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
