def test_del_annotation():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert str(seq.translate()) == str(prot_seq)
region = \
mutate.mutate_protein_from_transcript(
seq, 3, "GCTATT", "", padding = 8)
print(str(region))
assert region.annot == 'AI2del', region
def test_mutate_protein_from_transcript_snp():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert(str(seq.translate()) == str(prot_seq))
mutated_seq = Seq("AATGCTATTCGTAGT").translate()
region = mutate.mutate_protein_from_transcript(
seq, 1, 'C', 'A', padding = 8)
print(str(region))
assert(region.seq[0] == 'N')
assert(str(mutated_seq) == str(region.seq))
assert(len(region.seq) == 5)
assert(region.annot == 'T1N')
def test_stop_codon_annotation():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert str(seq.translate()) == str(prot_seq)
stop_seq = Seq("ACTTAGCCCATTCGTAGT")
assert str(stop_seq.translate()) == str(Seq("T*PIRS"))
# change the 4th-6th chars to stop codon TAG
region = \
mutate.mutate_protein_from_transcript(
seq, 3, "GCT", "TAGCCC", padding = 8)
print(str(region))
assert region.seq == 'T', region.seq
assert region.annot == 'A2*', region
def test_mutate_protein_prefix_stop_codon():
seq = Seq("TAGGCTATTCGTAGT")
prot_seq = Seq("*AIRS")
assert(str(seq.translate()) == str(prot_seq))
mutated_seq = Seq("TAGGATATTCGTAGT").translate()
print (str(mutated_seq))
region = mutate.mutate_protein_from_transcript(
seq, 4, 'C', 'A', padding = 8)
print(str(region))
assert(region.seq[0] == 'D')
assert(region.seq[1] == 'I')
assert(str(region.seq) == str(mutated_seq[1:]))
assert(region.annot == 'A2D')
def test_mutate_protein_from_transcript_indel():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert(str(seq.translate()) == str(prot_seq))
mutated_seq = Seq("AAATGCTATTCGTAGT").translate()
print (str(mutated_seq))
region = mutate.mutate_protein_from_transcript(
seq, 1, 'C', 'AA', padding = 8)
print(str(region))
assert(region.seq[0] == 'K')
assert(region.seq[1] == 'C')
assert(region.seq[2] == 'Y')
assert(str(region.seq) == str(mutated_seq[:-1]))
assert(region.annot == 'T1fs')
def test_stop_codon_after_subst_annotation():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert str(seq.translate()) == str(prot_seq)
stop_seq = Seq("ACTCCCTAGATTCGTAGT")
assert str(stop_seq.translate()) == str(Seq("TP*IRS"))
# change the 4th-6th chars to stop codon TAG
region = \
mutate.mutate_protein_from_transcript(
seq, 3, "GCT", "CCCTAG", padding = 8)
print(str(region))
assert region.n_removed == 1
assert region.n_inserted == 1
assert region.seq == 'TP', region.seq
assert region.annot == 'A2P*', region
def test_mutate_protein_from_transcript_snp_coordinates():
seq = Seq("ACTGCTATTCGTAGT")
prot_seq = Seq("TAIRS")
assert(str(seq.translate()) == str(prot_seq))
mutated_seq = Seq("AATGCTATTCGTAGT").translate()
region = \
mutate.mutate_protein_from_transcript(
seq, 1, 'C', 'A', padding = 8)
print(str(region))
assert region.seq[0] == 'N'
assert str(mutated_seq) == str(region.seq)
assert len(region.seq) == 5
assert region.mutation_start == 0
assert region.n_removed == 1
assert region.n_inserted == 1
assert region.annot == 'T1N'
def test_get_transcript_and_mutate_vcf():
variant = {
'chr' : '10',
'pos' : 43617416,
'ref' : 'T',
'alt' : 'C'
}
vcf = pd.DataFrame.from_records([variant])
transcripts_ids = ensembl.annotate_vcf_transcripts(vcf)
transcript_ids = set(transcripts_ids['stable_id_transcript'])
assert( "ENST00000355710" in transcript_ids)
assert( "ENST00000340058" in transcript_ids)
transcript_id = "ENST00000355710"
cdna_idx = ensembl.get_transcript_index_from_pos(
variant['pos'], transcript_id, skip_untranslated_region = False)
assert cdna_idx is not None
assert cdna_idx < 5569
cdna_transcript = ref_data.get_cdna(transcript_id)
assert(cdna_transcript[cdna_idx] == variant['ref'])
cds_idx = ensembl.get_transcript_index_from_pos(
variant['pos'], transcript_id, skip_untranslated_region = True)
assert cds_idx is not None
cds_transcript = ref_data.get_cds(transcript_id)
assert(cds_transcript[cds_idx] == variant['ref'])
region = mutate_protein_from_transcript(
cds_transcript,
cds_idx,
variant['ref'],
variant['alt'],
padding = 10)
assert region is not None
assert len(region.seq) == 21, (region.seq, len(region.seq))
assert region.seq == 'RSQGRIPVKWTAIESLFDHIY'
def peptide_from_transcript_variant(transcript_id,
pos,
ref,
alt,
padding=None,
max_length=None):
