// ============================================================================
bool CGtfRecord::x_FeatureToPartial(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetPartial() && mapped_feature.GetPartial() ) {
return true;
}
return false;
}
// ============================================================================
string CGtfRecord::x_CdsToProteinId(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetProduct() ) {
return mapped_feature.GetProduct().GetId()->GetSeqIdString( true );
}
return "";
}
// ============================================================================
string CGtfRecord::x_FeatureToNote(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetComment() ) {
return mapped_feature.GetComment();
}
return "";
}
// ============================================================================
bool CGtfRecord::x_CdsToRibosomalSlippage(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetExcept_text() ) {
if ( mapped_feature.GetExcept_text() == "ribosomal slippage" ) {
return true;
}
}
return false;
}
// =============================================================================
string CGtfRecord::x_MrnaToTranscriptId(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetProduct() ) {
return mapped_feature.GetProduct().GetId()->GetSeqIdString( true );
}
else {
return x_GenericTranscriptId( mapped_feature );
}
}
CAnnotCompare::TCompareFlags
CAnnotCompare::CompareFeats(const CMappedFeat& feat1,
CScope& scope1,
const CMappedFeat& feat2,
CScope& scope2,
vector<ECompareFlags>* complex_flags,
list<string>* comments)
{
return CompareFeats(feat1.GetOriginalFeature(),
feat1.GetLocation(), scope1,
feat2.GetOriginalFeature(),
feat2.GetLocation(), scope2,
complex_flags, comments);
}
// ----------------------------------------------------------------------------
bool CGtfRecord::x_AssignAttributesFromAsnCore(
CMappedFeat mapped_feature )
// ----------------------------------------------------------------------------
{
const CSeq_feat& feature = mapped_feature.GetOriginalFeature();
if ( feature.CanGetQual() ) {
const vector< CRef< CGb_qual > >& quals = feature.GetQual();
vector< CRef< CGb_qual > >::const_iterator it = quals.begin();
for ( /*NOOP*/; it != quals.end(); ++it ) {
if ( (*it)->CanGetQual() && (*it)->CanGetVal() ) {
if ( (*it)->GetQual() == "ID" ) {
continue;
}
if ( (*it)->GetQual() == "Parent" ) {
continue;
}
if ( (*it)->GetQual() == "gff_type" ) {
continue;
}
if ( (*it)->GetQual() == "transcript_id" ) {
continue;
}
if ( (*it)->GetQual() == "gene_id" ) {
continue;
}
SetAttribute((*it)->GetQual(), (*it)->GetVal());
}
}
}
return true;
}
// ============================================================================
string CGtfRecord::x_FeatureToDbxref(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( mapped_feature.IsSetDbxref() ) {
const CSeq_feat::TDbxref& dbxrefs = mapped_feature.GetDbxref();
if ( dbxrefs.size() > 0 ) {
string value = s_GtfDbtag( *dbxrefs[ 0 ] );
for ( size_t i=1; i < dbxrefs.size(); ++i ) {
value += ";";
value += s_GtfDbtag( *dbxrefs[ i ] );
}
return value;
}
}
return "";
}
// ============================================================================
string CGtfRecord::x_MrnaToProduct(
CMappedFeat mapped_feature )
// ============================================================================
{
const CRNA_ref& rna = mapped_feature.GetData().GetRna();
if ( rna.IsSetExt() && rna.GetExt().IsName() ) {
return rna.GetExt().GetName();
}
return "";
}
// ============================================================================
string CGtfRecord::x_CdsToCode(
CMappedFeat mapped_feature )
// ============================================================================
{
const CCdregion& cdr = mapped_feature.GetData().GetCdregion();
if ( cdr.IsSetCode() ) {
return NStr::IntToString( cdr.GetCode().GetId() );
}
return "";
}
// ============================================================================
string CGtfRecord::x_CdsToProduct(
CMappedFeat mapped_feature )
// ============================================================================
{
if ( ! mapped_feature.IsSetXref() ) {
return "";
}
