def test_within_length(self):
"""within_length checks whether a flowgram is within a given length."""
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08") # len 7
flow2 = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1') # len 10
self.assertTrue(within_length(flow1, 0,10))
self.assertFalse(within_length(flow1, 10,20))
self.assertFalse(within_length(flow2, 0,5))
self.assertTrue(within_length(flow2, 5,20))
self.assertTrue(within_length(flow2, 5,11))
def test_within_length(self):
"""within_length checks whether a flowgram is within a given length."""
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08") # len 7
flow2 = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1') # len 10
self.assertTrue(within_length(flow1, 0, 10))
self.assertFalse(within_length(flow1, 10, 20))
self.assertFalse(within_length(flow2, 0, 5))
self.assertTrue(within_length(flow2, 5, 20))
self.assertTrue(within_length(flow2, 5, 11))
def test_filter_sff_file(self):
"""filter_sff_file filters out bad reads."""
try:
fh = open(self.tiny_test)
except IOError:
self.fail(
"Could not open test file %s. Skipping test" %
self.tiny_test)
# With no filters all flowgram should be in out file
flowgrams, header = lazy_parse_sff_handle(fh)
filter_list = []
fd, out_file_name = mkstemp(
prefix="test_filter_sff_file",
suffix=".sff.txt")
close(fd)
out_fh = open(out_file_name, "w")
l = filter_sff_file(flowgrams, header, filter_list, out_fh)
remove(out_file_name)
fh.close()
self.assertEqual(l, 114)
# With good filters some should survive
fh = open(self.tiny_test)
flowgrams, header = lazy_parse_sff_handle(fh)
filter_list = [lambda f:within_length(f, 100, 300)]
fd, out_file_name = mkstemp(
prefix="test_filter_sff_file",
suffix=".sff.txt")
close(fd)
out_fh = open(out_file_name, "w")
l = filter_sff_file(flowgrams, header, filter_list, out_fh)
remove(out_file_name)
fh.close()
self.assertEqual(l, 112)
# With strong filters nothing should be in
fh = open(self.tiny_test)
flowgrams, header = lazy_parse_sff_handle(fh)
filter_list = [lambda f:within_length(f, 0, 0)]
fd, out_file_name = mkstemp(
prefix="test_filter_sff_file",
suffix=".sff.txt")
close(fd)
out_fh = open(out_file_name, "w")
l = filter_sff_file(flowgrams, header, filter_list, out_fh)
remove(out_file_name)
self.assertEqual(l, 0)
