C++ (Cpp) CGff2Record::GetAttribute Examples

Example #1

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
bool CGtfReader::x_FeatureSetDataCDS(
    const CGff2Record& record,
    CRef< CSeq_feat > pFeature )
//  ----------------------------------------------------------------------------
{
    if ( ! CGff2Reader::x_FeatureSetDataCDS( record, pFeature ) ) {
        return false;
    }

    CCdregion& cdr = pFeature->SetData().SetCdregion();
    string strValue;
    if ( record.GetAttribute( "protein_id", strValue ) ) {
        CRef<CSeq_id> pId = CReadUtil::AsSeqId(strValue,m_iFlags);
        if (pId->IsGenbank()) {
            pFeature->SetProduct().SetWhole(*pId);
        }
    }
    if ( record.GetAttribute( "ribosomal_slippage", strValue ) ) {
        pFeature->SetExcept( true );
        pFeature->SetExcept_text( "ribosomal slippage" );
    }
    if ( record.GetAttribute( "transl_table", strValue ) ) {
        CRef< CGenetic_code::C_E > pGc( new CGenetic_code::C_E );
        pGc->SetId( NStr::StringToUInt( strValue ) );
        cdr.SetCode().Set().push_back( pGc );
    }
    return true;
}

Example #2

//  ----------------------------------------------------------------------------
bool CGff3Reader::x_UpdateAnnot(
    const CGff2Record& record,
    CRef< CSeq_annot > pAnnot )
//  ----------------------------------------------------------------------------
{
    string gbkey;
    record.GetAttribute("gbkey", gbkey);
    CRef< CSeq_feat > pFeature(new CSeq_feat);

    //  Round trip info:
    CRef< CGb_qual > pQual( new CGb_qual );
    pQual->SetQual( "gff_source" );
    pQual->SetVal( record.Source() );
    pFeature->SetQual().push_back( pQual );

    pQual.Reset( new CGb_qual );
    pQual->SetQual( "gff_type" );
    pQual->SetVal( record.Type() );
    pFeature->SetQual().push_back( pQual );

    if ( record.IsSetScore() ) {
        pQual.Reset( new CGb_qual );
        pQual->SetQual( "gff_score" );
        pQual->SetVal( NStr::DoubleToString( record.Score() ) );
        pFeature->SetQual().push_back( pQual );
    }

    //  Special case: exon feature belonging to an RNA we have already seen
    if (record.Type() == "exon") {
        string parent;
        if (record.GetAttribute("Parent", parent)) {
            IdToFeatureMap::iterator it = m_MapIdToFeature.find(parent);
            if (it != m_MapIdToFeature.end()) {
                return record.UpdateFeature(m_iFlags, it->second);
            }
        }
    }

    //  Special case: Piece of another feature we have already seen
    string id;
    if (record.GetAttribute("ID", id)) {
        IdToFeatureMap::iterator it = m_MapIdToFeature.find(id);
        if (it != m_MapIdToFeature.end()) {
            return record.UpdateFeature(m_iFlags, it->second);
        }
    }

    //  General case: brand new regular feature
    if (!record.InitializeFeature(m_iFlags, pFeature)) {
        return false;
    }

    string strId;
    if ( record.GetAttribute( "ID", strId ) ) {
        m_MapIdToFeature[ strId ] = pFeature;
    }
    return x_AddFeatureToAnnot( pFeature, pAnnot );
}

Example #3

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
string s_GeneKey(
    const CGff2Record& gff )
//  ----------------------------------------------------------------------------
{
    string strGeneId;
    if ( ! gff.GetAttribute( "gene_id", strGeneId ) ) {
        cerr << "Unexpected: GTF feature without a gene_id." << endl;
        return "gene_id";
    }
    return strGeneId;
}

Example #4

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
string s_FeatureKey(
    const CGff2Record& gff )
//  ----------------------------------------------------------------------------
{
    string strGeneId = s_GeneKey( gff );
    if ( gff.Type() == "gene" ) {
        return strGeneId;
    }

    string strTranscriptId;
    if ( ! gff.GetAttribute( "transcript_id", strTranscriptId ) ) {
        cerr << "Unexpected: GTF feature without a transcript_id." << endl;
        strTranscriptId = "transcript_id";
    }

    return strGeneId + "|" + strTranscriptId;
}

Example #5

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
bool CGtfReader::x_CdsIsPartial(
    const CGff2Record& record )
//  ----------------------------------------------------------------------------
{
    string strPartial;
//    if ( record.Type() != "CDS" ) {
//        return false;
//    }
    if ( record.GetAttribute( "partial", strPartial ) ) {
        return true;
    }
    CRef< CSeq_feat > mRna;
    if ( ! x_FindParentMrna( record, mRna ) ) {
        return false;
    }
    return ( mRna->IsSetPartial() && mRna->GetPartial() );
}

Example #6

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
bool CGtfReader::x_FeatureSetDataMRNA(
    const CGff2Record& record,
    CRef<CSeq_feat> pFeature)
//  ----------------------------------------------------------------------------
{
    if ( ! CGff2Reader::x_FeatureSetDataRna( 
            record, pFeature, CSeqFeatData::eSubtype_mRNA)) {
        return false;
    }
    
    CRNA_ref& rna = pFeature->SetData().SetRna();

    string strValue;
    if (record.GetAttribute("product", strValue)) {
        rna.SetExt().SetName(strValue);
    }

    return true;
}

Example #7

File: gtf_reader.cpp Project: svn2github/ncbi_tk

//  ----------------------------------------------------------------------------
bool CGtfReader::x_FeatureSetDataGene(
    const CGff2Record& record,
    CRef< CSeq_feat > pFeature )
//  ----------------------------------------------------------------------------
{
    if ( ! CGff2Reader::x_FeatureSetDataGene( record, pFeature ) ) {
        return false;
    }

    CGene_ref& gene = pFeature->SetData().SetGene();

    string strValue;
    if ( record.GetAttribute( "gene_synonym", strValue ) ) {
        gene.SetSyn().push_back( strValue );
    }
    //  mss-399: do -not- use gene_id for /gene_syn or /gene:
    //if ( record.GetAttribute( "gene_id", strValue ) ) {
    //    gene.SetSyn().push_front( strValue );
    //}
    return true;
}