const vector< CRef< CSeqFeatXref > > xref = mapped_feature.GetXref();
vector< CRef< CSeqFeatXref > >::const_iterator it = xref.begin();
for ( ; it != xref.end(); ++it ) {
const CSeqFeatXref& ref = **it;
if ( ref.IsSetData() && ref.GetData().IsProt() &&
ref.GetData().GetProt().IsSetName() )
{
return ref.GetData().GetProt().GetName().front();
}
}
return "";
}
// ============================================================================
string CGtfRecord::x_GenericTranscriptId(
CMappedFeat mapped_feat )
// ============================================================================
{
static unsigned int uId = 1;
string strTranscriptId = string( "unknown_transcript_" ) +
NStr::UIntToString( uId );
if ( mapped_feat.GetData().GetSubtype() == CSeq_feat::TData::eSubtype_cdregion ) {
uId++;
}
return strTranscriptId;
}
// ============================================================================
string CGtfRecord::x_GenericGeneId(
CMappedFeat mapped_feat )
// ============================================================================
{
static unsigned int uId = 1;
string strGeneId = string( "unknown_gene_" ) +
NStr::UIntToString( uId );
if ( mapped_feat.GetData().GetSubtype() == CSeq_feat::TData::eSubtype_gene ) {
uId++;
}
return strGeneId;
}
// ============================================================================
string CGtfRecord::x_GeneToGeneId(
CMappedFeat mapped_feature )
// ============================================================================
{
const CGene_ref& gene = mapped_feature.GetData().GetGene();
if ( gene.IsSetLocus_tag() ) {
return gene.GetLocus_tag();
}
if ( gene.IsSetSyn() ) {
return gene.GetSyn().front();
}
return x_GenericGeneId( mapped_feature );
}
// ============================================================================
string CGtfRecord::x_GeneToGeneSyn(
CMappedFeat mapped_feature )
// ============================================================================
{
const CGene_ref& gene = mapped_feature.GetData().GetGene();
if ( ! gene.IsSetSyn() ) {
return "";
}
if ( gene.IsSetLocus_tag() ) {
return gene.GetSyn().front();
}
CGene_ref::TSyn::const_iterator it = gene.GetSyn().begin();
++it;
if ( it != gene.GetSyn().end() ) {
return *it;
}
return "";
}
// ----------------------------------------------------------------------------
bool CGtfRecord::x_AssignAttributesFromAsnExtended(
CMappedFeat mapped_feature )
// ----------------------------------------------------------------------------
{
const CSeq_feat& feature = mapped_feature.GetOriginalFeature();
string strDbxref = x_FeatureToDbxref( mapped_feature );
if ( ! strDbxref.empty() ) {
SetAttribute("db_xref", strDbxref);
}
string strNote = x_FeatureToNote( mapped_feature );
if ( ! strNote.empty() ) {
SetAttribute("note", strNote);
}
if ( x_FeatureToPseudo( mapped_feature ) ) {
SetAttribute("pseudo", "");
}
if ( x_FeatureToPartial( mapped_feature ) ) {
SetAttribute("partial", "");
}
switch ( feature.GetData().GetSubtype() ) {
default:
break;
case CSeq_feat::TData::eSubtype_cdregion: {
m_strGeneId = x_CdsToGeneId( mapped_feature );
m_strTranscriptId = x_CdsToTranscriptId( mapped_feature );
string strProteinId = x_CdsToProteinId( mapped_feature );
if ( ! strProteinId.empty() ) {
SetAttribute("protein_id", strProteinId);
}
if ( x_CdsToRibosomalSlippage( mapped_feature ) ) {
SetAttribute("ribosomal_slippage", "");
}
string strProduct = x_CdsToProduct( mapped_feature );
if ( ! strProduct.empty() ) {
SetAttribute("product", strProduct);
}
string strCode = x_CdsToCode( mapped_feature );
if ( ! strCode.empty() ) {
SetAttribute("transl_table", strCode);
}
}
break;
case CSeq_feat::TData::eSubtype_mRNA: {
m_strGeneId = x_MrnaToGeneId( mapped_feature );
m_strTranscriptId = x_MrnaToTranscriptId( mapped_feature );
string strProduct = x_MrnaToProduct( mapped_feature );
if ( ! strProduct.empty() ) {
SetAttribute("product", strProduct);
}
}
break;
case CSeq_feat::TData::eSubtype_gene: {
m_strGeneId = x_GeneToGeneId( mapped_feature );
string strGeneSyn = x_GeneToGeneSyn( mapped_feature );
if ( ! strGeneSyn.empty() ) {
SetAttribute("gene_synonym", strGeneSyn);
}
}
break;
}
return true;
}
