mkkblastindex.cpp

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/*  $Id: mkkblastindex.cpp 92025 2020-12-17 15:27:50Z grichenk $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author: Tom Madden
 *
 * File Description:
 *   Produce database for kmer (minhash) search.
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <algo/blast/proteinkmer/blastkmerutils.hpp>
#include <algo/blast/proteinkmer/blastkmerindex.hpp>
 
#ifdef _OPENMP
#include <omp.h>
#endif
 
USING_NCBI_SCOPE;
USING_SCOPE(objects);
 
/////////////////////////////////////////////////////////////////////////////
//  CBlastKmerBuildIndexApplication::
 
 
class CBlastKmerBuildIndexApplication : public CNcbiApplication
{
private:
    virtual void Init(void);
    virtual int  Run(void);
    virtual void Exit(void);
};
 
/////////////////////////////////////////////////////////////////////////////
//  Init test for all different types of arguments
 
 
void CBlastKmerBuildIndexApplication::Init(void)
{
    HideStdArgs(fHideConffile | fHideFullVersion | fHideXmlHelp | fHideVersion | fHideDryRun);
    
    unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
 
    arg_desc->AddKey("db", "database_name", 
                     "BLAST database to read and create",
                     CArgDescriptions::eString);
    
    arg_desc->AddDefaultKey("samples", "buhler_samples", 
                     "Number of samples to check",
                     CArgDescriptions::eInteger,
                     "30");
    
     arg_desc->AddDefaultKey("kmer", "kmerNum",
                        "kmer size", CArgDescriptions::eInteger, "5");
    
    arg_desc->AddDefaultKey("width", "width_data", 
                     "Width of data arrays.  4 for an int, 2 for short(recommmended), 1 for byte",
                     CArgDescriptions::eInteger, "2");
    
    arg_desc->AddDefaultKey("threads", "number_threads", 
                     "Number of threads to use.",
                     CArgDescriptions::eInteger, "1");
    
    arg_desc->AddDefaultKey("hashes", "number_hashes", 
                     "Number of Hash functions to use.",
                     CArgDescriptions::eInteger, "32");
    
    arg_desc->AddDefaultKey("alphabet", "alphabet_choice", 
                     "0 (zero) for 15 letter alphabet, 1 for 10 letter alphabet",
                     CArgDescriptions::eInteger, "0");
    
    arg_desc->AddDefaultKey("kversion", "index_version", 
                     "1 for older LSH, 2 for Buhler LSH, 3 for one hash method",
                     CArgDescriptions::eInteger, "3");
    
     arg_desc->AddOptionalKey("output", "Outputfile",
                        "Index files", CArgDescriptions::eString);
    
    arg_desc->AddDefaultKey("logfile",
            "LogInformation",
            "File for logging errors",
            CArgDescriptions::eOutputFile,
            "mkkblastindex.log",
            CArgDescriptions::fAppend);
 
    arg_desc->SetUsageContext("mkkblastindex", "Index for protein kmer search");
    
    SetupArgDescriptions(arg_desc.release());
}
 
/////////////////////////////////////////////////////////////////////////////
//  Build a KMER index.
//
 
int CBlastKmerBuildIndexApplication::Run(void)
{
 
    SetDiagPostLevel(eDiag_Warning);
        SetDiagPostPrefix("mkkblastindex");
 
    int retval = 0;
    // blast database of sequences
    CRef<CSeqDB> seqdb(new CSeqDB(GetArgs()["db"].AsString(), CSeqDB::eProtein));
 
    int samples = GetArgs()["samples"].AsInteger();
    
    int kmerNum = GetArgs()["kmer"].AsInteger();
 
    int dataWidth = GetArgs()["width"].AsInteger();
 
    int numThreads = GetArgs()["threads"].AsInteger();
 
    int numHashes = GetArgs()["hashes"].AsInteger();
 
    int alphabet = GetArgs()["alphabet"].AsInteger();
 
    int version = GetArgs()["kversion"].AsInteger();
 
    CNcbiOstream * logFile = & (GetArgs()["logfile"].HasValue()
                   ? GetArgs()["logfile"].AsOutputFile()
                   : cout);
 
    *logFile <<  CTime(CTime::eCurrent).AsString() << ": Producing indices for " << GetArgs()["db"].AsString() << " using " << numThreads << " threads" << endl;
 
    try {
        CBlastKmerBuildIndex build_index(seqdb, kmerNum, numHashes, samples, dataWidth, alphabet, version);
        build_index.Build(numThreads);
    }
        catch (const CSeqDBException& e) {              
            *logFile << "CSeqDB Database error: " << e.GetMsg() << endl;   
            retval = 1;
        }                                  
        catch (const blast::CMinHashException& e)  {
            *logFile << "CMinHash error: " << e.GetMsg() << endl;        
                retval = 1;
        }
        catch (const CFileException& e)  {
            *logFile << "File error: " << e.GetMsg() << endl;
                retval = 1;
        }
        catch (const std::ios::failure&) {                    
            *logFile << "mkkblastindex failed to write output" << endl;
            retval = 1;
        }                                                    
        catch (const std::bad_alloc&) {                     
            *logFile << "mkkblastindex ran out of memory" << endl;
            retval = 1;
        }                                            
    catch (...)  {
                *logFile << "Unknown error" << endl;
                retval = 1;
    }
    return retval;
}
    
 
/////////////////////////////////////////////////////////////////////////////
//  Cleanup
 
 
void CBlastKmerBuildIndexApplication::Exit(void)
{
    SetDiagStream(0);
}
 
 
/////////////////////////////////////////////////////////////////////////////
//  MAIN
 
 
#ifndef SKIP_DOXYGEN_PROCESSING
int main(int argc, const char* argv[])
{
    // Execute main application function
    return CBlastKmerBuildIndexApplication().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */