def check_sub_prereqs(_options: ConfigType) -> List[str]:
""" Check if all required applications and datafiles are present.
options is irrelevant here
"""
# Tuple is ( binary_name, optional)
_required_binaries = [
('blastp', False),
('makeblastdb', False),
]
_required_files = [
('subclusterprots.fasta', False),
('subclusterprots.fasta.phr', False),
('subclusterprots.fasta.pin', False),
('subclusterprots.fasta.psq', False),
('subclusters.txt', False)
]
failure_messages = []
for binary_name, optional in _required_binaries:
if path.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
for file_name, optional in _required_files:
if path.locate_file(_get_datafile_path(file_name)) is None and not optional:
failure_messages.append("Failed to locate file: %r" % file_name)
return failure_messages
def check_prereqs() -> List[str]:
failure_messages = []
for binary_name, optional in [('hmmscan', False), ('hmmpress', False)]:
if path.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
markov_models = [path.get_full_path(__file__, 'data', filename) for filename in [
'abmotifs.hmm', 'dockingdomains.hmm',
'ksdomains.hmm', 'nrpspksdomains.hmm']]
binary_extensions = ['.h3f', '.h3i', '.h3m', '.h3p']
for hmm in markov_models:
if path.locate_file(hmm) is None:
failure_messages.append("Failed to locate file %r" % hmm)
continue
for ext in binary_extensions:
binary = "{}{}".format(hmm, ext)
if path.locate_file(binary) is None:
result = subprocessing.run_hmmpress(hmm)
if not result.successful():
failure_messages.append('Failed to hmmpress {!r}: {}'.format(hmm, result.stderr))
break
return failure_messages
def check_prereqs() -> List[str]:
"Check if all required applications are around"
options = get_config()
# Tuple is ( binary_name, optional)
_required_binaries = [
('blastp', False),
('makeblastdb', False),
('diamond', False),
]
_required_files = [
('geneclusterprots.dmnd', False),
('geneclusterprots.fasta', False),
('geneclusters.txt', False),
]
clusterblastdir = os.path.join(options.database_dir, "clusterblast")
failure_messages = []
for binary_name, optional in _required_binaries:
if path.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
for file_name, optional in _required_files:
if path.locate_file(os.path.join(clusterblastdir,
file_name)) is None and not optional:
failure_messages.append("Failed to locate file: %r" % file_name)
failure_messages.extend(check_known_prereqs(options))
failure_messages.extend(check_sub_prereqs(options))
return failure_messages
def check_prereqs():
""" Ensures all required external programs are available """
failure_messages = []
for binary_name in ['hmmpfam2']:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate executable for %r" %
binary_name)
return failure_messages
def check_prereqs() -> List[str]:
"Check if all required applications are around"
failure_messages = []
for binary_name in ['muscle', 'fasttree']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
return failure_messages
def check_prereqs() -> List[str]:
"Checks if all required files and applications are around"
_binary_extensions = ['.h3f', '.h3i', '.h3m', '.h3p']
failure_messages = []
for binary_name in ['hmmpfam2', 'hmmscan', 'hmmpress']:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate file: %r" % binary_name)
# Get all HMM profile names from XML file
for profile in ["PKSI-KR.hmm2", "PKSI-KS_N.hmm2", "PKSI-KS_C.hmm2", "PKSI-AT.hmm2",
"PKSI-ACP.hmm2", "PKSI-DH.hmm2", "Thioesterase.hmm2", "PKSI-ER.hmm2",
"aa-activating.aroundLys.hmm2", "p450.hmm2"]:
full_hmm_path = path.get_full_path(__file__, "data", profile)
if path.locate_file(full_hmm_path) is None:
failure_messages.append("Failed to locate file: %s" % profile)
continue
if profile.endswith(".hmm2"):
continue
for ext in _binary_extensions:
binary = "{hmm}{ext}".format(hmm=full_hmm_path, ext=ext)
if not path.locate_file(binary):
result = subprocessing.run_hmmpress(full_hmm_path)
if not result.successful():
failure_messages.append("Failed to hmmpress {!r}: {!r}".format(profile, result.stderr))
# hmmpress generates _all_ binary files in one go, so stop the loop
break
binary_mtime = os.path.getmtime(binary)
hmm_mtime = os.path.getmtime(full_hmm_path)
if hmm_mtime < binary_mtime:
# generated file younger than hmm profile, do nothing
continue
try:
for filename in glob.glob("{}.h3?".format(full_hmm_path)):
logging.debug("removing outdated file %r", filename)
os.remove(filename)
except OSError as err:
failure_messages.append("Failed to remove outdated binary file for %s: %s" %
(profile, err))
break
result = subprocessing.run_hmmpress(full_hmm_path)
if not result.successful():
failure_messages.append("Failed to hmmpress %r: %r" % (profile, result.stderr))
failure_messages.append("HMM binary files outdated. %s (changed: %s) vs %s (changed: %s)" %
(profile, datetime.datetime.fromtimestamp(hmm_mtime),
binary, datetime.datetime.fromtimestamp(binary_mtime)))
# hmmpress generates _all_ binary files in one go, so stop the loop
break
return failure_messages
def check_prereqs() -> List[str]:
"""Check for prerequisites"""
failure_messages = []
for binary_name, _ in [("meme", "4.11.1"), ("fimo", "4.11.1")]:
if path.locate_executable(binary_name) is None:
failure_messages.append(
"Failed to locate executable for {!r}".format(binary_name))
# TODO: Check binary version here
return failure_messages
def check_prereqs() -> List[str]:
""" Check prereqs
hmmpfam2: used to find extra HMM hits not in hmm_detection
"""
failure_messages = []
for binary_name in ['hmmpfam2']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
return failure_messages
def check_prereqs() -> List[str]:
""" Check the prerequisites.
