blast2seq.cpp

ncbi源码

    }

    if (args["xungap"].AsDouble()) {
        opt.SetXDropoff(args["xungap"].AsDouble());
    }

    if (args["ungapped"].AsBoolean()) {
        opt.SetGappedMode(false);
    }

    if (args["gopen"].AsInteger()) {
        opt.SetGapOpeningCost(args["gopen"].AsInteger());
    }
    if (args["gext"].AsInteger()) {
        opt.SetGapExtensionCost(args["gext"].AsInteger());
    }

    switch (args["greedy"].AsInteger()) {
    case 1: /* Immediate greedy gapped extension with traceback */
        opt.SetGapExtnAlgorithm(eGreedyWithTracebackExt);
        opt.SetUngappedExtension(false);
        break;
    case 2: /* Two-step greedy extension, no ungapped extension */
        opt.SetGapExtnAlgorithm(eGreedyExt);
        opt.SetUngappedExtension(false);
        break;
    case 3: /* Two-step greedy extension after ungapped extension*/
        opt.SetGapExtnAlgorithm(eGreedyExt);
        break;
    default: break;
    }


    if (args["xgap"].AsDouble()) {
        opt.SetGapXDropoff(args["xgap"].AsDouble());
    }
    if (args["xfinal"].AsDouble()) {
        opt.SetGapXDropoffFinal(args["xfinal"].AsDouble());
    }

    if (args["evalue"].AsDouble()) {
        opt.SetEvalueThreshold(args["evalue"].AsDouble());
    }

    if (args["searchsp"].AsDouble()) {
        opt.SetEffectiveSearchSpace((Int8) args["searchsp"].AsDouble());
    }
    if (args["perc"].AsDouble()) {
        opt.SetPercentIdentity(args["perc"].AsDouble());
    }

    if (args["gencode"].AsInteger()) {
        opt.SetQueryGeneticCode(args["gencode"].AsInteger());
    }
    if (args["dbgencode"].AsInteger()) {
        opt.SetDbGeneticCode(args["dbgencode"].AsInteger());
    }

    if (args["maxintron"].AsInteger()) {
        opt.SetLongestIntronLength(args["maxintron"].AsInteger());
    }
    if (args["frameshift"].AsInteger()) {
        opt.SetFrameShiftPenalty(args["frameshift"].AsInteger());
        opt.SetOutOfFrameMode();
    }

    return retval;
}

#ifndef NDEBUG
FILE*
CBlast2seqApplication::GetOutputFilePtr(void)
{
    FILE *retval = NULL;

    if (GetArgs()["out"].AsString() == "-")
        retval = stdout;    
    else
        retval = fopen((char *)GetArgs()["out"].AsString().c_str(), "a");

    ASSERT(retval);
    return retval;
}
#endif

/*****************************************************************************/

int CBlast2seqApplication::Run(void)
{
    try {
        InitObjMgr();
        int counter = 0;
        const CArgs args = GetArgs();
        Uint1 program_number;

        if (args["trace"])
            SetDiagTrace(eDT_Enable);

        BlastProgram2Number(args["program"].AsString().c_str(), 
                            &program_number);
        EProgram program = static_cast<EProgram>(program_number);
        ENa_strand query_strand = eNa_strand_unknown;
        ENa_strand subject_strand = eNa_strand_unknown;

        if (program == eBlastn || program == eBlastx) { 
            int cmdline_strand = args["strand"].AsInteger();

            if (cmdline_strand == 1)
                query_strand = eNa_strand_plus;
            else if (cmdline_strand == 2)
                query_strand = eNa_strand_minus;
            else
                query_strand = eNa_strand_both;
         }

        if (program == eBlastn ||
            program == eTblastn ||
            program == eTblastx)
            subject_strand = eNa_strand_plus;

        // Retrieve input sequences
        TSeqLocVector query_loc = 
            BLASTGetSeqLocFromStream(args["query"].AsInputFile(), *m_ObjMgr,
              query_strand, 0, 0, &counter, args["lcase"].AsBoolean());

