def test_mutate_reference_seqeunce(self, vt, start, end, ref, alt, start_exon_space, end_exon_space, mutated_seq_gt):
""" Test that we can render a mutated sequence with SNP, INS, and DEL
"""
# mutated_seq_gt is stranded and this is a "-" transcript
tx = self.retrieve_test_transcript_MAPK1()
observed_allele = Bio.Seq.reverse_complement(alt)
mutated_allele = TranscriptProviderUtils.mutate_reference_sequence(tx.get_seq()[start_exon_space : end_exon_space+1], start_exon_space, start_exon_space, end_exon_space, observed_allele, vt)
self.assertTrue(mutated_seq_gt == mutated_allele, "No match (gt/guess) %s/%s for %s." % (mutated_seq_gt, mutated_allele, str([vt, start, end, ref, alt, start_exon_space, end_exon_space, mutated_seq_gt])))
def _determine_de_novo_old(self, vc, transcript_position_start,
transcript_position_end, ref, alt, tx,
variant_type):
"""Returns input vc if not de Novo. Otherwise, returns updated variant classification.
:param vc: Current variant classification. Note that if this is not 5'UTR, this method will just return this input.
:param transcript_position_start:
:param transcript_position_end:
:param ref: (str) Does not take into account strandedness (e.g. m.ref_allele)
:param alt: (str) Does not take into account strandedness (e.g. m.alt_allele)
:param tx: transcript
:param variant_type:
Will always return original vc if the vc is not None."""
result = vc
if vc == VariantClassification.FIVE_PRIME_UTR and ref != alt:
observed_allele_stranded = self._determine_stranded_allele(
alt, tx.get_strand())
reference_allele_stranded = self._determine_stranded_allele(
ref, tx.get_strand())
tx_seq = tx.get_seq()
if variant_type == VariantClassification.VT_INS:
if tx.get_strand() == "-":
transcript_position_start = transcript_position_end
else:
transcript_position_end = transcript_position_start
utr_region_start, utr_region_end = transcript_position_start - 2, transcript_position_end + 2
# TODO: This may not work for "+" strand. Need unit test.
utr_region_seq = tx_seq[utr_region_start:utr_region_end + 1]
mutated_utr_region_seq = TranscriptProviderUtils.mutate_reference_sequence(
utr_region_seq, utr_region_start, transcript_position_start,
transcript_position_end, observed_allele_stranded,
variant_type)
# Check for Denovo
ATG_position = mutated_utr_region_seq.find('ATG')
if ATG_position > -1:
cds_start_in_exon_space, cds_end_in_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(
tx)
ATG_position = utr_region_start + ATG_position + 1
if (cds_start_in_exon_space - ATG_position) % 3 == 0:
frameness = 'InFrame'
else:
frameness = 'OutOfFrame'
result = 'De_novo_Start_' + frameness
return result
def _determine_de_novo_old(self, vc, transcript_position_start, transcript_position_end, ref, alt, tx, variant_type):
"""Returns input vc if not de Novo. Otherwise, returns updated variant classification.
:param vc: Current variant classification. Note that if this is not 5'UTR, this method will just return this input.
:param transcript_position_start:
:param transcript_position_end:
:param ref: (str) Does not take into account strandedness (e.g. m.ref_allele)
:param alt: (str) Does not take into account strandedness (e.g. m.alt_allele)
:param tx: transcript
:param variant_type:
Will always return original vc if the vc is not None."""
result = vc
if vc == VariantClassification.FIVE_PRIME_UTR and ref != alt:
observed_allele_stranded = self._determine_stranded_allele(alt, tx.get_strand())
reference_allele_stranded = self._determine_stranded_allele(ref, tx.get_strand())
tx_seq = tx.get_seq()
if variant_type == VariantClassification.VT_INS:
if tx.get_strand() == "-":
transcript_position_start = transcript_position_end
else:
transcript_position_end = transcript_position_start
utr_region_start, utr_region_end = transcript_position_start-2, transcript_position_end+2
# TODO: This may not work for "+" strand. Need unit test.
utr_region_seq = tx_seq[utr_region_start:utr_region_end+1]
mutated_utr_region_seq = TranscriptProviderUtils.mutate_reference_sequence(utr_region_seq, utr_region_start,
transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)
# Check for Denovo
ATG_position = mutated_utr_region_seq.find('ATG')
if ATG_position > -1:
cds_start_in_exon_space, cds_end_in_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
ATG_position = utr_region_start + ATG_position + 1
if (cds_start_in_exon_space - ATG_position) % 3 == 0:
frameness = 'InFrame'
else:
frameness = 'OutOfFrame'
result = 'De_novo_Start_' + frameness
return result
def _determine_vc_for_cds_overlap(self, start, end, ref_allele, alt_allele, is_frameshift_indel, is_splice_site, tx, variant_type, is_start_codon):
"""
Note: This method can also handle start and stop codons.
