def test_deletion__overlapping_features(self):
# Example based on intersection of nei and arbB genes in MG1655.
before_overlap = 'GCCCTGGCTGCCAGCA'
overlap = 'CTAG'
after_overlap = 'GCCGACCGCTTCGG'
raw_seq_str = before_overlap + overlap + after_overlap
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
feature_1_loc = FeatureLocation(0,
len(before_overlap) + len(overlap),
strand=1)
feature_1 = SeqFeature(feature_1_loc, type='CDS', id='1')
seq_record.features.append(feature_1)
feature_2_loc = FeatureLocation(len(before_overlap),
len(raw_seq_str),
strand=1)
feature_2 = SeqFeature(feature_2_loc, type='CDS', id='2')
seq_record.features.append(feature_2)
maker = VCFToGenbankMaker(seq_record, None, None)
maker._update_genome_record_for_variant(len(before_overlap), overlap,
'')
# Assert the sequence is correct.
EXPECTED_SEQ = before_overlap + after_overlap
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the feature annotations are still correct.
EXPECTED_FEATURE_1_SEQ = before_overlap
self.assertEqual(EXPECTED_FEATURE_1_SEQ,
str(feature_1.extract(seq_record.seq)))
EXPECTED_FEATURE_2_SEQ = after_overlap
self.assertEqual(EXPECTED_FEATURE_2_SEQ,
str(feature_2.extract(seq_record.seq)))
def test_update_genome_record_for_variant(self):
"""Tests handling a vcf record.
"""
before_variant = 'AAAAA'
variant = 'TTTT'
after_variant = 'CCCCCC'
variant_replacement = 'GGGGGGG'
raw_seq_str = before_variant + variant + after_variant
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
# Replace the variant
variant_position = len(before_variant)
maker._update_genome_record_for_variant(variant_position, variant,
variant_replacement)
# Assert the sequence is correct.
EXPECTED_SEQ = before_variant + variant_replacement + after_variant
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the liftover is correct.
EXPECTED_LIFTOVER_MAPPING_1 = ((0, len(before_variant) - 1),
(0, len(before_variant) - 1))
EXPECTED_LIFTOVER_MAPPING_2 = ((len(before_variant) + len(variant),
len(raw_seq_str) - 1),
(len(before_variant) +
len(variant_replacement),
(len(before_variant) +
len(variant_replacement) +
len(after_variant) - 1)))
EXPECTED_LIFTOVER = [
EXPECTED_LIFTOVER_MAPPING_1, EXPECTED_LIFTOVER_MAPPING_2
]
self.assertEqual(EXPECTED_LIFTOVER,
maker.runtime_liftover._interval_mapping)