tools/Dat2PCL/Dat2PCL.cpp

/*****************************************************************************
 * This file is provided under the Creative Commons Attribution 3.0 license.
 *
 * You are free to share, copy, distribute, transmit, or adapt this work
 * PROVIDED THAT you attribute the work to the authors listed below.
 * For more information, please see the following web page:
 * http://creativecommons.org/licenses/by/3.0/
 *
 * This file is a component of the Sleipnir library for functional genomics,
 * authored by:
 * Curtis Huttenhower (chuttenh@princeton.edu)
 * Mark Schroeder
 * Maria D. Chikina
 * Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
 *
 * If you use this library, the included executable tools, or any related
 * code in your work, please cite the following publication:
 * Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
 * Olga G. Troyanskaya.
 * "The Sleipnir library for computational functional genomics"
 *****************************************************************************/
#include "stdafx.h"
#include "cmdline.h"
#include "statistics.h"

int main(int iArgs, char** aszArgs) {
    gengetopt_args_info sArgs;
    CGenome Genome;
    CGenes Genes(Genome);       
    CPCL PCL;
    CPCL aPCL;
    CDat Dat;
    size_t i, j, iArg;
    bool fModified;
    vector<string> features;
    vector<string> input_files;
    
    if (cmdline_parser(iArgs, aszArgs, &sArgs)) {
        cmdline_parser_print_help();
        return 1;
    }
    CMeta Meta(sArgs.verbosity_arg);
    
    if(sArgs.input_given){
      if( !Dat.Open( sArgs.input_arg, false, 0, false, true)){
        cerr << "Could not open: " << sArgs.input_arg << endl;
        return 1; }
      
      PCL.Open( Dat.GetGeneNames( ), Dat.GetGeneNames( ), features);
    
      cerr << "Gene count: " << Dat.GetGenes() << endl;
    
      PCL.populate( sArgs.input_arg );
    }
    else{
      if(sArgs.inputs_num > 0){
        input_files.resize( sArgs.inputs_num );
        copy( sArgs.inputs, sArgs.inputs + sArgs.inputs_num, input_files.begin( ) );
        
        for( iArg = 0; iArg < input_files.size(); ++iArg ) {
          
          if( !aPCL.Open(input_files[ iArg ].c_str(), sArgs.skip_arg, false, sArgs.rPCL_flag ) ) {
        cerr << "Could not open: " << input_files[ iArg ] << endl;
        return 1; }
          
          cerr << "Open: " << input_files[ iArg ] << endl;
          
          if(iArg == 0)
        PCL.Open(aPCL);
          else{
        for( i = 0; i < PCL.GetGenes( ); ++i )
          for( j = 0; j < PCL.GetExperiments( ); ++j )
            PCL.Set(i,j, aPCL.Get(i,j)+PCL.Get(i,j) );
          }
        }
      }
      else{
        return 1;
      }
    }
    
    
    if (sArgs.output_arg) {   
      PCL.Save(sArgs.output_arg);
    } else {
      PCL.Save(cout, NULL);
      cout.flush();
    }   
    return 0;
}