def query_subject_example(scope="module"):
"""This fixture returns an example of a subject and query"""
subject = ContigRegion(911, 757, Context(9795, True), name="subjectexample", forward=False,
filename="templates/pRIAS (CC15).gb")
query = ContigRegion(1, 155, Context(22240, True), name="queryexample", forward=True,
filename="templates/pRasdfasdfaIAS (CC15).gb")
return [query, subject]
def test_subquery():
c1 = Context(10000, True)
c2 = Context(5000, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
contig = Contig(q1, s1, "BLAST")
sub_query1 = contig.sub_query(200, 250)
sub_query2 = contig.sub_query(220, 300)
assert len(sub_query1) == 51
assert len(sub_query2) == 81
def test_gap_cost_both_extendable():
subject = ContigRegion(1, 100, Context(9795, True))
query_context = Context(20000, True)
query = ContigRegion(1, 100, query_context)
left = BlastContig(query, subject, "test")
from matplotlib import pyplot as plt
for left_extendable, right_extendable, color in [(True, True, "blue"),
(False, True, "green"),
(False, False, "red")]:
X = []
Y = []
left.lp_extendable = left_extendable
left.rp_extendable = left_extendable
for right_start in range(1, 1000):
right = BlastContig(
ContigRegion(right_start, right_start + 99, query_context),
subject, "test")
right.lp_extendable = right_extendable
right.rp_extendable = right_extendable
gap_cost = Assembly._gap_cost(left, right)
left_end = left.query.end
right_start = right.query.start
distance = right_start - left_end
print(
f"{left_end} {right_start} Distance: {distance}, Gap_cost: {gap_cost}"
)
X.append(distance)
Y.append(gap_cost)
plt.scatter(X,
Y,
s=1.0,
c=[color] * len(Y),
label=f"{left_extendable + right_extendable}")
if False:
plt.ylim(0, 500)
plt.xlabel("Distance (bp)")
plt.ylabel("Gap Cost ($)")
plt.legend(loc=2)
plt.show()
def test_contig_schema():
c1 = Context(10000, True)
c2 = Context(5100, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
contig1 = Contig(q1, s1, "BLAST", data1=5)
schema = schemas.ContigSchema()
data = schema.dump(contig1)
assert data['query']['start'] == 100
assert data['query']['end'] == 300
assert data['query']['context']['length'] == 10000
assert data['subject']['start'] == 500
assert data['subject']['end'] == 700
assert data['subject']['context']['length'] == 5100
assert data['quality']
assert data['metadata'] == {'data1': 5}
assert data['alignment_length'] == 201
def test_contig_region_with_circular_context(circular_context):
"""This test instantiation of a contig region using a circular context."""
c = ContigRegion(1, 100, circular_context, name="example", forward=False, sequence="AGTCAGAGTCAG",
filename="somesequence2.gb")
assert c.start == 1
assert c.end == 100
assert c.circular
assert c.name == "example"
assert c.direction == Region.REVERSE
assert c.sequence == "AGTCAGAGTCAG"
assert c.filename == "somesequence2.gb"
def test_contig_region_with_linear_context(linear_context):
"""This tests instantiation of a contig region using a linear context."""
