def check_prereqs(options):
failure_msgs = []
if options.full_hmmer or options.inclusive:
failure_msgs.extend(fullhmmer.check_prereqs(options))
failure_msgs.extend(genefinding.check_prereqs(options))
failure_msgs.extend(hmm_detection.check_prereqs())
if options.smcogs:
failure_msgs.extend(smcogs.check_prereqs(options))
if options.clusterblast:
failure_msgs.extend(clusterblast.check_prereqs(options))
if options.subclusterblast:
failure_msgs.extend(subclusterblast.check_prereqs(options))
if options.knownclusterblast:
failure_msgs.extend(knownclusterblast.check_prereqs(options))
if options.coexpress:
failure_msgs.extend(coexpress.check_prereqs(options))
return failure_msgs
def check_prereqs(options):
failure_msgs = []
if options.full_hmmer or options.inclusive:
failure_msgs.extend(fullhmmer.check_prereqs(options))
failure_msgs.extend(genefinding.check_prereqs(options))
failure_msgs.extend(hmm_detection.check_prereqs())
if options.run_asf:
failure_msgs.extend(active_site_finder.check_prereqs(options))
if options.tta:
failure_msgs.extend(tta.check_prereqs(options))
if options.smcogs:
failure_msgs.extend(smcogs.check_prereqs(options))
if options.clusterblast:
failure_msgs.extend(clusterblast.check_prereqs(options))
if options.subclusterblast:
failure_msgs.extend(subclusterblast.check_prereqs(options))
if options.knownclusterblast:
failure_msgs.extend(knownclusterblast.check_prereqs(options))
if options.cassis:
failure_msgs.extend(cassis.check_prereqs(options))
return failure_msgs
def test_check_prereqs(self):
"Test fullhmmer.check_prereqs()"
config = Namespace()
trace = """ Called antismash.utils.locate_executable('hmmscan')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3f')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3i')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3m')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3p')"""
expected = []
returned = fullhmmer.check_prereqs(config)
self.assertListEqual(expected, returned)
assert_same_trace(self.tt, trace)
def test_check_prereqs_missing_exe(self):
"Test fullhmmer.check_prereqs() with a missing executable"
config = Namespace()
antismash.utils.locate_executable.mock_returns = None
trace = """ Called antismash.utils.locate_executable('hmmscan')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3f')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3i')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3m')
Called antismash.utils.locate_file(
'.../antismash/generic_modules/fullhmmer/Pfam-A.hmm.h3p')"""
expected = ["Failed to locate file: 'hmmscan'"]
returned = fullhmmer.check_prereqs(config)
self.assertListEqual(expected, returned)
assert_same_trace(self.tt, trace)