tools/BNConverter/BNConverter.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 void Evaluate( const IDataset*, const IBayesNet*, bool, ostream& );
static void DebugDataset( const IDataset* );

int main( int iArgs, char** aszArgs ) {
    CDatasetCompact     Data;
    CDatasetCompactMap  DataMap;
    CDataset            DataFull;
    CDataPair           Answers;
    CDataMask           Train, Test;
    IDataset*           pData;
    gengetopt_args_info sArgs;
    ofstream            ofsm;
    IBayesNet*          pNet;
    size_t              i;

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

    CBayesNetSmile  BNSmile( !!sArgs.group_flag ), BNDefault( !!sArgs.group_flag );
#ifdef PNL_ENABLED
    CBayesNetPNL    BNPNL( !!sArgs.group_flag );
#endif // PNL_ENABLED
    CBayesNetFN     BNFN;

    if( sArgs.function_flag ) {
        if( !BNFN.Open( sArgs.input_arg ) ) {
            cerr << "Couldn't open: " << sArgs.input_arg << endl;
            return 1; }
        pNet = &BNFN; }
    else {
        if( !BNSmile.Open( sArgs.input_arg ) ) {
            cerr << "Couldn't open: " << sArgs.input_arg << endl;
            return 1; }
        if( sArgs.default_arg ) {
            if( !BNDefault.Open( sArgs.default_arg ) ) {
                cerr << "Couldn't open: " << sArgs.default_arg << endl;
                return 1; }
            BNSmile.SetDefault( BNDefault ); }
#ifdef PNL_ENABLED
        if( sArgs.pnl_flag ) {
            BNSmile.Convert( BNPNL );
            pNet = &BNPNL; }
        else
#endif // PNL_ENABLED
            pNet = &BNSmile; }
    if( sArgs.randomize_flag )
        pNet->Randomize( );

    if( sArgs.dataset_arg ) {
        if( !DataMap.Open( sArgs.dataset_arg ) ) {
            cerr << "Couldn't open: " << sArgs.dataset_arg << endl;
            return 1; }

        if( sArgs.genes_arg && !DataMap.FilterGenes( sArgs.genes_arg, CDat::EFilterInclude ) ) {
            cerr << "Couldn't open: " << sArgs.genes_arg << endl;
            return 1; }
        if( sArgs.genet_arg && !DataMap.FilterGenes( sArgs.genet_arg, CDat::EFilterTerm ) ) {
            cerr << "Couldn't open: " << sArgs.genet_arg << endl;
            return 1; }
        if( sArgs.genex_arg && !DataMap.FilterGenes( sArgs.genex_arg, CDat::EFilterExclude ) ) {
            cerr << "Couldn't open: " << sArgs.genex_arg << endl;
            return 1; }
        DataMap.FilterAnswers( );
        pData = &DataMap; }
    else {
        if( !Answers.Open( sArgs.answers_arg, pNet->IsContinuous( 0 ) ) ) {
            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; }

        if( pNet->IsContinuous( ) ) {
            if( !DataFull.Open( Answers, sArgs.datadir_arg, pNet ) ) {
                cerr << "Couldn't open: " << sArgs.datadir_arg << endl;
                return 1; }
            pData = &DataFull; }
        else {
            if( !Data.Open( Answers, sArgs.datadir_arg, pNet ) ) {
                cerr << "Couldn't open: " << sArgs.datadir_arg << endl;
                return 1; }
            Data.FilterAnswers( );
            pData = &Data; } }

    if( sArgs.test_arg ) {
        Train.AttachRandom( pData, (float)( 1 - sArgs.test_arg ) );
        Test.AttachComplement( Train );
        pData = &Train; }
    if( sArgs.test_arg < 1 ) {
        if( sArgs.checkpoint_flag )
            for( i = 0; i < (size_t)sArgs.iterations_arg; ++i ) {
                pNet->Learn( pData, 1, !!sArgs.zero_flag, !!sArgs.elr_flag );
                cerr << "Iteration " << i << '/' << sArgs.iterations_arg << " complete" << endl;
                pNet->Save( sArgs.output_arg ); }
        else
            pNet->Learn( pData, sArgs.iterations_arg, !!sArgs.zero_flag, !!sArgs.elr_flag ); }

    if( sArgs.murder_given )
        pNet->Randomize( sArgs.murder_arg );
    pNet->Save( sArgs.output_arg );

    if( sArgs.eval_train_arg && ( sArgs.test_arg < 1 ) ) {
        ofsm.open( sArgs.eval_train_arg, ios_base::binary );
        Evaluate( pData, pNet, !!sArgs.zero_flag, ofsm );
        ofsm.close( ); }
    if( sArgs.eval_test_arg && sArgs.test_arg ) {
        ofsm.clear( );
        ofsm.open( sArgs.eval_test_arg, ios_base::binary );
        Evaluate( &Test, pNet, !!sArgs.zero_flag, ofsm );
        ofsm.close( ); }

    return 0; }

static void Evaluate( const IDataset* pData, const IBayesNet* pNet, bool fZero, ostream& ostm ) {
    size_t  i, j;
    float   d;
    CDat    Dat;

    Dat.Open( pData->GetGeneNames( ) );
    pNet->Evaluate( pData, Dat, fZero );
    if( !pNet->IsContinuous( ) )
        for( i = 0; i < Dat.GetGenes( ); ++i )
            for( j = ( i + 1 ); j < Dat.GetGenes( ); ++j )
                if( !CMeta::IsNaN( d = Dat.Get( i, j ) ) )
                    Dat.Set( i, j, 1 - d );
    Dat.Save( ostm ); }

static void DebugDataset( const IDataset* pData ) {
    size_t  i, j;

    for( i = 0; i < pData->GetGenes( ); ++i ) {
        for( j = ( i + 1 ); j < pData->GetGenes( ); ++j )
            cerr << ( pData->IsExample( i, j ) ? 1 : 0 );
        if( ( i + 1 ) < pData->GetGenes( ) )
            cerr << endl; } }