# sometimes empty strings get represented with a '.'
if ref == ".":
ref = ""
if alt == ".":
alt = ""
forward = annotation.is_forward_strand(transcript_id)
ref = ref if forward else annotation.reverse_complement(ref)
alt = alt if forward else annotation.reverse_complement(alt)
transcript = _ensembl.get_cds(transcript_id)
def error_result(msg, *args):
logging.warning(msg, *args)
return None, -1, -1, msg % args
if not transcript:
return error_result("Couldn't find transcript for ID %s",
transcript_id)
idx = annotation.get_transcript_index_from_pos(
pos, transcript_id, skip_untranslated_region=True)
if idx is None:
return error_result(
"Couldn't translate gene position %s into transcript index for %s",
pos, transcript_id)
elif idx >= len(transcript):
return error_result(
"Index %d longer than sequence (len %d) for transcript %s (%s)",
idx, len(transcript), transcript_id,
gene_mutation_description(pos, ref, alt))
idx = idx if forward else idx - len(ref) + 1
# 'ref' represents what the VCF file thought were the reference bases
# at this position, now we actually check to make sure the transcript
# agrees
transcript_ref = str(transcript[idx:idx + len(ref)])
if transcript_ref != ref:
mutation_description = gene_mutation_description(pos, ref, alt)
return error_result(
"VCF/MAF expected %s at idx %d of transcript %s, found %s (%s)" % \
(ref, idx, transcript_id, transcript_ref, mutation_description)
)
region = mutate_protein_from_transcript(transcript,
idx,
ref,
alt,
padding=padding)
start = region.mutation_start
stop = start + region.n_inserted
if max_length and len(region.seq) > max_length:
seq = region.seq[:max_length]
stop = min(stop, max_length)
else:
seq = region.seq
return seq, start, stop, region.annot
def peptide_from_transcript_variant(
transcript_id, pos, ref, alt,
padding = None,
max_length = None):
# sometimes empty strings get represented with a '.'
if ref == ".":
ref = ""
if alt == ".":
alt = ""
forward = annotation.is_forward_strand(transcript_id)
ref = ref if forward else annotation.reverse_complement(ref)
alt = alt if forward else annotation.reverse_complement(alt)
transcript = _ensembl.get_cds(transcript_id)
def error_result(msg, *args):
logging.warning(msg, *args)
return None, -1, -1, msg % args
if not transcript:
return error_result("Couldn't find transcript for ID %s", transcript_id)
idx = annotation.get_transcript_index_from_pos(
pos,
transcript_id,
skip_untranslated_region = True)
if idx is None:
return error_result(
"Couldn't translate gene position %s into transcript index for %s",
pos,
transcript_id)
elif idx >= len(transcript):
return error_result(
"Index %d longer than sequence (len %d) for transcript %s (%s)",
idx,
len(transcript),
transcript_id,
gene_mutation_description(pos, ref, alt))
idx = idx if forward else idx - len(ref) + 1
# 'ref' represents what the VCF file thought were the reference bases
# at this position, now we actually check to make sure the transcript
# agrees
transcript_ref = str(transcript[idx:idx+len(ref)])
if transcript_ref != ref:
mutation_description = gene_mutation_description(pos, ref, alt)
return error_result(
"VCF/MAF expected %s at idx %d of transcript %s, found %s (%s)" % \
(ref, idx, transcript_id, transcript_ref, mutation_description)
)
region = mutate_protein_from_transcript(
transcript,
idx,
ref,
alt,
padding = padding)
start = region.mutation_start
stop = start + region.n_inserted
if max_length and len(region.seq) > max_length:
seq = region.seq[:max_length]
stop = min(stop, max_length)
else:
seq = region.seq
return seq, start, stop, region.annot