def generate_codon_change_from_vc(self, t, start, end, vc): """ :param t: (Transcript) :param start: (int) :param end: (int) :param vc: (VariantClassification) :return: """ dist_from_exon = self._get_splice_site_coordinates(t, start, end, vc.get_exon_i()) exon_i = vc.get_exon_i() if vc.get_vc() == VariantClassification.SPLICE_SITE and vc.get_secondary_vc() == VariantClassification.INTRON: return TranscriptProviderUtils.render_intronic_splice_site_codon_change(dist_from_exon, exon_i) if vc.get_ref_codon_start_in_exon() == "" or vc.get_ref_codon_end_in_exon() == "": return "" codon_position_start_cds_space = int(vc.get_ref_codon_start_in_exon()) - int(vc.get_cds_start_in_exon_space())+1 codon_position_end_cds_space = int(vc.get_ref_codon_end_in_exon()) - int(vc.get_cds_start_in_exon_space())+1 ref_codon_seq = vc.get_ref_codon() alt_codon_seq = vc.get_alt_codon() result = TranscriptProviderUtils.render_codon_change(vc.get_vt(), vc.get_vc(), int(codon_position_start_cds_space), int(codon_position_end_cds_space), ref_codon_seq, alt_codon_seq, dist_from_exon, exon_i, vc.get_secondary_vc()) return result
def generate_codon_change_from_vc(self, t, start, end, vc): """ :param t: (Transcript) :param start: (int) :param end: (int) :param vc: (VariantClassification) :return: """ dist_from_exon = self._get_splice_site_coordinates( t, start, end, vc.get_exon_i()) exon_i = vc.get_exon_i() if vc.get_vc( ) == VariantClassification.SPLICE_SITE and vc.get_secondary_vc( ) == VariantClassification.INTRON: return TranscriptProviderUtils.render_intronic_splice_site_codon_change( dist_from_exon, exon_i) if vc.get_ref_codon_start_in_exon( ) == "" or vc.get_ref_codon_end_in_exon() == "": return "" codon_position_start_cds_space = int( vc.get_ref_codon_start_in_exon()) - int( vc.get_cds_start_in_exon_space()) + 1 codon_position_end_cds_space = int( vc.get_ref_codon_end_in_exon()) - int( vc.get_cds_start_in_exon_space()) + 1 ref_codon_seq = vc.get_ref_codon() alt_codon_seq = vc.get_alt_codon() result = TranscriptProviderUtils.render_codon_change( vc.get_vt(), vc.get_vc(), int(codon_position_start_cds_space), int(codon_position_end_cds_space), ref_codon_seq, alt_codon_seq, dist_from_exon, exon_i, vc.get_secondary_vc()) return result