source: plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc @ 1050

// $Id: qQN.cc 1050 2009-05-06 09:11:59Z jari $

/*
  Copyright (C) 2009 Jari Häkkinen

  This file is part of the Normalizers plug-in package for BASE
  (net.sf.based.normalizers). The package is available at
  http://baseplugins.thep.lu.se/ BASE main site is
  http://base.thep.lu.se/

  This 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 3 of the License, or
  (at your option) any later version.

  The software 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, see <http://www.gnu.org/licenses/>.
*/

#include <config.h> // this header file is created by configure

#include <yat/normalizer/ColumnNormalizer.h>
#include <yat/normalizer/qQuantileNormalizer.h>

#include <yat/utility/CommandLine.h>
#include <yat/utility/MatrixWeighted.h>
#include <yat/utility/OptionHelp.h>
#include <yat/utility/OptionInFile.h>
#include <yat/utility/OptionOutFile.h>
#include <yat/utility/OptionSwitch.h>

#include <cstdlib>
#include <fstream>
#include <iostream>
#include <stdexcept>

using namespace theplu::yat::normalizer;
using namespace theplu::yat::utility;


void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&);
void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&,
                                const std::string&);

void exp_numbers(MatrixWeighted&);
template<typename Iterator> void log_numbers(Iterator first, Iterator last);
void log_numbers(MatrixWeighted&);

/**
   writes the data values in the matrix ignoring the weights, i.e.,
   produces the same output as the Matrix output operator does.
 */
std::ostream& operator<< (std::ostream&, const MatrixWeighted&);


int main(int argc, char* argv[])
{
  CommandLine cmd;
  OptionInFile assay(cmd, "assay-data", "assay annotations");
  OptionInFile indata(cmd, "in-data", "data to be normalized");
  OptionOutFile outdata(cmd, "out-data", "normalized data");
  OptionHelp help(cmd);
  help.synopsis()=(std::string("See ") +
                   "http://baseplugins.thep.lu.se/net.sf.basedb.normalizers " +
                   "for\ndetails on this program\n");
  OptionSwitch version(cmd, "version", "output version and exit");
  std::stringstream copyright;
  copyright << PACKAGE_STRING << '\n'
            << "Copyright (C) 2009 Jari Häkkinen\n\n"
            << "This is free software see the source for copying "
            << "conditions. There is NO\nwarranty; not even for "
            << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n";
  try {
    cmd.parse(argc, argv);
  }
  catch (cmd_error& e) {
    if (version.present()) {
      std::cout << copyright.str();
      return EXIT_SUCCESS;
    }
    std::cout << e.what() << std::endl;
    return EXIT_FAILURE;
  }
  if (version.present()) {
    std::cout << copyright.str();
    return EXIT_SUCCESS;
  }
  std::ifstream* infile=NULL;
  std::streambuf* cin_buffer=NULL;
  if (indata.present()) {
    infile=new std::ifstream(indata.value().c_str());
    cin_buffer = std::cin.rdbuf(); // save cin's input buffer
    std::cin.rdbuf(infile->rdbuf());
  }
  MatrixWeighted m(std::cin,'\t');
  if (indata.present()) {
    std::cin.rdbuf(cin_buffer); // restore old input buffer
    infile->close();
    delete infile;
  }

  std::vector<double> target;
  ( assay.present() ? create_target_and_fix_nans(target,m,assay.value()) :
                      create_target_and_fix_nans(target,m) );
  log_numbers(target.begin(),target.end());
  log_numbers(m);
  qQuantileNormalizer qqn(target.begin(), target.end(), 100);
  ColumnNormalizer<qQuantileNormalizer> cn(qqn);
  MatrixWeighted result(m.rows(),m.columns());
  cn(m,result);
  exp_numbers(result);

  std::ofstream* outfile=NULL;
  std::streambuf* cout_buffer = std::cout.rdbuf();
  if (outdata.present()) {
    outfile=new std::ofstream(outdata.value().c_str());
    cout_buffer = std::cout.rdbuf(); // save cout's output buffer
    std::cout.rdbuf(outfile->rdbuf());
  }
  std::cout << result << std::endl;
  if (outdata.present()) {
    std::cout.rdbuf(cout_buffer); // restore old output buffer
    outfile->close();
    delete outfile;
  }

  return EXIT_SUCCESS;
}


void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m,
                                const std::string& assay)
{
  std::ifstream is(assay.c_str());
  std::string line;
  size_t column=0;
  std::vector<size_t> column_contribs(m.rows(),0);
  std::vector<double> temp_target(m.rows(),0.0);
  while (getline(is, line)) {
    size_t found=line.find("yes");

    if (found!=std::string::npos) {
      // use this assay as a part of reference
      for (size_t row=0; row<m.rows(); ++row)
        if (m(row,column).weight()) { // weight either 0 or 1
          temp_target[row]+=m(row,column).data();
          ++column_contribs[row];
        }
        else
          m(row,column).data()=0;
    }
    else
      // this assay as not a part of the reference but fix nan
      for (size_t row=0; row<m.rows(); ++row)
        if (!m(row,column).weight()) // weight either 0 or 1
          m(row,column).data()=0;

    ++column;
    if (column>m.columns())
      throw std::runtime_error("Too many annotation columns wrt data matrix");
  }
  t.reserve(m.rows());
  for (size_t row=0; row<m.rows(); ++row)
    if (column_contribs[row])
      t.push_back(temp_target[row]/=column_contribs[row]);
  if (!t.size())
    throw std::runtime_error("Not a well defined reference, aborting");
}


void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m)
{
  std::vector<double> temp_target(m.rows(),0.0);
  t.reserve(m.rows());
  for (size_t row=0; row<m.rows(); ++row) {
    size_t column_contribs=0;
    for (size_t column=0; column<m.columns(); ++column)
      if (m(row,column).weight()) { // weight either 0 or 1
        temp_target[row]+=m(row,column).data();
        ++column_contribs;
      }
      else
        m(row,column).data()=0;
    if (column_contribs)
      t.push_back(temp_target[row]/=column_contribs);
  }
  if (!t.size())
    throw std::runtime_error("Not a well defined reference, aborting");
}


void exp_numbers(MatrixWeighted& m)
{
  MatrixWeighted::iterator i=m.begin();
  while (i!=m.end()) {
    i->data() =std::exp(i->data());
    ++i;
  }
}


template<typename Iterator> void log_numbers(Iterator i, Iterator last)
{
  while (i!=last) {
    *i=std::log(*i);
    ++i;
  }
}


void log_numbers(MatrixWeighted& m)
{
  MatrixWeighted::iterator i=m.begin();
  while (i!=m.end()) {
    i->data() =std::log(i->data());
    ++i;
  }
}


std::ostream& operator<< (std::ostream& s, const MatrixWeighted& m)
{
  s.setf(std::ios::dec);
  s.precision(12);
  for(size_t i=0, j=0; i<m.rows(); i++)
    for (j=0; j<m.columns(); j++) {
      if (m(i,j).weight())
        s << m(i,j).data();
      else
        s << "nan";
      if (j<m.columns()-1)
        s << s.fill();
      else if (i<m.rows()-1)
        s << "\n";
    }
  return s;
}