iostream>
#include <fstream>
#include <sstream>
#include <cassert>
#include <boost/algorithm/string.hpp>
#include <boost/assign.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include "getopt.h"
#include "utils.h"
#include "data_types.h"
#include "matrix.h"
using namespace std;
using namespace boost;
#include "template_utils.cpp"
//#define DEBUG
// Global variables
string tissue_markers_file="";
int num_tissues=0;
string reads_binning_file; //="stdin"; // default is "stdin"
string output_file="stdout"; // default is "stdout"
string output_type="tissueFraction"; // default is "tissueFraction"
double min_likelihood_ratio_cutoff=-1.0; // default is -1.0, which means "No reads filtering with likelihood ratio cutoff"
string em_algorithm_type="em.global.unknown"; // default is "the EM algorithm with unknown class", whose short name: "em.global.unknown". Other option is "em_known"
int em_max_iterations=100; // default is 100 iterations
/*-----------------------------------
command line parser's data structure
-----------------------------------*/
struct option longopts[] =
{
/* name, has_arg, flag, val */ /* longind */
{ "help", no_argument, 0, 'h' }, /* 0 */
{ "reads_binning_file", required_argument, 0, 'r' }, /* 2 */
{ "tissue_markers_file", required_argument, 0, 't' }, /* 1 */
{ "num_tissues", required_argument, 0, 'T' }, /* 1 */
{ "min_likelihood_ratio_cutoff", required_argument, 0, 'p' }, /* 1 */
{ "em_algorithm", required_argument, 0, 'a' }, /* 3 */
{ "em_max_iterations", required_argument, 0, 'x' }, /* 3 */
{ "output_file", required_argument, 0, 'o' }, /* 3 */
{ "output_type", required_argument, 0, 'O' }, /* 3 */
/* end-of-list marker */
{ 0, 0, 0, 0 }
};
// char *shortopts = "hr:t:T:a:p:x:o:O:"; /* short options string */
int longind = 0; /* long option list index */
void print_usage() {
Rcpp::Rcerr << "Calculate tissue-specific likelihood for each sequencing read and perform EM algorithm on all reads to obtain model parameters, then compute and output the tissue-specific read counts for each marker" << endl << endl;
Rcpp::Rcerr << "USAGE: tissue_deconv [options]" << endl << endl;
Rcpp::Rcerr << " Options:" << endl;
Rcpp::Rcerr << " -a [string]: read-based tissue deconvolution EM algorithm type: em.global.unknown (default), em.global.known, em.local.unknown, em.local.known." << endl;
Rcpp::Rcerr << " -r [FILE]: reads binning file (default: stdin)" << endl;
Rcpp::Rcerr << " -o [FILE]: output file (default: stdout)" << endl;
Rcpp::Rcerr << " -O [FILE]: output type tissueFraction (default), tissueFraction+readCountRaw, tissueFraction+readCountPerMillion, tissueFraction+readCountPerBillion" << endl;
Rcpp::Rcerr << " -T [positive integer]: number of tissue types." << endl;
Rcpp::Rcerr << " -p [positive real value]: all reads with likelihood ratio < cutoff (default: -1.0, meanin no reads filtering is used) will not be used. Likelihood ratio is the max(all tissues' likelihoods)/min(all tissues' likelihoods)" << endl;
Rcpp::Rcerr << " -t [FILE]: tissue markers file: each marker for each tissue type has either a median beta value or a paired shape parameters of beta-distribution from the tissue population of tissue types." << endl;
Rcpp::Rcerr << " -x [positive integer]: EM algorithm maximum iteration number: 100 (default)." << endl;
Rcpp::Rcerr << endl;
//cerr << "version 1.0, January 22, 2020" << endl;
//cerr << "By Wenyuan Li" << endl;
Rcpp::Rcerr << endl;
}
void parse_command_line(string reads_binning_file, int num_tissues, double min_likelihood_ratio_cutoff, string tissue_markers_file,
string em_algorithm_type, string output_file, string output_type, int em_max_iterations)
{
if (output_type!="tissueFraction" && output_type!="tissueFraction+readCountRaw" && output_type!="tissueFraction+readCountPerMillion" && output_type!="tissueFraction+readCountPerBillion") {
Rcpp::Rcerr << endl << "Error: output types should take one of four values: tissueFraction, tissueFraction+readCountRaw, tissueFraction+readCountPerMillion and tissueFraction+readCountPerBillion!" << endl << endl;
print_usage();
// exit(EXIT_FAILURE);
}
if (em_algorithm_type.compare("em.global.known")!=0 && em_algorithm_type.compare("em.global.unknown")!=0 && em_algorithm_type.compare("em.local.unknown")!=0 && em_algorithm_type.compare("em.local.unknown")!=0) {
Rcpp::Rcerr << endl << "Error: EM algorithm types should take one of three values: em.global.known, em.global.unknown, em.local.known, em.local.unknown!" << endl << endl;
print_usage();
