def test_make_targets():
rules = [MockRule(name="samtools_depth", output={"txt": "{version}/{end}/medium.depth.txt"}),
MockRule(name="samtools_rmdup", output={"txt": "{version}/{end}/medium.rmdup.txt"})]
conf = config.application_config()
tgt = helpers.make_targets(rules, conf, 'samtools', end='se')
# samtools_rmdup only available for version 1.3.1
assert len(tgt) == 3
def test_get_every_application_fixture():
conf = config.application_config()
for ad in config.APPLICATION_DIRECTORIES:
app = os.path.basename(ad)
version = conf[app]['_default']
for command in conf[app].keys():
if command.startswith("_"):
continue
af = config.get_application_fixture(app, command, version, 'se')
for x in af.values():
assert os.path.dirname(x).startswith(os.path.join(app, str(version)))
def application_output(application, command, version, end="se", **kwargs):
"""
Fixture factory to generate application output.
Params:
application (str): application name
command (str): application command name
version (str): application version
end (str): paired end or single end
Returns:
func: a filetype fixture function
"""
from pytest_ngsfixtures.config import application_config
conf = application_config()
assert application in conf.keys(), "no such application '{}'".format(
application)
assert command in conf[application].keys(), "no such command '{}'".format(
command)
assert type(version) is str, "version must be string"
if "_versions" in conf[application][command].keys():
_versions = [str(x) for x in conf[application][command]["_versions"]]
else:
_versions = [str(x) for x in conf[application]["_versions"]]
assert version in _versions, "no such application output for version '{}', application '{}'".format(
version, application)
assert end in ["se", "pe"], "end must be either se or pe"
params = {'version': version, 'end': end}
output = [
x.format(**params)
for x in conf[application][command]['output'].values()
]
if len(output) == 1:
src = os.path.join("applications", application, output[0])
return filetype(src, **kwargs)
else:
src = [os.path.join("applications", application, x) for x in output]
return fileset(src, **kwargs)
def test_collect_samtools_config_application():
conf = config.application_config('samtools')
assert 'samtools' in conf.keys()
assert 'fastqc' not in conf.keys()
assert 'input' in conf.keys()
def test_collect_bwa_config_application():
conf = config.application_config('bwa')
assert 'bwa' in conf.keys()
assert 'fastqc' not in conf.keys()
assert 'input' in conf.keys()
def test_collect_config():
conf = config.application_config()
assert 'bwa' in conf.keys()
assert 'fastqc' in conf.keys()
assert 'input' in conf.keys()