:param start:
:param end:
:param ref_allele:
:param alt_allele:
:param is_frameshift_indel:
:param is_splice_site:
:param tx:
:param variant_type:
:return:
"""
observed_allele_stranded, reference_allele_stranded = self._get_stranded_alleles(ref_allele, alt_allele, tx)
transcript_position_start, transcript_position_end = TranscriptProviderUtils.convert_genomic_space_to_exon_space(
start, end, tx)
if tx.get_strand() == "+" and not variant_type == VariantClassification.VT_INS:
transcript_position_start -= 1
transcript_position_end -= 1
transcript_seq = tx.get_seq()
protein_seq = tx.get_protein_seq()
cds_start, cds_stop = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
protein_position_start, protein_position_end = TranscriptProviderUtils.get_protein_positions(
transcript_position_start,
transcript_position_end, cds_start)
new_ref_transcript_seq = transcript_seq
if (transcript_seq[transcript_position_start:transcript_position_end+1] != reference_allele_stranded) and variant_type != VariantClassification.VT_INS:
new_ref_transcript_seq = list(transcript_seq)
new_ref_transcript_seq[transcript_position_start:transcript_position_end+1] = reference_allele_stranded
new_ref_transcript_seq = ''.join(new_ref_transcript_seq)
ref_tx_seq_has_been_changed = True
else:
ref_tx_seq_has_been_changed = False
cds_codon_start, cds_codon_end = TranscriptProviderUtils.get_cds_codon_positions(protein_position_start, protein_position_end, cds_start)
if variant_type == "DEL":
reference_codon_seq = new_ref_transcript_seq[cds_codon_start:cds_codon_end+1].lower()
else:
reference_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(new_ref_transcript_seq[cds_codon_start:cds_codon_end+1].lower(), cds_codon_start, transcript_position_start, transcript_position_end, reference_allele_stranded, variant_type)
if variant_type == "INS" and tx.get_strand() == "-":
mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(reference_codon_seq.lower(), cds_codon_start - 1, transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)
else:
mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(reference_codon_seq.lower(), cds_codon_start, transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)
observed_aa = Bio.Seq.translate(mutated_codon_seq)
if ref_tx_seq_has_been_changed:
reference_aa = Bio.Seq.translate(reference_codon_seq)
else:
reference_aa = protein_seq[protein_position_start-1:protein_position_end]
if variant_type != VariantClassification.VT_SNP:
try:
reference_aa, observed_aa, protein_position_start, protein_position_end = \
self._adjust_protein_position_and_alleles(protein_seq, protein_position_start,
protein_position_end, reference_aa, observed_aa)
except InvalidVariantException as ive:
logging.getLogger(__name__).error("Could not properly adjust protein position for variant: %s, %s, %s, %s, %s VT: %s" % (tx.get_contig(), start, end, ref_allele, alt_allele, variant_type))
logging.getLogger(__name__).error(str(ive))
logging.getLogger(__name__).warn("Above error may not have exact start and end positions if this is a VCF input.")
logging.getLogger(__name__).warn("Variant type is likely incorrect. This can happen with some GATK VCFs")
logging.getLogger(__name__).warn(TranscriptProviderUtils.is_valid_xNP(variant_type, ref_allele, alt_allele))
logging.getLogger(__name__).warn("The protein_change annotation may not be properly rendered.")
vc_tmp, vc_tmp_secondary = self.infer_variant_classification(variant_type, reference_aa, observed_aa, ref_allele, alt_allele,
is_frameshift_indel=is_frameshift_indel, is_splice_site=is_splice_site, is_start_codon=is_start_codon)
cds_start_exon_space, cds_end_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
exon_i = TranscriptProviderUtils.determine_exon_index(int(start), int(end), tx, variant_type)
final_vc = VariantClassification(vc_tmp, variant_type, transcript_id=tx.get_transcript_id(), alt_codon=mutated_codon_seq, ref_codon=reference_codon_seq, ref_aa=reference_aa, ref_protein_start=protein_position_start, ref_protein_end=protein_position_end, alt_aa=observed_aa, alt_codon_start_in_exon=cds_codon_start, alt_codon_end_in_exon=cds_codon_end, ref_codon_start_in_exon=cds_codon_start, ref_codon_end_in_exon=cds_codon_end, cds_start_in_exon_space=cds_start_exon_space, ref_allele_stranded=reference_allele_stranded, alt_allele_stranded=observed_allele_stranded, exon_i=exon_i, vc_secondary=vc_tmp_secondary)
return final_vc
def _determine_vc_for_cds_overlap(self, start, end, ref_allele, alt_allele,
is_frameshift_indel, is_splice_site, tx,
variant_type, is_start_codon):
"""
Note: This method can also handle start and stop codons.