// exit(EXIT_FAILURE);
}
if (reads_binning_file.empty()) {
Rcpp::Rcerr << endl << "Error: input reads binning file is required!" << endl << endl;
print_usage();
// exit(EXIT_FAILURE);
}
if (num_tissues<=0) {
Rcpp::Rcerr << endl << "Error: number of tissue types must be >1!" << endl << endl;
print_usage();
}
if (tissue_markers_file.empty()) {
Rcpp::Rcerr << endl << "Error: input file of tissue markers is required!" << endl << endl;
print_usage();
// exit(EXIT_FAILURE);
}
}
// [[Rcpp::export]]
void read_deconvolution_cpp(std::string reads_binning_file, int num_tissues, double min_likelihood_ratio_cutoff, std::string tissue_markers_file,
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std::string em_algorithm_type, std::string output_file, std::string output_type, int em_max_iterations=100, int random_seed=0) {
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parse_command_line(reads_binning_file, num_tissues, min_likelihood_ratio_cutoff, tissue_markers_file,
em_algorithm_type, output_file, output_type, em_max_iterations);
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// Rcpp::Rcerr << "fragment-level methylation states file: " << reads_binning_file << endl;
// Rcpp::Rcerr << "marker file: " << tissue_markers_file << endl;
// Rcpp::Rcerr << "number of sample types: " << num_tissues << endl;
// if (min_likelihood_ratio_cutoff==-1.0)
// Rcpp::Rcerr << "No likilihood-ratio-based reads filtering" << endl;
// else
// Rcpp::Rcerr << "min likelihood ratio cutoff (for each read): " << min_likelihood_ratio_cutoff << endl;
// Rcpp::Rcerr << "read deconvolution algorithm: " << em_algorithm_type << endl;
// Rcpp::Rcerr << "EM max iterations: " << em_max_iterations << endl;
// Rcpp::Rcerr << "output type: " << output_type << endl;
// Rcpp::Rcerr << "output file: " << output_file << endl;
// Rcpp::Rcerr << endl;
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// Rcpp::Rcerr << "reading " << tissue_markers_file << " ..." << endl;
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string fileext_gzip = ".gz";
Bins2Values marker2beta;
vector<string> tissue_names;
if (str_ends_with(tissue_markers_file,fileext_gzip)) {
// read_tissue_markers_gz_file(tissue_markers_file, 2, num_tissues, marker2beta, tissue_names);
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Rcpp::Rcout << "Input has to be a txt file" << endl;
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} else {
read_tissue_markers_txt_file(tissue_markers_file, 2, num_tissues, marker2beta, tissue_names);
}
//string debug_file="./debug.single_value.tissue_markers.txt";
//write_Bins2Values(marker2beta, tissue_names, debug_file, false);
//exit(EXIT_SUCCESS);
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// Rcpp::Rcerr << "calculating reads likelihoods ..." << endl;
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Matrix_Double reads_likelihoods((unsigned int)num_tissues);
Bins2UnsignedIntegers marker2rowindexes;
Bins2Value marker2ambiguousreadcounts;
vector<int> Rm, Rl;
unsigned long num_total_reads;
if (str_ends_with(reads_binning_file,fileext_gzip)) {
// num_total_reads = calc_read_probability_by_marker2beta_from_reads_binning_gzip_file(reads_binning_file, marker2beta, reads_likelihoods, marker2rowindexes, marker2ambiguousreadcounts, Rm, Rl, min_likelihood_ratio_cutoff);
Rcpp::Rcout << "Input has to be a txt file" << endl;
} else {
num_total_reads = calc_read_probability_by_marker2beta_from_reads_binning_text_file(reads_binning_file, marker2beta, reads_likelihoods, marker2rowindexes, marker2ambiguousreadcounts, Rm, Rl, min_likelihood_ratio_cutoff);
}
int num_reads_non_ambiguous = (int)reads_likelihoods.get_row_num();
int num_reads_ambiguous = 0;
Bins2Value::iterator m2amb_iter;
for (m2amb_iter=marker2ambiguousreadcounts.begin(); m2amb_iter!=marker2ambiguousreadcounts.end(); m2amb_iter++) {
num_reads_ambiguous += (int)(m2amb_iter->second);
}
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// Rcpp::Rcerr << "#reads_total: " << num_total_reads << endl;
// Rcpp::Rcerr << "#reads_covering_markers (non-ambiguous): " << num_reads_non_ambiguous << endl;
// Rcpp::Rcerr << "#reads_covering_markers (ambiguous): " << num_reads_ambiguous << endl;
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//////////////////////////////
////// begin for debug
#ifdef DEBUG
Rcpp::Rcout << "reads likelihoods: " << endl;
Rcpp::Rcout << reads_likelihoods << endl;
Rcpp::Rcout << "marker2ambiguousreadcounts: " << endl;
Rcpp::Rcout << marker2ambiguousreadcounts << endl;