c = ContigRegion(1, 100, linear_context, name="example", forward=True, sequence="AGTCAG",
filename="somesequence.gb")
assert c.start == 1
assert c.end == 100
assert not c.circular
assert c.name == "example"
assert c.direction == Region.FORWARD
assert c.sequence == "AGTCAG"
assert c.filename == "somesequence.gb"
def test_divide_contigs():
c1 = Context(10000, True)
c2 = Context(8000, True)
q1 = ContigRegion(1000, 3000, context=c1, forward=True)
s1 = ContigRegion(5000, 7000, context=c2, forward=True)
contig = Contig(q1, s1, "BLAST")
# not including self
divided_contigs = contig.divide_contig(
[1100, 1200],
[2000, 2200, 2300],
include_self=False)
assert len(divided_contigs) == 12
# including self
divided_contigs = contig.divide_contig(
[1100, 1200],
[2000, 2200, 2300],
include_self=True)
assert len(divided_contigs) == 13
def _overlap_range(left, right):
"""Gap span range between a left and right contig"""
# primers are 60bp, 20bp are annealed, leaving 40bp
max_primer_extension = 40.0
gap_span = ContigRegion.get_gap_span(left.query, right.query)
if gap_span is not None:
extension = max_primer_extension * left.end_extendable
extension += max_primer_extension * right.start_extendable
min_overlap = -1.0 * gap_span
max_overlap = -1.0 * gap_span + extension
return (min_overlap, max_overlap, gap_span)
return None
def test_fuse():
# Test fuse
c1 = Context(10000, True)
c2 = Context(5100, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
q2 = ContigRegion(301, 600, context=c1, forward=True)
q3 = ContigRegion(301, 600, context=c2, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
s2 = ContigRegion(701, 1000, context=c2, forward=True)
s3 = ContigRegion(701, 1000, context=c2, forward=True)
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig1.fuse(contig2)
assert contig1.query.end == 600
# Raises error if one has sequence and other does not
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
a = "A"*contig1.query.length
b = "B"*contig1.subject.length
c = "C"*contig2.query.length
d = "D"*contig2.subject.length
contig1.query.sequence = a
contig1.subject.sequence = b
contig2.query.sequence = c
contig2.subject.sequence = d
contig1.fuse(contig2)
assert contig1.query.sequence == a + c
assert contig1.subject.sequence == b + d
# Raises error if one has sequence and other does not
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig1.query.sequence = "AGTCTGAGCTGTCGTGATAGTGCTGA"
contig1.subject.sequence = "AGTYAGYCHYAYHCYHYSCHYHAYCY"
with pytest.raises(ContigError):
contig1.fuse(contig2)
# Raise error if different contexts
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig3 = Contig(q3, s3, "BLAST")
with pytest.raises(ContigError):
contig3.fuse(contig2)
def perfect_matches(self, rc=True):
"""
Pseudo-blast for finding perfect sequence matches (i.e. primers)
:param rc:
:return:
"""
# Get primer sequences (defined in db)
out, seqs, metadata = self.concate_db_to_fsa()
contig_container = ContigContainer()
# Get the query sequence
query_seq = open_sequence(self.query)[0].seq
query_seq_str = str(query_seq)
query_seq_str = re.sub('[nN]', '.', query_seq_str).lower()
fwd_matches = []
rev_matches = []
for seq in seqs:
seq_str = str(seq.seq)
try:
rc_seq_str = dna_reverse_complement(seq_str)
except KeyError:
continue
seq_str = re.sub('[nN]', '.', seq_str).lower()
rc_seq_str = re.sub('[nN]', '.', rc_seq_str).lower()
for match in re.finditer(seq_str, query_seq_str):
subject = ContigRegion(
seq.id,
ContigRegion.START_INDEX,
len(seq),
len(seq),
False,
True,
sequence=seq_str,
)
query = ContigRegion(
self.query,
match.start() + ContigRegion.START_INDEX,
match.end() + ContigRegion.START_INDEX - 1,
self.query_length,
self.query_circular,
True,
)
c = Contig(query, subject, Contig.TYPE_PRIMER)
contig_container.contigs.append(c)
for match in re.finditer(rc_seq_str, query_seq_str):
subject = ContigRegion(
seq.id,
len(seq),
ContigRegion.START_INDEX,
len(seq),
False,
False,
sequence=seq_str,
)
query = ContigRegion(
self.query,
match.start() + ContigRegion.START_INDEX,
match.end() + ContigRegion.START_INDEX - 1,
self.query_length,
self.query_circular,
True,
)
c = Contig(query, subject, Contig.TYPE_PRIMER)
contig_container.contigs.append(c)
return contig_container