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_assembly_round2():
instream = kevlar.open(data_file('var1.round2.augfastq'), 'r')
graph = kevlar.ReadGraph()
graph.load(kevlar.parse_augmented_fastx(instream))
contig = graph.get_record('contig1')
read = graph.get_record('read22f start=5,mutations=0')
pair = calc_offset(contig, read, 'AAGTCTCGACTTTAAGGAAGTGGGCCTAC')
assert pair.tail == read
assert pair.head == contig
assert merge_pair(pair) == ('TATCACTGTCCTTACAGGTGGATAGTCGCTTTGTAATAAAAGAGT'
'TACACCCCGGTTTTTAGAAGTCTCGACTTTAAGGAAGTGGGCCTA'
'CGGCGGAAGCCGTC')
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')