//for (int z=0; z<Rm.size(); z++) {
//cerr << Rm[z] << "\t" << Rl[z] << endl;
//}
//cout << endl;
Rcpp::Rcout << "marker2rowindexes: " << endl;
print_Bins2UnsignedIntegers(marker2rowindexes);
Rcpp::Rcout << "c++_done" << endl;
#endif
//// end for debug
//////////////////////////////
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// Rcpp::Rcerr << "perform " << em_algorithm_type << " ..." << endl;
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vector<double> theta;
//cout << "debug before em_type.compare" << endl << flush;
if (em_algorithm_type.compare("em.global.known")==0) {
// create and initialize q with the same size of p and with all elements initialized as 0
Matrix_Double q(num_reads_non_ambiguous, num_tissues, 0);
// estimate tissue fractions (theta) and tissue-specific posterior probability matrix (q)
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double obj = em_supervise(reads_likelihoods, em_max_iterations, theta, q, random_seed);
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// output
if (output_type=="tissueFraction") {
ofstream fout(output_file.c_str());
if (fout.is_open()) {
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print_vec(fout, tissue_names, "\t");
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fout << endl;
fout.precision(6);
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print_vec(fout, theta, "\t");
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fout << endl; ////////RH
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// fout << "obj: " << obj << endl;
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// fout << endl << num_reads_ambiguous << endl;
// fout << endl << "#reads_total: " << num_total_reads << "\t#reads_covering_markers(non_ambiguous): " << num_reads_non_ambiguous << endl << "\t#reads_covering_markers(ambiguous): " << num_reads_ambiguous << endl;
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fout.close();
}
} else if (output_type.find("readCount")!=std::string::npos) {
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// Rcpp::Rcerr << "Count reads of each marker by reads posterior probabilities: " << output_type << " ..." << endl;
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double unit = 1e6 / num_total_reads; // default unit is readCountPerMillion
if (output_type.find("readCountPerMillion")!=std::string::npos) {
unit = 1e6 / num_total_reads;
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// Rcpp::Rcerr << " unit: 1e6 / #total_reads = " << unit << endl;
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} else if (output_type.find("readCountPerBillion")!=std::string::npos) {
unit = 1e9 / num_total_reads;
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// Rcpp::Rcerr << " unit: 1e9 / #total_reads = " << unit << endl;
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} else if (output_type.find("readCountRaw")!=std::string::npos) {
unit = 1.0;
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// Rcpp::Rcerr << " unit: " << unit << endl;
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}
q.set_row_labels(reads_likelihoods.get_row_labels());
Matrix_Double readCounts(num_tissues);
readCounts_by_reads_posterior_probability_version_regular(q, unit, readCounts);
ofstream fout(output_file.c_str());
if (fout.is_open()) {
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print_vec(fout, tissue_names, "\t");
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fout << endl;
fout.precision(6);
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print_vec(fout, theta, "\t");
// fout << endl << "#reads_total: " << num_total_reads << "\t#reads_covering_markers(non_ambiguous): " << num_reads_non_ambiguous << "\t#reads_covering_markers(ambiguous): " << num_reads_ambiguous << "\tunit: " << unit << endl;
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fout << readCounts;
fout.close();
}
}
//////////////////////////////
////// begin for debug
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// Rcpp::Rcerr << "tissue fractions: ";
// print_vec(Rcpp::Rcerr, theta, ", ");
// Rcpp::Rcerr << endl;
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////// end for debug
//////////////////////////////
}
if (em_algorithm_type.compare("em.global.unknown")==0) {
// create and initialize q with the same size of p and with all elements initialized as 0
Matrix_Double q(num_reads_non_ambiguous, num_tissues, 0);
// estimate tissue fractions (theta) and tissue-specific posterior probability matrix (q)
