def test_reference_bed_file_exists(args, tmpdir):
with pytest.raises(SystemExit) as pytest_wrapped_e:
args.return_value = ['file', 'gene', 'ensembl', False, 'hg38', tmpdir]
genome_annotations_filter.main()
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1
def test_case_two(args, tmpdir):
output_folder = tmpdir.mkdir('output')
args.return_value = [
reference_annotation_bed_file[0], 'intron', 'ensembl', 'ucsc', 'hg38',
output_folder
]
genome_annotations_filter.main()
assert len([name for name in os.listdir(output_folder)]) == 3
chromosome_1_json = os.path.join(output_folder, "chr=chr1", "intron.json")
num_lines = sum(1 for line in open(chromosome_1_json))
exon_number_chr1 = 5
assert num_lines == exon_number_chr1 - 1
chromosome_5_json = os.path.join(output_folder, "chr=chr5", "intron.json")
num_lines = sum(1 for line in open(chromosome_5_json))
exon_number_chr5 = 2
assert num_lines == exon_number_chr5 - 1
chromosome_11_json = os.path.join(output_folder, "chr=chr11",
"intron.json")
num_lines = sum(1 for line in open(chromosome_11_json))
exon_number_chr11 = 1
assert num_lines == exon_number_chr11 - 1
def test_output_folder_exists(args):
with pytest.raises(SystemExit) as pytest_wrapped_e:
args.return_value = args.return_value = [
reference_annotation_bed_file[0], 'gene', 'ensembl', False, 'hg38',
'output'
]
genome_annotations_filter.main()
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 3
def test_entity_type_exists(args, tmpdir):
with pytest.raises(SystemExit) as pytest_wrapped_e:
output_folder = tmpdir.mkdir('output')
args.return_value = args.return_value = [
reference_annotation_bed_file[0], 'asdasd', 'ensembl', False,
'hg38', output_folder
]
genome_annotations_filter.main()
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 4
def test_reference_bed_file_is_a_bed_file(args, tmpdir):
with pytest.raises(SystemExit) as pytest_wrapped_e:
fake_file = tmpdir.join("wrong_file.tsv")
fake_file.write("")
args.return_value = [
str(fake_file), 'gene', 'ensembl', False, 'hg38', tmpdir
]
genome_annotations_filter.main()
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 2