        TSeqLocVector subject_loc = 
            BLASTGetSeqLocFromStream(args["subject"].AsInputFile(), *m_ObjMgr,
              subject_strand, 0, 0, &counter);

        CBlastOptionsHandle& opt_handle = *ProcessCommandLineArgs();

#ifndef NDEBUG
        CStopWatch sw;
        sw.Start();
#endif

        CBl2Seq blaster(query_loc, subject_loc, opt_handle);
        TSeqAlignVector seqalignv = blaster.Run();

#ifndef NDEBUG
        double t = sw.Elapsed();
        cerr << "CBl2seq run took " << t << " seconds" << endl;
        if (seqalignv.size() == 0) {
            cerr << "Returned NULL SeqAlign!" << endl;
            exit(1);
        }
#endif

        // Our poor man's formatting ...  
        if (args["asnout"]) {
            auto_ptr<CObjectOStream> asnout(
                CObjectOStream::Open(args["asnout"].AsString(), eSerial_AsnText));
            for (unsigned int index = 0; index < seqalignv.size(); ++index)
                *asnout << *seqalignv[index];
        }

    } catch (const CException& e) {
        cerr << e.what() << endl;
    }

    return 0;
}

void CBlast2seqApplication::Exit(void)
{
    SetDiagStream(0);
}


int main(int argc, const char* argv[])
{
    return CBlast2seqApplication().AppMain(argc, argv, 0, eDS_Default, 0);
}