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double obj = em_supervise(reads_likelihoods, em_max_iterations, theta, q, random_seed);
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// adjust 'theta' and 'q' by "num_reads_non_ambiguous/(num_reads_ambiguous + num_reads_non_ambiguous)", because we consider 'theta_unknown'
double theta_unknown = (double)num_reads_ambiguous/(num_reads_ambiguous + num_reads_non_ambiguous);
double tmp = (double)num_reads_non_ambiguous/(num_reads_ambiguous + num_reads_non_ambiguous);
for (int i=0; i<theta.size(); i++) {
theta[i] *= tmp;
}
q.multipy_single_value(tmp);
// output
if (output_type=="tissueFraction") {
ofstream fout(output_file.c_str());
if (fout.is_open()) {
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print_vec(fout, tissue_names, "\t");
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fout << "\tunknown" << endl;
fout.precision(6);
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print_vec(fout, theta, "\t");
fout << "\t" << theta_unknown << endl;
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// fout << "obj: " << obj << endl;
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// fout << endl;
// fout << endl << num_reads_ambiguous << endl;
// fout << endl << "#total_reads: " << num_total_reads << "\t#reads_covering_markers(non_ambiguous): " << num_reads_non_ambiguous << endl << "\t#reads_covering_markers(ambiguous): " << num_reads_ambiguous << endl;
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fout.close();
}
} else if (output_type.find("readCount")!=std::string::npos) {
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// Rcpp::Rcerr << "Count reads of each marker by reads posterior probabilities: " << output_type << " ..." << endl;
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double unit = 1e6 / num_total_reads; // default unit is readCountPerMillion
if (output_type.find("readCountPerMillion")!=std::string::npos) {
unit = 1e6 / num_total_reads;
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// Rcpp::Rcerr << " unit: 1e6 / #total_reads = " << unit << endl;
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} else if (output_type.find("readCountPerBillion")!=std::string::npos) {
unit = 1e9 / num_total_reads;
//unit = 1.0; // for debug only
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// Rcpp::Rcerr << " unit: 1e9 / #total_reads = " << unit << endl;
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} else if (output_type.find("readCountRaw")!=std::string::npos) {
unit = 1.0;
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// Rcpp::Rcerr << " unit: " << unit << endl;
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}
q.set_row_labels(reads_likelihoods.get_row_labels());
Matrix_Double readCounts(num_tissues); // the last column is for the unknown class.
readCounts_by_reads_posterior_probability_version_regular(q, unit, readCounts); // collapse from reads to markers
//tmp = (double)num_reads_ambiguous/(num_reads_ambiguous + num_reads_non_ambiguous);
for (m2amb_iter=marker2ambiguousreadcounts.begin(); m2amb_iter!=marker2ambiguousreadcounts.end(); m2amb_iter++) {
m2amb_iter->second *= theta_unknown * unit;
}
ofstream fout(output_file.c_str());
if (fout.is_open()) {
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print_vec(fout, tissue_names, "\t");
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fout << "\tunknown" << endl;
fout.precision(6);
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print_vec(fout, theta, "\t");
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fout << "\t" << theta_unknown << endl;
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// fout << "#reads_total: " << num_total_reads << "\t#reads_covering_markers(non_ambiguous): " << num_reads_non_ambiguous << "\t#reads_covering_markers(ambiguous): " << num_reads_ambiguous << "\tunit: " << unit << endl;
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readCounts.print_with_additional_column_of_Bins2Value(fout, marker2ambiguousreadcounts);
//fout << readCounts;
fout.close();
}
}
//////////////////////////////
////// begin for debug
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// Rcpp::Rcerr << "tissue fractions: ";
// print_vec(Rcpp::Rcerr , theta, ", ");
// Rcpp::Rcerr << ", " << theta_unknown << endl;
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////// end for debug
//////////////////////////////
}
}
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