// ----------------------------------------------------------------------------
bool CGtfReader::xFeatureSetQualifiersGene(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
//
// Create GB qualifiers for the record attributes:
//
CRef< CGb_qual > pQual(0);
const CGff2Record::TAttributes& attrs = record.Attributes();
CGff2Record::TAttrCit it = attrs.begin();
for (/*NOOP*/; it != attrs.end(); ++it) {
// gtf genes don't get transcript_id
if (it->first == "transcript_id") {
continue;
}
// special case some well-known attributes
if (x_ProcessQualifierSpecialCase(it, pFeature)) {
continue;
}
// turn everything else into a qualifier
pQual.Reset(new CGb_qual);
pQual->SetQual(it->first);
pQual->SetVal(it->second);
pFeature->SetQual().push_back(pQual);
}
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 );
}
// ----------------------------------------------------------------------------
bool CGtfReader::x_ProcessQualifierSpecialCase(
CGff2Record::TAttrCit it,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
CRef<CGb_qual> pQual(0);
if (0 == NStr::CompareNocase(it->first, "exon_id")) {
return true;
}
if (0 == NStr::CompareNocase(it->first, "exon_number")) {
return true;
}
if ( 0 == NStr::CompareNocase( it->first, "note" ) ) {
pFeature->SetComment( it->second );
return true;
}
if ( 0 == NStr::CompareNocase( it->first, "dbxref" ) ||
0 == NStr::CompareNocase( it->first, "db_xref" ) )
{
vector< string > tags;
NStr::Split( it->second, ";", tags );
for ( vector<string>::iterator it = tags.begin();
it != tags.end(); ++it ) {
pFeature->SetDbxref().push_back( x_ParseDbtag( *it ) );
}
return true;
}
if ( 0 == NStr::CompareNocase( it->first, "pseudo" ) ) {
pFeature->SetPseudo( true );
return true;
}
if ( 0 == NStr::CompareNocase( it->first, "partial" ) ) {
pFeature->SetPartial( true );
return true;
}
//if (0 == NStr::CompareNocase(it->first, "protein_id")) {
// if (pFeature->IsSetProduct()) {
// return true;
// }
//}
return false;
}
