def test_positive_read_three(self, stdout):
region_filename = generate_random_filename()
seq_filename = generate_random_filename()
with open(region_filename, 'w') as file:
file.write("\t".join(["chr1", "0", "10", "name", "0", "+"]))
with open(seq_filename, 'w') as file:
file.write("\t".join(["chr1", "2", "9", "name", "0", "+"]))
metaplot.main(['three', region_filename, seq_filename])
# Get the result from stdout by splitting into a list and making the output floats where possible
result = [line for line in stdout.getvalue().split("\n") if line]
result[0] = result[0].split("\t")
for i, line in enumerate(result[1:]):
result[i + 1] = [float(val) for val in line.split()]
seq_file_basename = seq_filename.split("/")[-1]
expected = [[
"Position", seq_file_basename + " 3' sense strand",
seq_file_basename + " 3' divergent strand"
], [-5, 0, 0], [-4, 0, 0], [-3, 0, 0], [-2, 0, 0], [-1, 0, 0],
[1, 0, 0], [2, 0, 0], [3, 0, 0], [4, 1, 0], [5, 0, 0]]
remove_files(region_filename, seq_filename)
self.assertEqual(result, expected)
def test_complete_run(self, stdout):
reads_filename = generate_random_filename()
with open(reads_filename, 'w') as file:
file.write("chr1\t1\t10\tname\t0\t+\n")
file.write("chr1\t10\t20\tname\t0\t-\n")
regions_filename = generate_random_filename()
with open(regions_filename, 'w') as file:
file.write("chr1\t0\t20\tname\t0\t+\n")
metaplot.main(['whole', regions_filename, reads_filename])
output = stdout.getvalue().split("\n")[1:]
result = []
for line in output:
if line:
result.append(tuple([float(val) for val in line.split()]))
remove_files(reads_filename, regions_filename)
position = list(range(-10, 0)) + list(range(1, 11))
fw_expected = [0] + [1] * 9 + [0] * 10
rv_expected = [0] * 10 + [-1] * 10
expected = list(zip(position, fw_expected, rv_expected))
self.assertEqual(result, expected)
def test_two_sequencing_files(self, stdout):
reads_filename = generate_random_filename()
reads_filename_two = generate_random_filename()
with open(reads_filename, 'w') as file:
file.write("chr1\t1\t10\tname\t0\t+\n")
file.write("chr1\t10\t20\tname\t0\t-\n")
with open(reads_filename_two, 'w') as file:
file.write("chr1\t1\t10\tname\t0\t-\n")
file.write("chr1\t10\t20\tname\t0\t+\n")
regions_filename = generate_random_filename()
with open(regions_filename, 'w') as file:
file.write("chr1\t0\t20\tname\t0\t+\n")
metaplot.main(
['whole', regions_filename, reads_filename, reads_filename_two])
output = stdout.getvalue().split("\n")
header = output[0].split("\t")
reads_basename = reads_filename.split("/")[-1]
reads_basename_two = reads_filename_two.split("/")[-1]
expected_header = [
"Position", reads_basename + " whole sense strand",
reads_basename + " whole divergent strand",
reads_basename_two + " whole sense strand",
reads_basename_two + " whole divergent strand"
]
self.assertEqual(header, expected_header)
result = []
for line in output[1:]:
if line:
result.append(tuple([float(val) for val in line.split()]))
remove_files(reads_filename, regions_filename, reads_filename_two)
position = list(range(-10, 0)) + list(range(1, 11))
fw_expected = [0] + [1] * 9 + [0] * 10
rv_expected = [0] * 10 + [-1] * 10
fw_expected_two = [0] * 10 + [1] * 10
rv_expected_two = [0] + [-1] * 9 + [0] * 10
expected = list(
zip(position, fw_expected, rv_expected, fw_expected_two,
rv_expected_two))
self.assertEqual(result, expected)