process_gene_overlap.hpp

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/*  $Id: process_gene_overlap.hpp 91317 2020-10-08 18:29:47Z 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
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*  warranties of performance, merchantability or fitness for any particular
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* Author:
*
* File Description:
*
* ===========================================================================
*/
 
#ifndef __process_gene_overlap__hpp__
#define __process_gene_overlap__hpp__
 
//  ============================================================================
class CGeneOverlapProcess
//  ============================================================================
    : public CScopedProcess
{
public:
    //  ------------------------------------------------------------------------
    CGeneOverlapProcess()
    //  ------------------------------------------------------------------------
        : CScopedProcess()
        , m_out( 0 )
    {};
 
    //  ------------------------------------------------------------------------
    ~CGeneOverlapProcess()
    //  ------------------------------------------------------------------------
    {
    };
 
    //  ------------------------------------------------------------------------
    void ProcessInitialize(
        const CArgs& args )
    //  ------------------------------------------------------------------------
    {
        CScopedProcess::ProcessInitialize( args );
 
        m_out = args["o"] ? &(args["o"].AsOutputFile()) : &cout;
    };
 
    //  ------------------------------------------------------------------------
    void ProcessFinalize()
    //  ------------------------------------------------------------------------
    {
    }
 
    //  ------------------------------------------------------------------------
    virtual void SeqEntryInitialize(
        CRef<CSeq_entry>& se )
    //  ------------------------------------------------------------------------
    {
        CScopedProcess::SeqEntryInitialize( se );
    };
 
    //  ------------------------------------------------------------------------
    void SeqEntryProcess()
    //  ------------------------------------------------------------------------
    {
        try {
            VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY (bit, *m_entry) {
                const CBioseq& bioseq = *bit;
                if (bioseq.IsSetInst()) {
                    const CSeq_inst& inst = bioseq.GetInst();
                    if (inst.IsSetMol()) {
                        TSEQ_MOL mol = inst.GetMol();
                        if (mol == CSeq_inst::eMol_aa) {
                            continue;
                        }
                    }
                }
 
                CBioseq_Handle bsh = m_scope->GetBioseqHandle(bioseq);
                SAnnotSelector sel;
                sel.SetLimitTSE(bsh.GetTSE_Handle());
                sel.SetResolveDepth(0);
 
                for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) {
                    const CMappedFeat mf = *feat_it;
                    const CSeq_feat& feat = mf.GetOriginalFeature();
                    TestFeatureGeneOverlap( feat );
                    ++m_objectcount;
                }
 
                /*
                FOR_EACH_SEQANNOT_ON_BIOSEQ ( ait, bioseq ) {
                    const CSeq_annot& annot = **ait;
                    FOR_EACH_SEQFEAT_ON_SEQANNOT ( fit, annot ) {
                        const CSeq_feat& feat = **fit;
                        TestFeatureGeneOverlap( feat );
                        ++m_objectcount;
                    }
                }
                VISIT_ALL_FEATURES_WITHIN_SEQENTRY (fit, *m_entry) {
                    const CSeq_feat& feat = *fit;
                    TestFeatureGeneOverlap( feat );
                    ++m_objectcount;
                }
                */
            }
        }
        catch (CException& e) {
            ERR_POST(Error << "error processing seqentry: " << e.what());
        }
    };
 
protected:
    //  ------------------------------------------------------------------------
    void TestFeatureGeneOverlap (
        const CSeq_feat& f )
    //  ------------------------------------------------------------------------
    {
        if ( f.GetData().Which() == CSeqFeatData::e_Gene ) {
            return;
        }
        ++m_objectcount;
        const CSeq_feat_Base::TLocation& locbase = f.GetLocation();
        CConstRef<CSeq_feat> ol = sequence::GetOverlappingGene( 
            locbase, *m_scope );
        if ( ! ol ) {
            return;
        }
        const CGene_ref& gene = ol->GetData().GetGene();
        if (gene.IsSetLocus()) {
            *m_out << "Gene locus " << gene.GetLocus() << endl;
        }
        if (gene.IsSetLocus_tag()) {
            *m_out << "Gene locus_tag " << gene.GetLocus_tag() << endl;
        }
        /*
        *m_out << SeqLocString( locbase ) << " -> " 
               << SeqLocString( ol->GetLocation() ) << endl;
        */
    }
 
