def test_convert_target_position_to_source(self):
"""Simple test for converting a position in the target (new) genome
back to the corresponding position in the original source genome.
"""
before_insertion = 'AAAAAAAAAAAAA'
after_insertion = 'CCCCCCCCCCCCCC'
raw_seq_str = before_insertion + after_insertion
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
INSERTION_BASE = 'T'
INSERTION_POSITION = len(before_insertion)
insertion_data = {
'position': INSERTION_POSITION,
'sequence': INSERTION_BASE
}
maker.handle_insertion(insertion_data)
self.assertEqual(
3, maker.runtime_liftover.convert_target_position_to_source(3))
self.assertIsNone(
maker.runtime_liftover.convert_target_position_to_source(
INSERTION_POSITION))
self.assertEqual(
INSERTION_POSITION,
maker.runtime_liftover.convert_target_position_to_source(
INSERTION_POSITION + 1))
def test_insertion__greater_than_one_base(self):
"""Tests insertion with more than one base.
"""
before_insertion = 'AAAAAAAAAAAAA'
after_insertion = 'CCCCCCCCCCCCCC'
raw_seq_str = before_insertion + after_insertion
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
INSERTION_SEQ = 'TT'
insertion_data = {
'position': len(before_insertion),
'sequence': INSERTION_SEQ
}
maker.handle_insertion(insertion_data)
# Assert the resulting sequence is correct.
EXPECTED_SEQ = before_insertion + INSERTION_SEQ + after_insertion
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the liftover is correct.
EXPECTED_LIFTOVER_MAPPING_1 = ((0, len(before_insertion) - 1),
(0, len(before_insertion) - 1))
EXPECTED_LIFTOVER_MAPPING_2 = ((len(before_insertion),
len(raw_seq_str) - 1),
(len(before_insertion) + 2,
len(raw_seq_str) + 1))
EXPECTED_LIFTOVER = [
EXPECTED_LIFTOVER_MAPPING_1, EXPECTED_LIFTOVER_MAPPING_2
]
self.assertEqual(EXPECTED_LIFTOVER,
maker.runtime_liftover._interval_mapping)
def test_insertion__simple(self):
"""Tests insertion.
Makes sure both the Genbank and the liftover file look correct.
"""
before_insertion = 'AAAAAAAAAAAAA'
after_insertion = 'CCCCCCCCCCCCCC'
raw_seq_str = before_insertion + after_insertion
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
INSERTION_BASE = 'T'
insertion_data = {
'position': len(before_insertion),
'sequence': INSERTION_BASE
}
maker.handle_insertion(insertion_data)
EXPECTED_SEQ = before_insertion + INSERTION_BASE + after_insertion
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the liftover is correct.
EXPECTED_LIFTOVER_MAPPING_1 = ((0, len(before_insertion) - 1),
(0, len(before_insertion) - 1))
EXPECTED_LIFTOVER_MAPPING_2 = ((len(before_insertion),
len(raw_seq_str) - 1),
(len(before_insertion) + 1,
len(raw_seq_str)))
EXPECTED_LIFTOVER = [
EXPECTED_LIFTOVER_MAPPING_1, EXPECTED_LIFTOVER_MAPPING_2
]
self.assertEqual(EXPECTED_LIFTOVER,
maker.runtime_liftover._interval_mapping)
def test_deletion__greater_than_one_base__3_bases(self):
"""Tests a deletion of 3 bases.
"""
before_deletion = 'AAAAA'
deleted_bases = 'TTT'
after_deletion = 'GGGGGGGGGGG'
raw_seq_str = before_deletion + deleted_bases + after_deletion
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
deletion_data = {
'interval':
(len(before_deletion), len(before_deletion) + len(deleted_bases))
}
maker.handle_deletion(deletion_data)
# Assert the sequence is correct.
EXPECTED_SEQ = before_deletion + after_deletion
self.assertEqual(len(EXPECTED_SEQ), len(seq_record.seq))
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the liftover is correct.
EXPECTED_LIFTOVER = [((0, 4), (0, 4)), ((8, 18), (5, 15))]
self.assertEqual(EXPECTED_LIFTOVER,
maker.runtime_liftover._interval_mapping)
def test_combo__reverse_operations(self):
"""Tests a combination of insertions and deletions, similar to above,
but with operations applied in reverse order.
"""
before_deletion = 'AAAAA'
deleted_bases = 'TTT'
after_deletion = 'GGGGGGGGGGG'
insertion = 'AAA'
after_insertion = 'TTTTT'
raw_seq_str = (before_deletion + deleted_bases + after_deletion +
after_insertion)
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
insertion_start = (len(before_deletion) + len(deleted_bases) +
len(after_deletion))
insertion_1_data = {'position': insertion_start, 'sequence': insertion}
maker.handle_insertion(insertion_1_data)
deletion_data = {
'interval':
(len(before_deletion), len(before_deletion) + len(deleted_bases))
}
maker.handle_deletion(deletion_data)
EXPECTED_SEQ = (before_deletion + after_deletion + insertion +
after_insertion)
self.assertEqual(len(EXPECTED_SEQ), len(seq_record.seq))
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
def test_deletion__multiple_positions(self):
"""Tests multiple deletions.
