tools/DataDumper/DataDumper.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"

static const char   c_acDab[]   = ".dab";

int main( int iArgs, char** aszArgs ) {
    gengetopt_args_info sArgs;
    size_t                      i, j, k, iPairs, iPair, iArg;
    map<string,size_t>          mapZeros;
    vector<string>              vecstrNames;
    CDataPair                   Answers;
    CFullMatrix<unsigned char>  MatData;
    vector<size_t>              veciGenes;
    float                       d;

    if( cmdline_parser( iArgs, aszArgs, &sArgs ) ) {
        cmdline_parser_print_help( );
        return 1; }
    CMeta Meta( sArgs.verbosity_arg );

    if( sArgs.zeros_arg ) {
        ifstream        ifsm;
        vector<string>  vecstrZeros;
        char            acLine[ 1024 ];

        ifsm.open( sArgs.zeros_arg );
        if( !ifsm.is_open( ) ) {
            cerr << "Couldn't open: " << sArgs.zeros_arg << endl;
            return 1; }
        while( !ifsm.eof( ) ) {
            ifsm.getline( acLine, ARRAYSIZE(acLine) - 1 );
            acLine[ ARRAYSIZE(acLine) - 1 ] = 0;
            vecstrZeros.clear( );
            CMeta::Tokenize( acLine, vecstrZeros );
            if( vecstrZeros.empty( ) )
                continue;
            mapZeros[ vecstrZeros[ 0 ] ] = atoi( vecstrZeros[ 1 ].c_str( ) ); } }

    if( !Answers.Open( sArgs.answers_arg, false ) ) {
        cerr << "Couldn't open: " << sArgs.answers_arg << endl;
        return 1; }
    if( sArgs.genes_arg && !Answers.FilterGenes( sArgs.genes_arg, CDat::EFilterInclude ) ) {
        cerr << "Couldn't open: " << sArgs.genes_arg << endl;
        return 1; }
    if( sArgs.genet_arg && !Answers.FilterGenes( sArgs.genet_arg, CDat::EFilterTerm ) ) {
        cerr << "Couldn't open: " << sArgs.genet_arg << endl;
        return 1; }
    if( sArgs.genex_arg && !Answers.FilterGenes( sArgs.genex_arg, CDat::EFilterExclude ) ) {
        cerr << "Couldn't open: " << sArgs.genex_arg << endl;
        return 1; }

    for( iPairs = i = 0; i < Answers.GetGenes( ); ++i )
        for( j = ( i + 1 ); j < Answers.GetGenes( ); ++j )
            if( !CMeta::IsNaN( Answers.Get( i, j ) ) )
                iPairs++;
    MatData.Initialize( iPairs, sArgs.inputs_num );
    MatData.Clear( );

    veciGenes.resize( Answers.GetGenes( ) );
    for( iArg = 0; iArg < sArgs.inputs_num; ++iArg ) {
        CDatasetCompact                     Data;
        size_t                              iOne, iTwo, iZero, iVal;
        map<string,size_t>::const_iterator  iterZero;

        vecstrNames.clear( );
        vecstrNames.push_back( sArgs.inputs[ iArg ] );
        if( !Data.Open( Answers, vecstrNames, true ) ) {
            cerr << "Couldn't open: " << sArgs.inputs[ iArg ] << endl;
            return 1; }
        vecstrNames[ 0 ] = CMeta::Filename( CMeta::Deextension( CMeta::Basename( vecstrNames[ 0 ].c_str( ) ) ) );
        iZero = ( ( iterZero = mapZeros.find( vecstrNames[ 0 ] ) ) == mapZeros.end( ) ) ? -1 :
            iterZero->second;
        for( i = 0; i < veciGenes.size( ); ++i )
            veciGenes[ i ] = Data.GetGene( Answers.GetGene( i ) );
        for( iPair = i = 0; i < veciGenes.size( ); ++i ) {
            iOne = veciGenes[ i ];
            for( j = ( i + 1 ); j < veciGenes.size( ); ++j ) {
                if( CMeta::IsNaN( Answers.Get( i, j ) ) )
                    continue;
                if( ( iOne != -1 ) && ( ( iTwo = veciGenes[ j ] ) != -1 ) ) {
                    iVal = Data.GetDiscrete( iOne, iTwo, 1 );
                    if( ( iVal != -1 ) || ( ( iVal = iZero ) != -1 ) || ( sArgs.zero_flag && !( iVal = 0 ) ) )
                        MatData.Set( iPair, iArg, (unsigned char)( iVal + 1 ) ); }
                iPair++; } } }

    cout << "Gene 1 Gene 2  Answer";
    for( i = 0; i < sArgs.inputs_num; ++i )
        cout << '\t' << sArgs.inputs[ i ];
    cout << endl;
    for( iPair = i = 0; i < Answers.GetGenes( ); ++i )
        for( j = ( i + 1 ); j < Answers.GetGenes( ); ++j ) {
            if( CMeta::IsNaN( d = Answers.Get( i, j ) ) )
                continue;
            cout << Answers.GetGene( i ) << '\t' << Answers.GetGene( j ) << '\t' << d;
            for( k = 0; k < MatData.GetColumns( ); ++k )
                cout << '\t' << ( (int)MatData.Get( iPair, k ) - 1 );
            cout << endl;
            iPair++; }

    return 0; }