def __call__(self, snv):
self._clean_filter(snv)
seq_name = snv.chrom
seq_ref = self.ref_index[seq_name]
aminos = None
try:
seq_estscan = self.orf_seq_index[seq_name + self.orf_suffix]
except KeyError:
return
try:
aminos = get_amino_change(seq_ref, seq_estscan, snv)
except IsIndelError:
snv.add_filter(self.name)
snv.add_info(info=self.info_id, value='INDEL')
except BetweenSegments:
pass
except OutsideAlignment:
pass
if aminos is None:
return
if set(aminos['ref_amino']) != set(aminos['alt_amino']):
snv.add_filter(self.name)
info_val = '{}->{}'.format(aminos['ref_amino'],
','.join(aminos['alt_amino']))
snv.add_info(info=self.info_id, value=info_val)
def __call__(self, snv):
self._clean_filter(snv)
seq_name = snv.chrom
seq_ref = self.ref_index[seq_name]
aminos = None
try:
seq_estscan = self.orf_seq_index[seq_name + self.orf_suffix]
except KeyError:
return
try:
aminos = get_amino_change(seq_ref, seq_estscan, snv)
except IsIndelError:
snv.add_filter(self.name)
except BetweenSegments:
pass
except OutsideAlignment:
pass
if aminos is None:
return
ref_aa = aminos['ref_amino']
alt_aas = aminos['alt_amino']
if set(ref_aa) == set(alt_aas):
return snv
if any([self._is_severe(ref_aa, alt_aa) for alt_aa in alt_aas]):
snv.add_filter(self.name)
def test_get_aminos(self):
# test using
seq_ref = """>SEUC00016_TC01
CACGCTAAACAACGATCATTGTCATCGGTACCGATTGTTACAAGTTGTGTGCAGTGTCGT
GCTATTTGTGTGTACATTCCTTCTAAGATGTCGTCAACAAAGTGGTTGGTGTGTGCGCTA
GTGGTGGTGTGCGTGAGCGTAAGGCAAGCAACATCTGCGCCGGCGCCGCAGGAACAAGAA
TACCCGCCTATGCCCTACGAGTACAAATATGACGTTGAAGATCAAGAGCTTGAAGAGAAA
GCTCTCTACTTCGGAGCCAACGAAGCAGGAGATGCCCAGGGCAAGGTCATCGGAGGATAC
CGAGTTCTCCTCCCCGATGGTCGTCTTATGACCGTCGAGTACAGTGTGGAGGGAGAAAGC
GGTTTCGTTCCCAAAATCACCTTCGAAGACAACGCCAGCCCCTTCGGCAAAGGAAAGTAG
ACCTTATAACGACGCCTACAAGACTGGTACCGCGATCAATTGATACTAGTTCAATTTGAT
TTCTGAATTCTATGCCGTAAAACATTTTCTTTTATTAATTATACCGATTTCGATAAATAG
ACATCTTTACCTACTTAACGAATTTCTCATAGGATTCAGAAGTCGAAACCGAAAAAAGTT
ACTTCAGTTTTCATTAGATTGTAAATGTGTGTAAATTATTATTATTATTATATCAGGGAT
CCTTAAGTTGATATTAGTGGTGATATAAACGATATTTATGAACGACAATCAGGTATCGTC
ACTGGCTTGAGTAATGTTAGAAAAAATATAATTTTACCGAAAGCATTAGTAACTTTTTTC
ACGATTATAATCTCCCATACATACTGTATACTTACGTTACGTATAATAATTTTGATTGTC
TTCATAGTGTACTCTATAATATATGTAGGTGTAGGCAAAACTCATTCGCCAATAAGATAA
TATGTACAGTCAGCGATTTCTAAGATAAATTTGTACCGCAAATATCGAGTTACCGATACT
GTGATCAATTAGAACG"""
orf_seq = """>SEUC00016_TC01_orf_seq start=89 end=421 strand=forward
ATGTCGTCAACAAAGTGGTTGGTGTGTGCGCTAGTGGTGGTGTGCGTGAGCGTAAGGCAAGCAACATCTGCGCC
GGCGCCGCAGGAACAAGAATACCCGCCTATGCCCTACGAGTACAAATATGACGTTGAAGATCAAGAGCTTGAAG
AGAAAGCTCTCTACTTCGGAGCCAACGAAGCAGGAGATGCCCAGGGCAAGGTCATCGGAGGATACCGAGTTCTC
CTCCCCGATGGTCGTCTTATGACCGTCGAGTACAGTGTGGAGGGAGAAAGCGGTTTCGTTCCCAAAATCACCTT
CGAAGACAACGCCAGCCCCTTCGGCAAAGGAAAGTAG"""
seq_ref = StringIO(seq_ref)
orf_seq = StringIO(orf_seq)
seq_ref = SeqIO.read(seq_ref, "fasta")
orf_seq = SeqIO.read(orf_seq, "fasta")
record = FakeClass()
record.is_indel = False
record.pos = 111
record.alleles = ["T", "C"]
aminos = get_amino_change(seq_ref, orf_seq, record)
assert aminos == {"ref_amino": "C", "alt_amino": ["R"]}
record = FakeClass()
record.is_indel = True
record.pos = 110
try:
aminos = get_amino_change(seq_ref, orf_seq, record)
raise RuntimeError("We should not reach here")
except IsIndelError:
pass
record = FakeClass()
record.is_indel = False
record.pos = 111
record.alleles = ["T", "C", "A"]
aminos = get_amino_change(seq_ref, orf_seq, record)
assert aminos == {"ref_amino": "C", "alt_amino": ["R", "S"]}
# Outside orf
seq_ref = "ATCTAGGCTGCTACGATTAGCTGACGATGTTATCGTAGATCTAGCTGATCATCTAGCT"
seq_ref += "GATCG"
orf_seq = "AGGCTCTACGATTAGCTGATCGATGTTATC"
seq_ref = SeqRecord(seq=Seq(seq_ref), id="ref")
orf_seq = SeqRecord(seq=Seq(orf_seq), id="orf")
record = FakeClass()
record.is_indel = False
record.pos = 34
record.alleles = ["G", "C"]
try:
aminos = get_amino_change(seq_ref, orf_seq, record)
self.fail()
except OutsideAlignment:
pass
# frameshift
record = FakeClass()
record.is_indel = False
record.pos = 9
record.alleles = ["G", "C"]
try:
aminos = get_amino_change(seq_ref, orf_seq, record)
self.fail()
except BetweenSegments:
pass