// ----------------------------------------------------------------------------
bool CGtfReader::x_CreateFeatureLocation(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
CRef<CSeq_id> pId = CReadUtil::AsSeqId(
record.Id(), m_iFlags & fAllIdsAsLocal);
CSeq_interval& location = pFeature->SetLocation().SetInt();
location.SetId( *pId );
location.SetFrom( record.SeqStart() );
if (record.Type() != "mRNA") {
location.SetTo(record.SeqStop());
}
else {
// place holder
// actual location will be computed from the exons and CDSs living on
// this feature.
location.SetTo(record.SeqStart());
}
if ( record.IsSetStrand() ) {
location.SetStrand( record.Strand() );
}
return true;
}
// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
bool CGtfReader::x_MergeFeatureLocationMultiInterval(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
CRef<CSeq_id> pId = CReadUtil::AsSeqId(
record.Id(), m_iFlags & fAllIdsAsLocal);
CRef< CSeq_loc > pLocation( new CSeq_loc );
pLocation->SetInt().SetId( *pId );
pLocation->SetInt().SetFrom( record.SeqStart() );
pLocation->SetInt().SetTo( record.SeqStop() );
if ( record.IsSetStrand() ) {
pLocation->SetInt().SetStrand( record.Strand() );
}
pLocation = pLocation->Add(
pFeature->SetLocation(), CSeq_loc::fSortAndMerge_All, 0 );
pFeature->SetLocation( *pLocation );
return true;
}
// ----------------------------------------------------------------------------
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;
}