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import random
import pytest
from bx.seq import twobit
def quick_fasta_iter(f):
current_header = None
current_sequence = []
for line in f:
if line.startswith("#"):
continue
if line.startswith(">"):
if current_sequence:
yield current_header, "".join(current_sequence)
current_sequence = []
current_header = line.strip()[1:]
else:
current_sequence.append("".join(line.split()))
if current_sequence:
yield current_header, "".join(current_sequence)
current_sequence = []
@pytest.mark.parametrize("filename", ["test", "testN", "testMask"])
def test_random_subseq_matches(filename):
test_fa = f"test_data/seq_tests/{filename}.fa"
test_twobit = f"test_data/seq_tests/{filename}.2bit"
# Load Fasta data
expected = {}
with open(test_fa) as f:
for h, s in quick_fasta_iter(f):
expected[h] = s
# Open 2bit
with open(test_twobit, "rb") as f:
t = twobit.TwoBitFile(f)
for k, s in expected.items():
assert k in t.index
# assert t.index[k].size == len(s)
length = len(s)
for _ in range(100):
start = random.randint(0, length - 2)
end = random.randint(start + 1, length)
assert t[k].get(start, end) == s[start:end]
assert t[k][start:end] == s[start:end], "seq: %s, start: %d, end: %d\nExpected:\n%s\nActual:\n%s\n" % (
k,
start,
end,
s[start:end],
t.get(k, start, end),
)
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