"""
before_deletion = 'AAAAA'
deleted_bases = 'TTT'
after_deletion = 'GGGGGGGGGGG'
other_deletion = 'C'
after_other_deletion = 'TTTTT'
raw_seq_str = (before_deletion + deleted_bases + after_deletion +
other_deletion + after_other_deletion)
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
deletion_data = {
'interval':
(len(before_deletion), len(before_deletion) + len(deleted_bases))
}
maker.handle_deletion(deletion_data)
other_deletion_start = (len(before_deletion) + len(deleted_bases) +
len(after_deletion))
other_deletion_end = other_deletion_start + len(other_deletion)
other_deletion_data = {
'interval': (other_deletion_start, other_deletion_end)
}
maker.handle_deletion(other_deletion_data)
EXPECTED_SEQ = before_deletion + after_deletion + after_other_deletion
self.assertEqual(len(EXPECTED_SEQ), len(seq_record.seq))
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
def test_insertion__multiple(self):
"""Tests insertion for multiple inserts.
Makes sure both the Genbank and the liftover file look correct.
"""
before_insertion_1 = 'AAAAAAAAAAAAA'
after_insertion_1 = 'CCCCCCCCCCCCCC'
before_insertion_2 = 'AAAAAAAAAAAAAAAAAA'
after_insertion_2 = 'CCCCCCCCCCCCCCCC'
raw_seq_str = (before_insertion_1 + after_insertion_1 +
before_insertion_2 + after_insertion_2)
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
INSERTION_1_BASE = 'T'
insertion_1_data = {
'position': len(before_insertion_1),
'sequence': INSERTION_1_BASE
}
maker.handle_insertion(insertion_1_data)
INSERTION_2_BASE = 'G'
insertion_2_data = {
'position': (len(before_insertion_1) + len(after_insertion_1) +
len(before_insertion_2)),
'sequence':
INSERTION_2_BASE
}
maker.handle_insertion(insertion_2_data)
EXPECTED_SEQ = (before_insertion_1 + INSERTION_1_BASE +
after_insertion_1 + before_insertion_2 +
INSERTION_2_BASE + after_insertion_2)
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
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)
def test_deletion__simple(self):
"""Tests a single deletion.
"""
before_deletion = 'AAAAA'
deleted_base = 'T'
after_deletion = 'GGGGGGGGGGG'
raw_seq_str = before_deletion + deleted_base + after_deletion
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
deletion_data = {
'interval': (len(before_deletion), len(before_deletion) + 1)
}
maker.handle_deletion(deletion_data)
# Assert the sequence is correct.
EXPECTED_SEQ = before_deletion + after_deletion
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))
# Assert the liftover is correct.
EXPECTED_LIFTOVER = [((0, 4), (0, 4)), ((6, 16), (5, 15))]
self.assertEqual(EXPECTED_LIFTOVER,
maker.runtime_liftover._interval_mapping)
def test_combo(self):
"""Tests a combination of insertions, deletions, and snps.
"""
before_deletion = 'AAAAA'
deleted_bases = 'TTT'
after_deletion = 'GGGGGGGGGGG'
after_deletion_with_snp = 'GGGCGGGGGGG'
insertion = 'AAA'
after_insertion = 'TTTTT'
raw_seq_str = (before_deletion + deleted_bases + after_deletion +
after_insertion)
seq = Seq(raw_seq_str, generic_dna)
seq_record = SeqRecord(seq)
maker = VCFToGenbankMaker(seq_record, None, None)
# Make deletion.
deletion_data = {
'interval':
(len(before_deletion), len(before_deletion) + len(deleted_bases))
}
maker.handle_deletion(deletion_data)
# Make insertion.
insertion_start = (len(before_deletion) + len(deleted_bases) +
len(after_deletion))
insertion_1_data = {'position': insertion_start, 'sequence': insertion}
maker.handle_insertion(insertion_1_data)
# Make SNP.
insertion_start = (len(before_deletion) + len(deleted_bases) +
after_deletion_with_snp.index('C'))
snp_data = {'position': insertion_start, 'ref': 'G', 'alt': 'C'}
maker.handle_snp(snp_data)
EXPECTED_SEQ = (before_deletion + after_deletion_with_snp + insertion +
after_insertion)
self.assertEqual(len(EXPECTED_SEQ), len(seq_record.seq))
self.assertEqual(EXPECTED_SEQ, str(seq_record.seq))