def test_merge_targets():
"""Identify cluster for merging"""
uid1 = "ACCT"
uid2 = "GGGG"
uid3 = "AAGG"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
seq2 = ["ACTGTTTTTCTAAGC"] * 5
qual2 = ['I' * len(seq2[0])] * len(seq2)
seq3 = ["ACTGTTTTTCTAAGC"] * 2
qual3 = ['I' * len(seq3[0])] * len(seq3)
clusters = create_consensus([uid1 + uid1]*len(seq1) + \
[uid2 + uid2]*len(seq2),
['I'*(len(uid1)*2)]*(len(seq1) + len(seq2)),
seq1 + seq2, qual1 + qual2)
seq3 = [
pseq.SequenceWithQuality(seq, qual) for seq, qual in zip(seq3, qual3)
]
uid = pseq.SequenceWithQuality(uid2 + uid3, 'I' * (len(uid2) + len(uid3)))
cand = clusters.merge_target(uid, seq3[0], {}, 2)
assert cand == uid2 + uid2, "%r != %r" % (cand, uid2 + uid2)
cand = clusters.merge_target(uid, seq3[0], {}, 1)
assert cand is None, "%r != %r" % (cand, None)
def test_merge_diff(idx):
"""Propagate diffs when merging clusters"""
uid1 = "ACCT"
uid2 = "ACTT"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
seq2 = ["ACTGTTTTTCTAAGC"] * 5
qual2 = ['I' * len(seq2[0])] * len(seq2)
seq3 = ["ACTGTTTTTCTAAGC"] * 2
qual3 = ['I' * len(seq3[0])] * len(seq3)
seq4 = ["ACTGTTTGTGTAAGC", "ACTGTTTGTGTAAGC", "ACTGTTTGTATAAGC"]
qual4 = ['I' * len(seq4[0])] * len(seq4)
clusters = create_consensus([uid1 + uid2]*len(seq1) + \
[uid2 + uid1]*len(seq2) + \
[uid2 + uid2]*len(seq3) + \
[uid1 + uid1]*len(seq4),
['I'*(len(uid1)*2)]*(len(seq1) + len(seq2) + \
len(seq3) + len(seq4)),
seq1 + seq2 + seq3 + seq4,
qual1 + qual2 + qual3 + qual4)
ids = [uid1 + uid2, uid2 + uid1, uid2 + uid2, uid1 + uid1]
centres = [clusters[ids[i]] for i in idx]
merged = centres[0]
for i in range(1, len(clusters)):
success = merged.merge(centres[i], 2, max_dist=0.5)
assert success
expect = "+8G4T7 10C9G2"
obs = str(merged).splitlines()
assert merged.size == 11, "%r != %r" % (merged.size, 11)
assert obs[2] == expect, "%r != %r" % (obs[2], expect)
def test_keys():
"""Retrieve cluster IDs"""
uid1 = "ACCT"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
clusters = create_consensus([uid1 + uid1] * len(seq1),
['I' * (len(uid1) * 2)] * len(seq1), seq1,
qual1)
assert list(clusters.keys()) == [
'ACCTACCT'
], "%r != %r" % (list(clusters.keys()), ['ACCTACCT'])
def test_values():
"""Retrieve cluster consensus"""
uid1 = "ACCT"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
clusters = create_consensus([uid1 + uid1] * len(seq1),
['I' * (len(uid1) * 2)] * len(seq1), seq1,
qual1)
values = list(clusters.values())
assert len(values) == 1, "%r != %r" % (len(values), 1)
assert values[0].sequence.sequence == "ACTGTTTGTCTAAGC", "%r != %r" % \
(values[0].sequence.sequence, ['ACCTACCT'])
def test_iteritems():
"""Retrieve cluster IDs"""
uid1 = "ACCT"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
clusters = create_consensus([uid1 + uid1] * len(seq1),
['I' * (len(uid1) * 2)] * len(seq1), seq1,
qual1)
expected = [('ACCTACCT', "ACTGTTTGTCTAAGC")]
for (obs, expect) in zip(clusters.items(), expected):
assert obs[0] == expect[0], "%r != %r" % (obs[0], expect[0])
assert obs[1].sequence.sequence == expect[1], "%r != %r" % \
(obs[1].sequence.sequence, expect[1])
def test_write():
"""Write fastq output"""
uid1 = "ACCT"
seq1 = ["ACTGTTTGTCTAAGC"] * 2
qual1 = ['I' * len(seq1[0])] * len(seq1)
clusters = create_consensus([uid1 + uid1] * len(seq1),
['I' * (len(uid1) * 2)] * len(seq1), seq1,
qual1)
clusters.write(TMP + "write.fastq")
expect = str(clusters['ACCTACCT']).split("\n")
with open(TMP + "write.fastq") as output:
for (i, (out_line, expect_line)) in enumerate(zip(output, expect), 1):
out_line = out_line.strip("\n")
assert out_line == expect_line, "Error in line %r of fastq record:\n%r\n !=\n%r" % \
(i, out_line, expect_line)