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from nose.tools import assert_equal, assert_true, assert_false
import sys, numpy as np
from tempfile import NamedTemporaryFile
from pbcore.io.align._bgzf import BgzfReader, BgzfWriter
# TODO: did Biopython have tests for it?
class TestBgzf(object):
def __init__(self):
pass
def roundTripData(self, size, sizeToRead=None):
if sizeToRead is None: sizeToRead = size
data = (np.sin(np.arange(size))*100).astype(np.int8).tostring()
assert size == len(data)
with NamedTemporaryFile() as compressionOutput:
with BgzfWriter(compressionOutput.name, compresslevel=1) as writer:
writer.write(data)
with BgzfReader(compressionOutput.name) as reader:
decompressionOutput = reader.read(sizeToRead)
assert_equal(data[:sizeToRead], decompressionOutput)
def test_small_data(self):
self.roundTripData(0)
for i in xrange(8):
self.roundTripData(10**i)
def test_partial_reads(self):
self.roundTripData(10**7, (10**7)/2)
# def test_big_data(self):
# # This breaks because of recursion depth limit in
# # implementation from Biopython.
# self.roundTripData(10**8)
if __name__ == "__main__":
size = int(sys.argv[1])
TestBgzf().roundTripData(size)
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