def test_arguments(self):
# Should print the usage
with self.assertRaises(SystemExit):
with Quieter():
tps_distance_per_gene.parse_args([])
with self.assertRaises(SystemExit):
with Quieter():
tps_distance_per_gene.parse_args(["regions filename"])
regions_file = generate_random_filename()
with open(regions_file, 'w') as file:
file.write(
"\t".join(['chr1', '1', '3', 'name', '0', '+'])
)
max_threads = multiprocessing.cpu_count()
result = tps_distance_per_gene.parse_args([regions_file, 'seq_file'])
self.assertEqual(result, (regions_file, ['seq_file'], 2, max_threads))
result = tps_distance_per_gene.parse_args([regions_file, 'seq_file', '-t', '2'])
self.assertEqual(result, (regions_file, ['seq_file'], 2, 2))
result = tps_distance_per_gene.parse_args([regions_file, 'seq_file', '--threads', '2'])
self.assertEqual(result, (regions_file, ['seq_file'], 2, 2))
def test_arguments(self):
with self.assertRaises(SystemExit):
with Quieter():
sequence_from_region_around_max_tss.parse_args([])
with self.assertRaises(SystemExit):
with Quieter():
sequence_from_region_around_max_tss.parse_args(
["max_tss_file"])
with self.assertRaises(SystemExit):
with Quieter():
sequence_from_region_around_max_tss.parse_args(
["max_tss_file", 'left'])
max_tss_file = generate_random_filename()
with open(max_tss_file, 'w') as file:
file.write(
"\t".join(["chr16", "53607", "53608", "POLR3K", "0", "-"]) +
"\n" +
"\t".join(["chr16", "53872", "53873", "SNRNP25", "0", "+"]) +
"\n")
result = sequence_from_region_around_max_tss.parse_args(
[max_tss_file, '-5', '10'])
search = [["-", 5], ['+', 10]]
self.assertEqual(result, (False, max_tss_file, search))
remove_files(max_tss_file)
def test_incorrect_number_of_arguments(self):
with self.assertRaises(SystemExit):
with Quieter():
nucleotide_heatmap.parse_args([])
with self.assertRaises(SystemExit):
with Quieter():
nucleotide_heatmap.parse_args(["max_tss_file"])
with self.assertRaises(SystemExit):
with Quieter():
nucleotide_heatmap.parse_args(["max_tss_file", "region_width"])
with self.assertRaises(SystemExit):
with Quieter():
nucleotide_heatmap.parse_args(["max_tss_file", "region_width", "vertical_average", "extra"])
max_tss_file = generate_random_filename()
with open(max_tss_file, 'w') as file:
file.write(
"\t".join(['chr1', '1', '2', 'name', '0', '+'])
)
result = nucleotide_heatmap.parse_args([max_tss_file, '50', '2000', '2'])
self.assertEqual(result, (max_tss_file, 50, 2000, 2))
remove_files(max_tss_file)
def test_no_input(self):
with self.assertRaises(SystemExit):
with Quieter():
make_regions_file_centered_on_max_tss.parse_args([])
with self.assertRaises(SystemExit):
with Quieter():
make_regions_file_centered_on_max_tss.parse_args(['truQuant_file'])
result = make_regions_file_centered_on_max_tss.parse_args(['truQuant_file', '10'])
self.assertEqual(result, ('truQuant_file', 10, False))
def test_arguments(self):
with self.assertRaises(SystemExit):
with Quieter():
read_through_transcription.parse_input([
'Regions Filename', 'TSR Filename', '1000', '50000', '50'
])
with self.assertRaises(SystemExit):
with Quieter():
read_through_transcription.parse_input(
['Regions Filename', 'TSR Filename', '1000', '50000'])
with self.assertRaises(SystemExit):
with Quieter():
read_through_transcription.parse_input(
['Regions Filename', 'TSR Filename', '1000'])
with self.assertRaises(SystemExit):
with Quieter():
read_through_transcription.parse_input(
['Regions Filename', 'TSR Filename'])
with self.assertRaises(SystemExit):
with Quieter():
read_through_transcription.parse_input(['Regions Filename'])
max_threads = multiprocessing.cpu_count()
result = read_through_transcription.parse_input([
'Regions Filename', 'TSR Filename', '1000', '50000', '50',
'seq_file'
])
self.assertEqual(result, ('Regions Filename', 'TSR Filename', 1000,
50000, 50, ['seq_file'], max_threads))
# Test threading works
result = read_through_transcription.parse_input([
'Regions Filename', 'TSR Filename', '1000', '50000', '50',
'seq_file', '-t', '4'
])
self.assertEqual(result, ('Regions Filename', 'TSR Filename', 1000,
50000, 50, ['seq_file'], 4))
result = read_through_transcription.parse_input([
'Regions Filename', 'TSR Filename', '1000', '50000', '50',
'seq_file', '--threads', '4'
])
self.assertEqual(result, ('Regions Filename', 'TSR Filename', 1000,
50000, 50, ['seq_file'], 4))
def test_parse_input(self):
# No arguments throws error
with self.assertRaises(SystemExit):
with Quieter():
metaplot.parse_input([])
# Needs a region file and at least one seq file
regions_file = generate_random_filename()
with open(regions_file, 'w') as file:
file.write("\t".join(['chr1', '1', '3', 'name', '0', '+']))
region_length = 2
max_threads = multiprocessing.cpu_count()
