コード例 #1
0
//  ----------------------------------------------------------------------------
bool CGff3Reader::x_UpdateFeatureCds(
    const CGff2Record& gff,
    CRef<CSeq_feat> pFeature)
//  ----------------------------------------------------------------------------
{
    CRef<CSeq_feat> pAdd = CRef<CSeq_feat>(new CSeq_feat);
    if (!x_FeatureSetLocation(gff, pAdd)) {
        return false;
    }
    pFeature->SetLocation().Add(pAdd->GetLocation());
    return true;
}
コード例 #2
0
ファイル: gtf_reader.cpp プロジェクト: svn2github/ncbi_tk
//  ----------------------------------------------------------------------------
bool CGtfReader::x_MergeFeatureLocationSingleInterval(
    const CGff2Record& record,
    CRef< CSeq_feat > pFeature )
//  ----------------------------------------------------------------------------
{
    const CSeq_interval& gene_int = pFeature->GetLocation().GetInt();
    if ( gene_int.GetFrom() > record.SeqStart() -1 ) {
        pFeature->SetLocation().SetInt().SetFrom( record.SeqStart() );
    }
    if ( gene_int.GetTo() < record.SeqStop() - 1 ) {
        pFeature->SetLocation().SetInt().SetTo( record.SeqStop() );
    }
    if (record.Type() == "CDS"  &&  pFeature->GetData().IsCdregion()) {
        return x_FeatureTrimQualifiers(record, pFeature);
    }
    return true;
}
コード例 #3
0
ファイル: gtf_reader.cpp プロジェクト: svn2github/ncbi_tk
//  ----------------------------------------------------------------------------
bool CGtfReader::x_UpdateAnnotCds(
    const CGff2Record& gff,
    CRef< CSeq_annot > pAnnot )
//  ----------------------------------------------------------------------------
{
    //
    // If there is no gene feature to go with this CDS then make one. Otherwise,
    //  make sure the existing gene feature includes the location of the CDS.
    //
    CRef< CSeq_feat > pGene;
    if ( ! x_FindParentGene( gff, pGene ) ) {
        if ( ! x_CreateParentGene( gff, pAnnot ) ) {
            return false;
        }
    }
    else {
        if ( ! x_MergeParentGene( gff, pGene ) ) {
            return false;
        }
    }
    
    //
    // If there is no CDS feature with this gene_id|transcript_id then make one.
    //  Otherwise, fix up the location of the existing one.
    //
    CRef< CSeq_feat > pCds;
    if ( ! x_FindParentCds( gff, pCds ) ) {
        //
        // Create a brand new CDS feature:
        //
        if ( ! x_CreateParentCds( gff, pAnnot ) ) {
            return false;
        }
        x_FindParentCds( gff, pCds );
    }
    else {
        //
        // Update an already existing CDS features:
        //
        if ( ! x_MergeFeatureLocationMultiInterval( gff, pCds ) ) {
            return false;
        }
        if (!x_FeatureTrimQualifiers(gff, pCds)) {
            return false;
        }
    }

    if ( x_CdsIsPartial( gff ) ) {
        CRef<CSeq_feat> pParent;
        if ( x_FindParentMrna( gff, pParent ) ) {
            CSeq_loc& loc = pCds->SetLocation();
            size_t uCdsStart = gff.SeqStart();
            size_t uMrnaStart = pParent->GetLocation().GetStart( eExtreme_Positional );
            if ( uCdsStart == uMrnaStart ) {
                loc.SetPartialStart( true, eExtreme_Positional );
//                cerr << "fuzzed down: " << gff.SeqStart() << "  " << gff.SeqStop() << " vs. " << uMrnaStart << endl;
            }

            size_t uCdsStop =  gff.SeqStop();
            size_t uMrnaStop = pParent->GetLocation().GetStop( eExtreme_Positional );
            if ( uCdsStop == uMrnaStop  && gff.Type() != "stop_codon" ) {
                loc.SetPartialStop( true, eExtreme_Positional );
//                cerr << "fuzzed up  : " << gff.SeqStart() << "  " << gff.SeqStop() << " vs. " << uMrnaStop << endl;
            }
        }
    }
    return true;
}