def test_merge_pair(record1, record2, record4):
"""
Assemble a compatible overlapping read pair.
GCTGCACCGATGTACGCAAA
||||| --> GCTGCACCGATGTACGCAAAGCTATTTAAAACC
ACGCAAAGCTATTTAAAACC
"""
pair = OverlappingReadPair(tail=record1,
head=record2,
offset=13,
overlap=7,
sameorient=True,
swapped=False)
assert merge_pair(pair) == 'GCTGCACCGATGTACGCAAAGCTATTTAAAACC'
pair = OverlappingReadPair(tail=record1,
head=record4,
offset=13,
overlap=7,
sameorient=True,
swapped=False)
with pytest.raises(AssertionError) as ae:
contig = merge_pair(pair)
assert 'attempted to assemble incompatible reads' in str(ae)
def test_merge_contained_with_offset_and_error(record7, record12):
"""
Test merge with containment, offset, and a sequencing error.
CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCTCAAGGTATGTGAGGCGATAACTCAA
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
CCCGGATACTTGAAGCAGGCAcC
||||||||||||||||| *
"""
pair = calc_offset(record7, record12, 'CCCGGATACTTGAAGCA')
assert pair == INCOMPATIBLE_PAIR
pair = OverlappingReadPair(tail=record7,
head=record12,
offset=10,
overlap=23,
sameorient=True,
swapped=False)
with pytest.raises(AssertionError) as ae:
newrecord = merge_and_reannotate(pair, 'WontWork')
assert 'attempted to assemble incompatible reads' in str(ae)
def test_merge_and_reannotate_contained(record7, record10):
"""
Test merge/reannotation with containment.
CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCTCAAGGTATGTGAGGCGATAACTCAA
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCT
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
"""
pair = OverlappingReadPair(tail=record7,
head=record10,
offset=0,
overlap=35,
sameorient=True,
swapped=False)
newrecord = merge_and_reannotate(pair, 'ContainedAtOne')
assert newrecord.name == 'ContainedAtOne'
assert newrecord.sequence == record7.sequence
assert newrecord.ikmers == record7.ikmers
def test_merge_and_reannotate_edge_case_opposite_orientation(record7, record9):
"""
Test merge/reannotation with edge cases to check for fencepost errors.
CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCTCAAGGTATGTGAGGCGATAACTCAA
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
reverse complement -----> GTATGTGAGGCGATAACTCAAGACCACGGGAGCTCACTTCGTTGACGCGAGCGCCTTGCT
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
|||||||||||||||||
""" # noqa
pair = OverlappingReadPair(tail=record7,
head=record9,
offset=39,
overlap=21,
sameorient=False,
swapped=False)
newrecord = merge_and_reannotate(pair, 'SoMeCoNtIg')
assert newrecord.name == 'SoMeCoNtIg'
assert newrecord.sequence == ('CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCTCAAGGTAT'
'GTGAGGCGATAACTCAAGACCACGGGAGCTCACTTCGTTGACG'
'CGAGCGCCTTGCT')
assert len(newrecord.ikmers) == 8
testseqs = [
'TCCCCACCCGGATACTT',
'CCCCACCCGGATACTTG',
'CCCGGATACTTGAAGCA',
'GGTATGTGAGGCGATAA',
'GTATGTGAGGCGATAAC',
'TATGTGAGGCGATAACT',
]
testoffsets = [4, 5, 10, 38, 39, 40, 81, 82]
for kmer, seq, offset in zip(newrecord.ikmers, testseqs, testoffsets):
assert kmer.sequence == seq
assert kmer.offset == offset
def test_merge_and_reannotate_opposite_orientation(record1, record3):
"""
Assemble a read pair and re-annotate the associated interesting k-mers.
GCTGCACCGATGTACGCAAA
||||| --> GCTGCACCGATGTACGCAAAGCTATTTAAAACC
ACGCAAAGCTATTTAAAACC ***** *****
"""
pair = OverlappingReadPair(tail=record1,
head=record3,
offset=13,
overlap=7,
sameorient=False,
swapped=False)
newrecord = merge_and_reannotate(pair, 'contig1')
assert newrecord.name == 'contig1'
assert newrecord.sequence == 'GCTGCACCGATGTACGCAAAGCTATTTAAAACC'
assert len(newrecord.ikmers) == 2
assert newrecord.ikmers[0].offset == 14
assert newrecord.ikmers[1].offset == 27
def test_graph_init():
"""Test graph initialization."""
instream = kevlar.open(data_file('var1.reads.augfastq'), 'r')
graph = kevlar.ReadGraph()
graph.load(kevlar.parse_augmented_fastx(instream))
graph.populate_edges(strict=True)
# 10 reads in the file, but read16f has no valid connections due to error
assert len(graph.nodes()) == 10
# The given read shares its interesting k-mer and has compatible overlaps
# with 6 other reads (read13f and read15f have errors).
r23name = 'read23f start=67,mutations=0'
assert len(graph[r23name]) == 6
# Test the values of one of the edges.
r35name = 'read35f start=25,mutations=0'
assert graph[r23name][r35name]['offset'] == 42
assert graph[r23name][r35name]['overlap'] == 58
# Should all be a single CC
assert len(list(connected_components(graph))) == 2
assert len([p for p in graph.partitions()]) == 1
r8name = 'read8f start=8,mutations=0'
r37name = 'read37f start=9,mutations=0'
assert graph[r37name][r8name]['offset'] == 1
assert graph[r37name][r8name]['overlap'] == 99
pair = OverlappingReadPair(tail=graph.get_record(r8name),
head=graph.get_record(r37name),
offset=1,
overlap=99,
sameorient=True,
swapped=False)
assert merge_pair(pair) == ('CACTGTCCTTACAGGTGGATAGTCGCTTTGTAATAAAAGAGTTAC'
'ACCCCGGTTTTTAGAAGTCTCGACTTTAAGGAAGTGGGCCTACGG'
'CGGAAGCCGTC')