java: NRPSPredictor, sandpuma
muscle: sandpuma, at_analysis, kr_analysis, minowa, orderfinder
hmmsearch: minowa
"""
failure_messages = []
for binary_name in ["hmmsearch", "muscle", "java"]:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
return failure_messages
def check_prereqs() -> List[str]:
""" Checks if the required external programs are available """
failure_messages = []
for binary_name, optional in [('hmmpfam2', False), ('fimo', True)]:
present = True
if path.locate_executable(binary_name) is None:
present = False
if not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
if binary_name == "fimo":
get_config().fimo_present = present
return failure_messages
def check_known_prereqs(options: ConfigType) -> List[str]:
""" Determines if any prerequisite data files or executables are missing
Arguments:
options: antismash Config
Returns:
a list of error messages, one for each failing prequisite check
"""
failure_messages = []
for binary_name in ['blastp', 'makeblastdb', options.cb_diamond_executable]:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
return failure_messages
def check_prereqs() -> List[str]:
""" Check that prereqs are satisfied. hmmpress is only required if the
databases have not yet been generated.
"""
failure_messages = []
for binary_name in ["hmmsearch", "hmmpress"]:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate executable for %r" % binary_name)
# no point checking the data if we can't use it
if failure_messages:
return failure_messages
failure_messages.extend(prepare_data(logging_only=True))
return failure_messages
def check_prereqs() -> List[str]:
""" Make sure the external tools to use are available """
failure_messages = []
options = get_config()
if options.genefinding_tool in ['none']:
return failure_messages
binaries = []
if options.genefinding_tool in ['prodigal', 'prodigal-m']:
binaries = ['prodigal']
elif options.taxon == 'fungi':
binaries = ['glimmerhmm']
for binary_name in binaries:
if not locate_executable(binary_name):
failure_messages.append("Failed to locate executable for %r" % binary_name)
return failure_messages
def check_prereqs() -> List[str]:
""" Ensure at least one database exists and is valid """
failure_messages = []
for binary_name in ['hmmscan']:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate executable: %r" % binary_name)
data_dir = get_config().database_dir
try:
version = pfamdb.find_latest_database_version(data_dir)
except ValueError as err:
failure_messages.append(str(err))
return failure_messages
data_path = os.path.join(data_dir, "pfam", version)
failure_messages.extend(pfamdb.check_db(data_path))
return failure_messages
def check_prereqs() -> List[str]:
"""Check for prerequisites
"""
failure_messages = []
for binary_name in ['hmmscan', 'hmmpress']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
database = os.path.join(get_config().database_dir, 'resfam', 'Resfams.hmm')
if path.locate_file(database) is None:
failure_messages.append('Failed to locate Resfam database in %s' %
database)
failure_messages.extend(prepare_data(logging_only=True))
return failure_messages
def check_prereqs() -> List[str]:
""" Check that prereqs are satisfied. hmmpress is only required if the
databases have not yet been generated.
"""
failure_messages = []
for binary_name, optional in [('hmmsearch', False), ('hmmpress', False)]:
if path.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
profiles = None
# Check that hmmdetails.txt is readable and well-formatted
try:
profiles = get_signature_profiles()
except ValueError as err:
failure_messages.append(str(err))
# the path to the markov model
hmm = path.get_full_path(__file__, 'data', 'bgc_seeds.hmm')
hmm_files = [os.path.join("data", sig.hmm_file) for sig in profiles]
if path.locate_file(hmm) is None:
# try to generate file from all specified profiles in hmmdetails
try:
with open(hmm, 'w') as all_hmms_handle:
for hmm_file in hmm_files:
with open(path.get_full_path(__file__, hmm_file),
'r') as handle:
all_hmms_handle.write(handle.read())
except OSError:
failure_messages.append('Failed to generate file {!r}'.format(hmm))
# if previous steps have failed, the remainder will too, so don't try
if failure_messages:
return failure_messages
binary_extensions = ['.h3f', '.h3i', '.h3m', '.h3p']
for ext in binary_extensions:
binary = "{}{}".format(hmm, ext)
if path.locate_file(binary) is None:
result = run_hmmpress(hmm)
if not result.successful():
failure_messages.append('Failed to hmmpress {!r}: {}'.format(
hmm, result.stderr))
break
return failure_messages
def check_prereqs() -> List[str]:
""" Checks the prereqs for the lanthipeptide module.
