def test_help():
try:
main.main([prog, '--help'])
assert False
except SystemExit:
pass
else:
raise Exception
def test_help():
try:
main.main([prog, '--help'])
assert False
except SystemExit:
pass
else:
raise Exception
def test_mutually_exclusive():
try:
main.main([
prog, '--pipeline', 'quality_control', '--info', "quality_control"
])
assert False
except SystemExit:
assert True
def _test_with_cluster_config(tmpdir):
directory = tmpdir.mkdir("analysis2")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
main.main([prog, "--pipeline", "rnaseq", "--file1", file1, "--snakemake-cluster",
'"sbatch --mem={cluster.ram}"',"--force",
"--working-directory", name])
with open("%s/runme.sh" % name) as fh:
assert "cluster_config" in fh.read()
def _test_with_cluster_config(tmpdir):
directory = tmpdir.mkdir("analysis2")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
main.main([
prog, "--pipeline", "rnaseq", "--file1", file1, "--snakemake-cluster",
'"sbatch --mem={cluster.ram}"', "--force", "--working-directory", name
])
with open("%s/runme.sh" % name) as fh:
assert "cluster_config" in fh.read()
def test_config_params(tmpdir):
directory = tmpdir.mkdir("analysis3")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
main.main([prog, "--pipeline", "quality_control", "--force", "--file1", file1,
"--no-adapters", "--config-params", "bwa_mem_phix:threads:4" ,
"--working-directory", name])
try:
main.main([prog, "--pipeline", "quality_control", "--force", "--file1", file1,
"--no-adapters", "--config-params", "bwa_mem_phix",
"--working-directory", name])
assert False
except:
assert True
def test_input(tmpdir):
directory = tmpdir.mkdir("analysis0")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
file2 = sequana_data('Hm2_GTGAAA_L005_R2_001.fastq.gz', 'data')
main.main([
prog, "--pipeline", "quality_control", "--file1", file1, "--file2",
file2, "--no-adapters", "--force", "--working-directory", name
])
try:
main.main([
prog, "--pipeline", "quality_control", "--file1", file1 + "dummy",
"--no-adapters", "--force", "--working-directory", name
])
assert False
except ValueError:
assert True
try:
main.main([
prog, "--pipeline", "quality_control", "--file1", file1,
"--no-adapters", "--force", "--file2", file2 + "duly",
"--working-directory", name
])
assert False
except ValueError:
assert True
try:
main.main([
prog, "--pipeline", "quality_control", "--file1", file1,
"--no-adapters", "--force", "--file2", file2,
"--working-directory", name, "--kraken", "dummy"
])
assert False
except ValueError:
assert True
try:
main.main([
prog, "--pipeline", "quality_control", "--file1", file1,
"--no-adapters", "--force", "--file2", file2,
"--working-directory", name, "--kraken", "dummy"
])
assert False
except ValueError:
assert True
def test_config_params(tmpdir):
directory = tmpdir.mkdir("analysis3")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
main.main([
prog, "--pipeline", "quality_control", "--force", "--file1", file1,
"--no-adapters", "--config-params", "bwa_mem_phix:threads:4",
"--working-directory", name
])
try:
main.main([
prog, "--pipeline", "quality_control", "--force", "--file1", file1,
"--no-adapters", "--config-params", "bwa_mem_phix",
"--working-directory", name
])
assert False
except:
assert True
def test_input(tmpdir):
directory = tmpdir.mkdir("analysis0")
name = directory.__str__()
file1 = sequana_data('Hm2_GTGAAA_L005_R1_001.fastq.gz', 'data')
file2 = sequana_data('Hm2_GTGAAA_L005_R2_001.fastq.gz', 'data')
main.main([prog, "--pipeline", "quality_control", "--file1",
file1, "--file2", file2, "--no-adapters" , "--force",
"--working-directory", name])
try:
main.main([prog, "--pipeline", "quality_control", "--file1",
file1+"dummy", "--no-adapters" , "--force",
"--working-directory", name])
assert False
except ValueError:
assert True
try:
main.main([prog, "--pipeline", "quality_control", "--file1",
file1, "--no-adapters" , "--force", "--file2",
file2+"duly","--working-directory", name])
assert False
except ValueError:
assert True
try:
main.main([prog, "--pipeline", "quality_control", "--file1",
file1, "--no-adapters" , "--force", "--file2",
file2,"--working-directory", name, "--kraken", "dummy"])
assert False
except ValueError:
assert True
try:
main.main([prog, "--pipeline", "quality_control", "--file1",
file1, "--no-adapters" , "--force", "--file2",
file2,"--working-directory", name, "--kraken", "dummy"])
assert False
except ValueError:
assert True
def test_init(mocker):
try:
# py3
with mocker.patch('builtins.input', return_value="y"):
try:
main.main([prog, '--pipeline', "qualitydummy"])
assert False
except:
assert True
except:
# py2
with mocker.patch('__builtin__.input', return_value="y"):
main.main([prog, '--pipeline', "quality_control"])
with mocker.patch('__builtin__.input', return_value="y"):
try:
main.main([prog, '--pipeline', "qualitydummy"])
assert False
except:
assert True
def test_init(mocker):
try:
# py3
with mocker.patch('builtins.input', return_value="y"):
try:
main.main([prog, '--pipeline', "qualitydummy"])
assert False
except:
assert True
except:
# py2
with mocker.patch('__builtin__.input', return_value="y"):
main.main([prog, '--pipeline', "quality_control"])
with mocker.patch('__builtin__.input', return_value="y"):
try:
main.main([prog, '--pipeline', "qualitydummy"])
assert False
except:
assert True
def test_main():
main.main([prog])
def test_show_pipelines():
main.main([prog, '--show-pipelines'])
def _test_issue(mocker):
def func(*args, **kwargs):
pass
with patch('easydev.onweb', func):
main.main([prog, '--issue'])
def test_info(mocker):
def func(*args, **kwargs):
pass
with patch('easydev.onweb', func):
main.main([prog, '--info', "quality_control"])
def test_get_config():
main.main([prog, "--pipeline", "quality_control",
"--get-config"])
import os
os.remove("config.yaml")
def test_info(mocker):
def func(*args, **kwargs):
pass
with patch('easydev.onweb', func ):
main.main([prog, '--info', "quality_control"])
def test_get_config():
main.main([prog, "--pipeline", "quality_control", "--get-config"])
import os
os.remove("config.yaml")
def _test_issue(mocker):
def func(*args, **kwargs):
pass
with patch('easydev.onweb', func ):
main.main([prog, '--issue'])
def test_version():
main.main([prog, '--version'])
def test_show_pipelines():
main.main([prog, '--show-pipelines'])
def test_mutually_exclusive():
try:
main.main([prog, '--pipeline', 'quality_control', '--info', "quality_control"])
assert False
except SystemExit:
assert True
def test_main():
main.main([prog])
def test_version():
main.main([prog, '--version'])