    //  ------------------------------------------------------------------------
    string SeqLocString( const CSeq_loc& loc )
    //  ------------------------------------------------------------------------
    {
        string str;
        loc.GetLabel(&str);
        return str;
    }
 
    //  ------------------------------------------------------------------------
    //  Data:
    //  ------------------------------------------------------------------------
protected:
    CNcbiOstream* m_out;
};
 
//  ============================================================================
class CGeneFeatTreeProcess
//  ============================================================================
    : public CScopedProcess
{
public:
    //  ------------------------------------------------------------------------
    CGeneFeatTreeProcess()
    //  ------------------------------------------------------------------------
        : CScopedProcess()
        , m_out( 0 )
    {};
 
    //  ------------------------------------------------------------------------
    ~CGeneFeatTreeProcess()
    //  ------------------------------------------------------------------------
    {
    };
 
    //  ------------------------------------------------------------------------
    void ProcessInitialize(
        const CArgs& args )
    //  ------------------------------------------------------------------------
    {
        CScopedProcess::ProcessInitialize( args );
 
        m_out = args["o"] ? &(args["o"].AsOutputFile()) : &cout;
    };
 
    //  ------------------------------------------------------------------------
    void ProcessFinalize()
    //  ------------------------------------------------------------------------
    {
    }
 
    //  ------------------------------------------------------------------------
    virtual void SeqEntryInitialize(
        CRef<CSeq_entry>& se )
    //  ------------------------------------------------------------------------
    {
        CScopedProcess::SeqEntryInitialize( se );
    };
 
    //  ------------------------------------------------------------------------
    void SeqEntryProcess()
    //  ------------------------------------------------------------------------
    {
        try {
            VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY (bit, *m_entry) {
                const CBioseq& bioseq = *bit;
                if (bioseq.IsSetInst()) {
                    const CSeq_inst& inst = bioseq.GetInst();
                    if (inst.IsSetMol()) {
                        TSEQ_MOL mol = inst.GetMol();
                        if (mol == CSeq_inst::eMol_aa) {
                            continue;
                        }
                    }
                }
 
                CBioseq_Handle bsh = m_scope->GetBioseqHandle(bioseq);
                SAnnotSelector sel;
                sel.SetLimitTSE(bsh.GetTSE_Handle());
                sel.SetResolveDepth(0);
 
                for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) {
                    const CMappedFeat mf = *feat_it;
                    m_featTree.AddFeature(mf);
                }
 
                for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) {
                    const CMappedFeat mf = *feat_it;
                    TestFeatureGeneTree( mf );
                    ++m_objectcount;
                }
            }
        }
        catch (CException& e) {
            ERR_POST(Error << "error processing seqentry: " << e.what());
        }
    };
 
protected:
    //  ------------------------------------------------------------------------
    void TestFeatureGeneTree (
        const CMappedFeat mf )
    //  ------------------------------------------------------------------------
    {
        if ( mf.GetData().GetSubtype() == CSeqFeatData::eSubtype_gene ) {
            return;
        }
        ++m_objectcount;
        CMappedFeat best = feature::GetBestGeneForFeat(mf, &m_featTree);
        if (best) {
            const CGene_ref& gene = best.GetData().GetGene();
            if (gene.IsSetLocus()) {
                *m_out << "Gene locus " << gene.GetLocus() << endl;
            }
            if (gene.IsSetLocus_tag()) {
                *m_out << "Gene locus_tag " << gene.GetLocus_tag() << endl;
            }
        }
    }
 
    //  ------------------------------------------------------------------------
    string SeqLocString( const CSeq_loc& loc )
    //  ------------------------------------------------------------------------
    {
        string str;
        loc.GetLabel(&str);
        return str;
    }
 
    //  ------------------------------------------------------------------------
    //  Data:
    //  ------------------------------------------------------------------------
protected:
    CNcbiOstream* m_out;
    feature::CFeatTree m_featTree;
};
 
#endif