// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
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 );
}
// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
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() );
}
// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
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;
}