fimo is optional, having it available increases accuracy in the RODEO
subsection
"""
failure_messages = []
for binary_name, optional in [('hmmpfam2', False), ('fimo', True)]:
present = True
if path.locate_executable(binary_name) is None:
present = False
if not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
slot = '{}_present'.format(binary_name)
conf = get_config()
if hasattr(conf, slot):
setattr(conf, slot, present)
return failure_messages
def check_prereqs() -> List[str]:
"Check if all required applications are around"
options = get_config()
# Tuple is ( binary_name, optional)
_required_binaries = [
'blastp',
'makeblastdb',
options.cb_diamond_executable,
]
failure_messages = []
for binary_name in _required_binaries:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
failure_messages.extend(prepare_data(logging_only=True))
failure_messages.extend(check_known_prereqs(options))
failure_messages.extend(check_sub_prereqs(options))
return failure_messages
def check_prereqs() -> List[str]:
"Checks if all required files and applications are around"
failure_messages = []
for binary_name in ['hmmpfam2', 'hmmscan', 'hmmpress']:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate file: %r" % binary_name)
# Get all HMM profile names from XML file
for profile in [
"PKSI-KR.hmm2", "PKSI-KS_N.hmm2", "PKSI-KS_C.hmm2", "PKSI-AT.hmm2",
"PKSI-ACP.hmm2", "PKSI-DH.hmm2", "Thioesterase.hmm2",
"PKSI-ER.hmm2", "p450.hmm2"
]:
full_hmm_path = path.get_full_path(__file__, "data", profile)
if path.locate_file(full_hmm_path) is None:
failure_messages.append("Failed to locate file: %s" % profile)
continue
return failure_messages
def check_prereqs() -> List[str]:
"Check if all required applications are around"
failure_messages = []
for binary_name in ['muscle', 'hmmscan', 'hmmpress', 'fasttree', 'java']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
for hmm in ['smcogs.hmm']:
hmm = path.get_full_path(__file__, 'data', hmm)
if path.locate_file(hmm) is None:
failure_messages.append("Failed to locate file %r" % hmm)
continue
for ext in ['.h3f', '.h3i', '.h3m', '.h3p']:
binary = "%s%s" % (hmm, ext)
if path.locate_file(binary) is None:
# regenerate them
result = subprocessing.run_hmmpress(hmm)
if not result.successful():
failure_messages.append("Failed to hmmpress %s: %s" %
(hmm, result.stderr.rstrip()))
break
return failure_messages
def check_prereqs() -> List[str]:
""" Check the prerequisites.
hmmscan: domain detection
blastp: CLF and starter unit analysis
HMMs: t2pks.hmm
Returns:
a list of strings describing any errors, if they occurred
"""
failure_messages = []
for binary_name in ['hmmscan', "hmmpress", 'blastp']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
for blastdb in ['KSIII', 'AT', 'LIG']:
for ext in ['.fasta', '.phr', '.pin', '.psq']:
dbfile = path.get_full_path(__file__, 'data', blastdb + ext)
if path.locate_file(dbfile) is None:
failure_messages.append("Failed to locate file %r" % dbfile)
failure_messages.extend(prepare_data(logging_only=True))
return failure_messages
def check_known_prereqs(_options: ConfigType) -> List[str]:
""" Determines if any prerequisite data files or executables are missing
Arguments:
options: antismash Config
Returns:
a list of error messages, one for each failing prequisite check
"""
failure_messages = []
for binary_name, optional in [('blastp', False), ('makeblastdb', False),
('diamond', False)]:
if path.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
for file_name, optional in [('knownclusterprots.fasta', False),
('knownclusterprots.dmnd', False),
('knownclusters.txt', False)]:
if path.locate_file(
_get_datafile_path(file_name)) is None and not optional:
failure_messages.append("Failed to locate file: %r" % file_name)
return failure_messages
def check_prereqs() -> List[str]:
""" Check the prerequisites.
hmmscan: domain detection
blastp: CLF and starter unit analysis
HMMs: t2pks.hmm
Returns:
a list of strings describing any errors, if they occurred
"""
failure_messages = []
for binary_name in ['hmmscan', 'blastp']:
if path.locate_executable(binary_name) is None:
failure_messages.append("Failed to locate file: %r" % binary_name)
for hmm in ['t2pks.hmm']:
hmm = path.get_full_path(__file__, 'data', hmm)
if path.locate_file(hmm) is None:
failure_messages.append("Failed to locate file %r" % hmm)
continue
for ext in ['.h3f', '.h3i', '.h3m', '.h3p']:
binary = "%s%s" % (hmm, ext)
if path.locate_file(binary) is None:
# regenerate them
result = subprocessing.run_hmmpress(hmm)
if not result.successful():
failure_messages.append("Failed to hmmpress %s: %s" %
(hmm, result.stderr.rstrip()))
break
for blastdb in ['KSIII', 'AT', 'LIG']:
for ext in ['.fasta', '.phr', '.pin', '.psq']:
dbfile = path.get_full_path(__file__, 'data', blastdb + ext)
if path.locate_file(dbfile) is None:
failure_messages.append("Failed to locate file %r" % dbfile)
continue
return failure_messages
