tools/Data2DB/Data2DB.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"


int main( int iArgs, char** aszArgs ) {
    static const size_t c_iBuffer   = 1024;
#ifdef WIN32
    pthread_win32_process_attach_np( );
#endif // WIN32
    gengetopt_args_info sArgs;
    ifstream            ifsm;
    istream*            pistm;
    vector<string>      vecstrLine, vecstrGenes, vecstrDatasets;
    char                acBuffer[ c_iBuffer ];
    CBayesNetSmile      BNSmile;
    size_t              i;
    map<string, size_t> mapstriZeros;

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

    if( sArgs.input_arg ) {
        ifsm.open( sArgs.input_arg );
        pistm = &ifsm; }
    else
        pistm = &cin;
    while( !pistm->eof( ) ) {
        pistm->getline( acBuffer, c_iBuffer - 1 );
        acBuffer[ c_iBuffer - 1 ] = 0;
        vecstrLine.clear( );
        CMeta::Tokenize( acBuffer, vecstrLine );
        if( vecstrLine.size( ) < 2 ) {
            cerr << "Ignoring line: " << acBuffer << endl;
            continue; }
        if( !( i = atoi( vecstrLine[ 0 ].c_str( ) ) ) ) {
            cerr << "Illegal gene ID: " << vecstrLine[ 0 ] << " for " << vecstrLine[ 1 ] << endl;
            return 1; }
        i--;
        if( vecstrGenes.size( ) <= i )
            vecstrGenes.resize( i + 1 );
        vecstrGenes[ i ] = vecstrLine[ 1 ]; }
    if( sArgs.input_arg )
        ifsm.close( );

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

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


    bool useNibble = false;
    if(sArgs.use_nibble_flag==1){
        useNibble = true;
    }

    CDatabase DB(useNibble);
    DB.SetMemmap( !!sArgs.memmap_flag );
    DB.SetBuffer( !!sArgs.buffer_flag );
    DB.SetBlockOut( sArgs.block_files_arg );
    DB.SetBlockIn( sArgs.block_datasets_arg );

    if(sArgs.network_arg){
        if(sArgs.dataset_arg){
            cerr << "Confused. Only network OR dataset list." << endl;
            return 1;
        }

        if( !BNSmile.Open( sArgs.network_arg ) ) {
            cerr << "Could not open: " << sArgs.network_arg << endl;
            return 1; }
        if( !DB.Open( vecstrGenes, sArgs.dir_in_arg, &BNSmile, sArgs.dir_out_arg, min((size_t)sArgs.files_arg,
            vecstrGenes.size( )), mapstriZeros ) ) {
            cerr << "Could not open data" << endl;
            return 1;
        }

    }else if(sArgs.dataset_arg){

        ifsm.open(sArgs.dataset_arg);
        while(!pistm->eof()){
            pistm->getline(acBuffer, c_iBuffer -1);
            if(acBuffer[0]==0)
                break;
            acBuffer[c_iBuffer-1] = 0;
            //If line contains multiple columns,
            //use the first column, which is the dataset column
            vector<string> tok;
            CMeta::Tokenize(acBuffer, tok, " \t");
            vecstrDatasets.push_back(tok[0]);
        }
        vecstrDatasets.resize(vecstrDatasets.size());
        ifsm.close();

        if( !DB.Open( vecstrGenes, vecstrDatasets, sArgs.dir_in_arg, sArgs.dir_out_arg, min((size_t)sArgs.files_arg,
            vecstrGenes.size( )), mapstriZeros ) ) {
            cerr << "Could not open data" << endl;
            return 1;
        }

    }else{
        cerr << "Must give a network or a dataset list." << endl;
        return 1;

    }

#ifdef WIN32
    pthread_win32_process_detach_np( );
#endif // WIN32
    return 0; }