tools/BNEvaluator/BNEvaluator.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 int Genes( const char*, CGenes& );

int main( int iArgs, char** aszArgs ) {
    IBayesNet*          pBN;
    gengetopt_args_info sArgs;
    CPCL                PCLOut;
    CPCLPair            PCLIn;
    CGenome             Genome;
    CGenes              GenesIn( Genome ), GenesEx( Genome );
    size_t              i, j;
    int                 iRet;
    vector<string>      vecstrGenes, vecstrExperiments, vecstrNodes, vecstrFeatures;
    vector<size_t>      veciGenes;
    ofstream            ofsm;

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

    CBayesNetSmile  BNSmile( !!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; }
        pBN = &BNFN; }
    else {
        if( !BNSmile.Open( sArgs.input_arg ) ) {
            cerr << "Couldn't open: " << sArgs.input_arg << endl;
            return 1; }
#ifdef PNL_ENABLED
        if( sArgs.pnl_flag ) {
            BNSmile.Convert( BNPNL );
            pBN = &BNPNL; }
        else
#endif // PNL_ENABLED
            pBN = &BNSmile; }

    if( ( iRet = Genes( sArgs.genes_arg, GenesIn ) ) ||
        ( iRet = Genes( sArgs.genex_arg, GenesEx ) ) )
        return iRet;
    if( !PCLIn.Open( sArgs.data_arg, sArgs.skip_arg ) ) {
        cerr << "Couldn't open: " << ( sArgs.data_arg ? sArgs.data_arg : "PCL" ) << endl;
        return 1; }

    for( i = 0; i < PCLIn.GetGenes( ); ++i ) {
        if( GenesIn.GetGenes( ) && !GenesIn.IsGene( PCLIn.GetGene( i ) ) )
            continue;
        if( GenesEx.GetGenes( ) && GenesEx.IsGene( PCLIn.GetGene( i ) ) )
            continue;
        veciGenes.push_back( i );
        vecstrGenes.push_back( PCLIn.GetGene( i ) ); }

    pBN->GetNodes( vecstrNodes );
    for( i = 0; i < vecstrNodes.size( ); ++i ) {
        for( j = 0; j < PCLIn.GetExperiments( ); ++j )
            if( vecstrNodes[ i ] == PCLIn.GetExperiment( j ) )
                break;
        if( j < PCLIn.GetExperiments( ) )
            continue;
        for( j = 0; j < pBN->GetValues( i ); ++j ) {
            char    acTmp[ 1024 ];

#pragma warning( disable : 4996 )
            sprintf( acTmp, "%s:%d", vecstrNodes[ i ].c_str( ), j );
#pragma warning( default : 4996 )
            vecstrExperiments.push_back( acTmp ); } }

    PCLOut.Open( vecstrGenes, vecstrExperiments, vecstrFeatures );
    pBN->Evaluate( PCLIn, PCLOut, !!sArgs.zero_flag, sArgs.algorithm_arg );
    if( sArgs.output_arg )
        ofsm.open( sArgs.output_arg );
    PCLOut.Save( sArgs.output_arg ? (ostream&)ofsm : cout );
    if( sArgs.output_arg )
        ofsm.close( );

    return 0; }

static int Genes( const char* szGenes, CGenes& Genes ) {
    ifstream    ifsm;

    if( !szGenes )
        return 0;

    ifsm.open( szGenes );
    if( !Genes.Open( ifsm ) ) {
        cerr << "Couldn't open: " << szGenes << endl;
        return 1; }
    ifsm.close( );
    return 0; }