blast_sample.cpp

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/*  $Id: blast_sample.cpp 90001 2020-05-04 12:53:02Z ivanov $
 * ===========================================================================
 *
 *                            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:  Christiam Camacho
 *
 * File Description:
 *   Demo of using the CBl2Seq class to compare two sequences using the BLAST
 *   algorithm
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
 
// Objects includes
#include <objects/seqloc/Seq_loc.hpp>
 
// Object Manager includes
#include <objtools/simple/simple_om.hpp>
 
// BLAST includes
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/sseqloc.hpp>
 
USING_NCBI_SCOPE;
USING_SCOPE(objects);
 
 
/////////////////////////////////////////////////////////////////////////////
//  CBlastSampleApplication::
 
class CBlastSampleApplication : public CNcbiApplication
{
private:
    virtual void Init(void);
    virtual int  Run(void);
    virtual void Exit(void);
 
    enum ESeqType {
        eQuery,
        eSubject
    };
    blast::SSeqLoc* x_CreateSSeqLoc(ESeqType st);
};
 
 
blast::SSeqLoc*
CBlastSampleApplication::x_CreateSSeqLoc(CBlastSampleApplication::ESeqType st)
{
    // Get the gi
    TGi gi;
    if (st == eQuery) {
        gi = GI_FROM(TIntId, GetArgs()["query"].AsIntId());
    } else {
        gi = GI_FROM(TIntId, GetArgs()["subject"].AsIntId());
    }
    CRef<CSeq_loc> seqloc(new CSeq_loc);
    seqloc->SetWhole().SetGi(gi);
 
    // Setup the scope
    CRef<CScope> scope(CSimpleOM::NewScope());
 
    return new blast::SSeqLoc(seqloc, scope);
}
 
 
/////////////////////////////////////////////////////////////////////////////
//  Init test for all different types of arguments
 
void CBlastSampleApplication::Init(void)
{
    HideStdArgs(fHideLogfile | fHideConffile | fHideFullVersion | fHideXmlHelp | fHideVersion);
 
    // Create command-line argument descriptions class
    unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
 
    // Specify USAGE context
    arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
      "CBl2Seq demo to compare 2 sequences using BLAST");
 
    // Program type
    arg_desc->AddKey("program", "p", "Type of BLAST program", CArgDescriptions::eString);
    arg_desc->SetConstraint
        ("program", &(*new CArgAllow_Strings, 
                "blastp", "blastn", "blastx", "tblastn", "tblastx"));
 
    // Identifier for the query sequence
    arg_desc->AddKey("query", "QuerySequenceID", 
                    "GI of the query sequence",
                    CArgDescriptions::eIntId);
 
    // Identifier for the subject sequence
    arg_desc->AddKey("subject", "SubjectSequenceID", 
                     "GI of the subject sequence",
                     CArgDescriptions::eIntId);
 
    // Output file
    arg_desc->AddDefaultKey("out", "OutputFile", 
        "File name for writing the Seq-align results in ASN.1 form",
        CArgDescriptions::eOutputFile, "-", CArgDescriptions::fPreOpen);
 
    // Setup arg.descriptions for this application
    SetupArgDescriptions(arg_desc.release());
}
 
 
 
/////////////////////////////////////////////////////////////////////////////
//  Run demo
 
int CBlastSampleApplication::Run(void)
{
    int retval = 0;
    try {
        // Obtain the query, subject, and program from command line
        // arguments...
        unique_ptr<blast::SSeqLoc> query(x_CreateSSeqLoc(eQuery));
        unique_ptr<blast::SSeqLoc> subject(x_CreateSSeqLoc(eSubject));
        blast::EProgram program = blast::ProgramNameToEnum(GetArgs()["program"].AsString());
 
        /// ... and BLAST the sequences!
        blast::CBl2Seq blaster(*query, *subject, program);
        blast::TSeqAlignVector alignments = blaster.Run();
 
        /// Display the alignments in text ASN.1
        CNcbiOstream& out = GetArgs()["out"].AsOutputFile();
        for (const auto& it : alignments)
            out << MSerial_AsnText << *it;
 
    } catch (const CException& e) {
        ERR_POST(e);
        retval = 1;
    }
 
    return retval;
}
 
 
/////////////////////////////////////////////////////////////////////////////
//  Cleanup
 
void CBlastSampleApplication::Exit(void)
{
    // Do your after-Run() cleanup here
}
 
 
/////////////////////////////////////////////////////////////////////////////
//  MAIN
 
#ifndef SKIP_DOXYGEN_PROCESSING
int NcbiSys_main(int argc, ncbi::TXChar* argv[])
{
    // Execute main application function
    return CBlastSampleApplication().AppMain(argc, argv);
}
#endif /* SKIP_DOXYGEN_PROCESSING */