# These will work!!
result = metaplot.parse_input(['five', regions_file, 'seq_file'])
self.assertEqual(result,
('five', regions_file, ['seq_file'], 2, max_threads))
result = metaplot.parse_input(['three', regions_file, 'seq_file'])
self.assertEqual(result,
('three', regions_file, ['seq_file'], 2, max_threads))
# Test the threading is working
result = metaplot.parse_input(
['five', regions_file, 'seq_file', '-t', '4'])
self.assertEqual(result, ('five', regions_file, ['seq_file'], 2, 4))
result = metaplot.parse_input(
['three', regions_file, 'seq_file', '--threads', '4'])
self.assertEqual(result, ('three', regions_file, ['seq_file'], 2, 4))
remove_files(regions_file)
def test_arguments(self):
# No arguments throws an error
with self.assertRaises(SystemExit):
with Quieter():
base_distribution.parse_args([])
regions_file = generate_random_filename()
with open(regions_file, 'w') as file:
file.write("\t".join(['chr1', '1', '3', 'name', '0', '+']))
# Regions file works file
result = base_distribution.parse_args([regions_file])
self.assertEqual(result, (regions_file, 2))
# Multiple arguments throws an error
with self.assertRaises(SystemExit):
with Quieter():
base_distribution.parse_args(['first', 'second'])
remove_files(regions_file)
def test_arguments(self):
with self.assertRaises(SystemExit):
with Quieter():
truQuant.parse_input([])
seq_file_for_annotation = generate_random_filename()
with open(seq_file_for_annotation, 'w') as file:
file.write("\t".join(['chr1', '1', '3', 'name', '0', '+']))
max_threads = multiprocessing.cpu_count()
result = truQuant.parse_input([seq_file_for_annotation])
self.assertEqual(result, ([seq_file_for_annotation], 1000, 0.3, 75,
(150, 20, 30, 600), max_threads))
result = truQuant.parse_input([
seq_file_for_annotation, '-a', '500', '-b'
'0.6', '-r', '10', '-t', '20'
])
self.assertEqual(result, ([seq_file_for_annotation], 500, 0.6, 10,
(150, 20, 30, 600), 20))
result = truQuant.parse_input([
seq_file_for_annotation, '-a', '500', '--blacklist_percent', '0.6',
'-r', '10', '-t', '20'
])
self.assertEqual(result, ([seq_file_for_annotation], 500, 0.6, 10,
(150, 20, 30, 600), 20))
# Try making the blacklist percent greater than one
with self.assertRaises(SystemExit):
with Quieter():
truQuant.parse_input([seq_file_for_annotation, '-b', '1.5'])
remove_files(seq_file_for_annotation)
def test_arguments(self):
with self.assertRaises(SystemExit):
with Quieter():
pausing.parse_input(['regions_filename'])
regions_file = generate_random_filename()
with open(regions_file, 'w') as file:
file.write("\t".join(['chr1', '1', '3', 'name', '0', '+']))
max_threads = multiprocessing.cpu_count()
result = pausing.parse_input([regions_file, 'seq_file'])
self.assertEqual(result,
(regions_file, ['seq_file'], 100, max_threads))
# Test the threading option
result = pausing.parse_input([regions_file, 'seq_file', '-t', '2'])
self.assertEqual(result, (regions_file, ['seq_file'], 100, 2))
result = pausing.parse_input(
[regions_file, 'seq_file', '--threads', '2'])
self.assertEqual(result, (regions_file, ['seq_file'], 100, 2))
remove_files(regions_file)
def test_invalid_number_of_arguments(self):
# Should print the usage
with self.assertRaises(SystemExit):
with Quieter():
TES_fold_change_heatmap.main([])
def test_search_not_in_region(self):
# Should raise an InvalidSearch error because polr2a file is -10 to +10
with self.assertRaises(InvalidSearchException):
with Quieter():
sequence_searches.parse_input(
[self.polr2a_region_file, 'TATA,-20:-10'])
def test_incorrect_search(self):
# Should raise an InvalidSearch error because of the underscore
with self.assertRaises(InvalidSearchException):
with Quieter():
sequence_searches.parse_input(
[self.polr2a_region_file, 'TATA,-5_7'])
def test_only_regions_file(self):
# Should print the usage
with self.assertRaises(SystemExit):
with Quieter():
sequence_searches.parse_input([self.polr2a_region_file])
def test_no_arguments(self):
# Should print the usage
with self.assertRaises(SystemExit):
with Quieter():
sequence_searches.parse_input([])