source: plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc @ 1034

// $Id: qQN.cc 1034 2009-04-07 21:22:26Z 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/Matrix.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(std::vector<double>&, const Matrix&);
void create_target(std::vector<double>&, const Matrix&, const std::string&);


int main(int argc, char* argv[])
{
  CommandLine cmd;
  OptionInFile assay(cmd, "assay-data", "assay annotations", true);
  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;
  }

  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());
  }
  Matrix m(std::cin,'\t');
  if (indata.present()) {
    std::cin.rdbuf(cin_buffer); // restore old input buffer
    infile->close();
    delete infile;
  }

  std::vector<double> target(m.rows(),0);
  ( assay.present() ? create_target(target,m,assay.value()) :
                      create_target(target,m) );
  qQuantileNormalizer qqn(target.begin(), target.end(), 100);
  ColumnNormalizer<qQuantileNormalizer> cn(qqn);
  Matrix result(m.rows(),m.columns());
  cn(m,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(std::vector<double>& t, const Matrix& m,
                   const std::string& assay)
{
  std::ifstream is(assay.c_str());
  std::string line;
  size_t column=0;
  size_t yes=0;
  for (size_t row=0; row<m.rows(); ++row)
    t[row]=0;
  while (getline(is, line)) {
    size_t found=line.find("yes");
    if (found!=std::string::npos) {
      for (size_t row=0; row<m.rows(); ++row)
        t[row]+=m(row,column);
      ++yes;
    }
    ++column;
    if (column>m.columns())
      throw std::runtime_error("Too many annotation columns wrt data matrix");
  }
  if (!yes)
    throw std::runtime_error("No columns marked as reference");
  for (size_t row=0; row<m.rows(); ++row)
    t[row]/=yes;
}


void create_target(std::vector<double>& t, const Matrix& m)
{
  for (size_t row=0; row<m.rows(); ++row) {
    t[row]=0;
    for (size_t column=0; column<m.columns(); ++column)
      t[row]+=m(row,column);
    t[row]/=m.columns();
  }
}