tools/DBCombiner/DBCombiner.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, vecstrDBs;
    char                acBuffer[ c_iBuffer ];
    size_t              i;

    if( cmdline_parser( iArgs, aszArgs, &sArgs ) ) {
        cmdline_parser_print_help( );
        return 1; }

    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( );

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

    if(sArgs.reorganize_flag==1){
        vector<string> vecstrDataset;
        ifstream ifsm2;
        ifsm2.open(sArgs.dataset_arg);
        while(!ifsm2.eof()){
            ifsm2.getline(acBuffer, c_iBuffer-1);
            if(acBuffer[0]==0) break;
            acBuffer[c_iBuffer-1] = 0;
            vector<string> vecstrLine;
            CMeta::Tokenize(acBuffer, vecstrLine);
            vecstrDataset.push_back(vecstrLine[0]);
        }
        ifsm2.close();

        if(useNibble){
            fprintf(stderr, "The use of nibble flag is not supported for --reorganize mode\n");
            return 1;
        }
        CDatabase db(false);
        db.Open(sArgs.db_dir_arg, vecstrGenes, vecstrDataset.size(), 
            sArgs.src_db_num_arg);
        db.Reorganize(sArgs.dest_db_dir_arg, sArgs.dest_db_num_arg);
        return 0;
    }

    if(sArgs.combine_flag==1){
        CDatabase DB(useNibble);

        bool fSplit = false;
        if(sArgs.split_flag==1){
            fSplit = true;
        }

        if(sArgs.db_arg){
            ifsm.open(sArgs.db_arg);
            while(!pistm->eof()){
                pistm->getline(acBuffer, c_iBuffer -1);
                if(acBuffer[0]==0){
                    break;
                }
                acBuffer[c_iBuffer-1] = 0;
                vecstrDBs.push_back(acBuffer);
            }
            vecstrDBs.resize(vecstrDBs.size());
            ifsm.close();

            //printf("Reading DBS"); getchar();
            vector<CDatabaselet*> DBS;
            DBS.resize(vecstrDBs.size());
            for(i=0; i<vecstrDBs.size(); i++){
                DBS[i] = new CDatabaselet(useNibble);
                DBS[i]->Open(vecstrDBs[i]);
            }
            //printf("Finished reading DBS"); getchar();

            CDatabaselet::Combine(DBS, sArgs.dir_out_arg, vecstrGenes, fSplit);
            for(i=0; i<vecstrDBs.size(); i++){
                free(DBS[i]);
            }

        }else{
            cerr << "Must give a db list." << endl;
            return 1;

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