/*
 * ===========================================================================
 * $Log: blast2seq.cpp,v $
 * Revision 1000.5  2004/06/01 18:06:32  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.46
 *
 * Revision 1.46  2004/05/21 21:41:02  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.45  2004/05/19 14:52:02  camacho
 * 1. Added doxygen tags to enable doxygen processing of algo/blast/core
 * 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
 *    location
 * 3. Added use of @todo doxygen keyword
 *
 * Revision 1.44  2004/05/17 15:33:57  madden
 * Int algorithm_type replaced with enum EBlastPrelimGapExt
 *
 * Revision 1.43  2004/04/30 15:56:31  papadopo
 * Plus/minus/both strands are acceptable for any blast program
 * that takes a nucleotide query
 *
 * Revision 1.42  2004/04/23 13:51:56  papadopo
 * handle strands for blastx correctly
 *
 * Revision 1.41  2004/04/19 21:35:23  papadopo
 * explicitly calculate strands for input sequences
 *
 * Revision 1.40  2004/03/26 18:50:32  camacho
 * Use CException::what() in catch block
 *
 * Revision 1.39  2004/03/17 20:09:08  dondosha
 * Use CBlastNucleotideOptionsHandle method to set both extension method and scan step, instead of directly calling CalculateBestStride
 *
 * Revision 1.38  2004/03/11 17:27:41  camacho
 * Minor change to avoid confusing doxygen
 *
 * Revision 1.37  2004/03/09 18:55:34  dondosha
 * Fix: set out-of-frame mode boolean option in addition to the frame shift penalty
 *
 * Revision 1.36  2004/02/13 03:31:51  camacho
 * 1. Use CBlastOptionsHandle class (still needs some work)
 * 2. Remove dead code, clean up, add @todo doxygen tags
 *
 * Revision 1.35  2004/01/05 18:50:27  vasilche
 * Fixed path to include files.
 *
 * Revision 1.34  2003/12/31 20:05:58  dondosha
 * For discontiguous megablast, set extension method and scanning stride correctly
 *
 * Revision 1.33  2003/12/09 15:13:58  camacho
 * Use difference scopes for queries and subjects
 *
 * Revision 1.32  2003/12/04 17:07:51  camacho
 * Remove yet another unused variable
 *
 * Revision 1.31  2003/11/26 18:36:45  camacho
 * Renaming blast_option*pp -> blast_options*pp
 *
 * Revision 1.30  2003/11/26 18:24:32  camacho
 * +Blast Option Handle classes
 *
 * Revision 1.29  2003/11/03 15:20:39  camacho
 * Make multiple query processing the default for Run().
 *
 * Revision 1.28  2003/10/27 20:52:29  dondosha
 * Made greedy option an integer, to specify number of extension stages
 *
 * Revision 1.27  2003/10/24 20:55:30  camacho
 * Rename GetDefaultStride
 *
 * Revision 1.26  2003/10/22 16:48:09  dondosha
 * Changed "ag" option to "scantype";
 * Use function from core library to calculate default value of stride if AG
 * scanning method is used.
 *
 * Revision 1.25  2003/10/21 22:15:33  camacho
 * Rearranging of C options structures, fix seed extension method
 *
 * Revision 1.24  2003/10/21 17:34:34  camacho
 * Renaming of gap open/extension accessors/mutators
 *
 * Revision 1.23  2003/10/17 18:22:28  dondosha
 * Use separate variables for different initial word extension options
 *
 * Revision 1.22  2003/10/08 15:27:02  camacho
 * Remove unnecessary conditional
 *
 * Revision 1.21  2003/10/07 17:37:10  dondosha
 * Lower case mask is now a boolean argument in call to BLASTGetSeqLocFromStream
 *
 * Revision 1.20  2003/09/26 21:36:29  dondosha
 * Show results for all queries in multi-query case
 *
 * Revision 1.19  2003/09/26 15:42:23  dondosha
 * Added second argument to SetExtendWordMethod, so bit can be set or unset
 *
 * Revision 1.18  2003/09/11 17:46:16  camacho
 * Changed CBlastOption -> CBlastOptions
 *
 * Revision 1.17  2003/09/09 15:43:43  ucko
 * Fix #include directive for blast_input.hpp.
 *
 * Revision 1.16  2003/09/05 18:24:28  camacho
 * Restoring printing of SeqAlign, fix setting of default word extension method
 *
 * Revision 1.15  2003/08/28 23:17:20  camacho
 * Add processing of command-line options
 *
 * Revision 1.14  2003/08/19 20:36:44  dondosha
 * EProgram enum type is no longer part of CBlastOptions class
 *
 * Revision 1.13  2003/08/18 20:58:57  camacho
 * Added blast namespace, removed *__.hpp includes
 *
 * Revision 1.12  2003/08/18 17:07:42  camacho
 * Introduce new SSeqLoc structure (replaces pair<CSeq_loc, CScope>).
 * Change in function to read seqlocs from files.
 *
 * Revision 1.11  2003/08/15 16:03:00  dondosha
 * TSeqLoc and TSeqLocVector types no longer belong to class CBl2Seq, but are common to all BLAST applications
 *
 * Revision 1.10  2003/08/11 20:16:43  camacho
 * Change return type of BLASTGetSeqLocFromStream and fix namespaces
 *
 * Revision 1.9  2003/08/11 15:26:30  dondosha
 * BLASTGetSeqLocFromStream function moved to blast_input.cpp
 *
 * Revision 1.8  2003/08/08 20:46:08  camacho
 * Fix to use new ReadFasta arguments
 *
 * Revision 1.7  2003/08/08 20:24:31  dicuccio
 * Adjustments for Unix build: rename 'ncmimath' -> 'ncbi_math'; fix #include in demo app
 *
 * Revision 1.6  2003/08/01 22:38:31  camacho
 * Added conditional compilation to write seqaligns
 *
 * Revision 1.5  2003/07/30 16:33:31  madden
 * Remove C toolkit dependencies
 *
 * Revision 1.4  2003/07/16 20:25:34  camacho
 * Added dummy features argument to C formatter
 *
 * Revision 1.3  2003/07/14 21:53:32  camacho
 * Minor
 *
 * Revision 1.2  2003/07/11 21:22:57  camacho
 * Use same command line option as blast to display seqalign
 *
 * Revision 1.1  2003/07/10 18:35:58  camacho
 * Initial revision
 *
 * ===========================================================================
 */