:param start:
:param end:
:param ref_allele:
:param alt_allele:
:param is_frameshift_indel:
:param is_splice_site:
:param tx:
:param variant_type:
:return:
"""
observed_allele_stranded, reference_allele_stranded = self._get_stranded_alleles(
ref_allele, alt_allele, tx)
transcript_position_start, transcript_position_end = TranscriptProviderUtils.convert_genomic_space_to_exon_space(
start, end, tx)
if tx.get_strand(
) == "+" and not variant_type == VariantClassification.VT_INS:
transcript_position_start -= 1
transcript_position_end -= 1
transcript_seq = tx.get_seq()
protein_seq = tx.get_protein_seq()
cds_start, cds_stop = TranscriptProviderUtils.determine_cds_in_exon_space(
tx)
protein_position_start, protein_position_end = TranscriptProviderUtils.get_protein_positions(
transcript_position_start, transcript_position_end, cds_start)
new_ref_transcript_seq = transcript_seq
if (transcript_seq[transcript_position_start:transcript_position_end +
1] != reference_allele_stranded
) and variant_type != VariantClassification.VT_INS:
new_ref_transcript_seq = list(transcript_seq)
new_ref_transcript_seq[
transcript_position_start:transcript_position_end +
1] = reference_allele_stranded
new_ref_transcript_seq = ''.join(new_ref_transcript_seq)
ref_tx_seq_has_been_changed = True
else:
ref_tx_seq_has_been_changed = False
cds_codon_start, cds_codon_end = TranscriptProviderUtils.get_cds_codon_positions(
protein_position_start, protein_position_end, cds_start)
if variant_type == "DEL":
reference_codon_seq = new_ref_transcript_seq[
cds_codon_start:cds_codon_end + 1].lower()
else:
reference_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(
new_ref_transcript_seq[cds_codon_start:cds_codon_end +
1].lower(), cds_codon_start,
transcript_position_start, transcript_position_end,
reference_allele_stranded, variant_type)
if variant_type == "INS" and tx.get_strand() == "-":
mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(
reference_codon_seq.lower(), cds_codon_start - 1,
transcript_position_start, transcript_position_end,
observed_allele_stranded, variant_type)
else:
mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(
reference_codon_seq.lower(), cds_codon_start,
transcript_position_start, transcript_position_end,
observed_allele_stranded, variant_type)
observed_aa = MutUtils.translate_sequence(mutated_codon_seq)
if ref_tx_seq_has_been_changed:
reference_aa = MutUtils.translate_sequence(reference_codon_seq)
else:
reference_aa = protein_seq[protein_position_start -
1:protein_position_end]
if variant_type != VariantClassification.VT_SNP:
try:
reference_aa, observed_aa, protein_position_start, protein_position_end = \
self._adjust_protein_position_and_alleles(protein_seq, protein_position_start,
protein_position_end, reference_aa, observed_aa)
except InvalidVariantException as ive:
logging.getLogger(__name__).error(
"Could not properly adjust protein position for variant: %s, %s, %s, %s, %s VT: %s"
% (tx.get_contig(), start, end, ref_allele, alt_allele,
variant_type))
logging.getLogger(__name__).error(str(ive))
logging.getLogger(__name__).warn(
"Above error may not have exact start and end positions if this is a VCF input."
)
logging.getLogger(__name__).warn(
"Variant type is likely incorrect. This can happen with some GATK VCFs"
)
logging.getLogger(__name__).warn(
TranscriptProviderUtils.is_valid_xNP(
variant_type, ref_allele, alt_allele))
logging.getLogger(__name__).warn(
"The protein_change annotation may not be properly rendered."
)
vc_tmp, vc_tmp_secondary = self.infer_variant_classification(
variant_type,
reference_aa,
observed_aa,
ref_allele,
alt_allele,
is_frameshift_indel=is_frameshift_indel,
is_splice_site=is_splice_site,
is_start_codon=is_start_codon)
cds_start_exon_space, cds_end_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(
tx)
exon_i = TranscriptProviderUtils.determine_exon_index(
int(start), int(end), tx, variant_type)
final_vc = VariantClassification(
vc_tmp,
variant_type,
transcript_id=tx.get_transcript_id(),
alt_codon=mutated_codon_seq,
ref_codon=reference_codon_seq,
ref_aa=reference_aa,
ref_protein_start=protein_position_start,
ref_protein_end=protein_position_end,
alt_aa=observed_aa,
alt_codon_start_in_exon=cds_codon_start,
alt_codon_end_in_exon=cds_codon_end,
ref_codon_start_in_exon=cds_codon_start,
ref_codon_end_in_exon=cds_codon_end,
cds_start_in_exon_space=cds_start_exon_space,
ref_allele_stranded=reference_allele_stranded,
alt_allele_stranded=observed_allele_stranded,
exon_i=exon_i,
vc_secondary=vc_tmp_secondary)
return final_vc
