def check_prereqs(options):
"Check if all required applications are around"
failure_messages = []
if options.genefinding == 'none':
return failure_messages
basedir = utils.get_genefinding_basedir(options)
for binary_name, optional in _required_binaries:
new_binary_name = path.join(basedir, binary_name)
if locate_executable(new_binary_name) is None and not optional:
if locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
return failure_messages
def check_prereqs():
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
cfg = config.get_config()
cfg.cdh_use_binary = True
#Check if cd-hit binary exist
if cfg.enable_cdhit:
if utils.locate_executable("cd-hit") is None:
cfg.cdh_use_binary = False
logging.info(
"Cannot locate cd-hit binary, using ps-cd-hit algorithm instead"
)
for hmm_model in cfg.enabled_detection_models:
#Check if hmmdetails.txt is readable and well-formatted
dir_path = path.dirname(path.abspath(__file__))
model_name = ""
if not hmm_model is "default":
dir_path = path.join(dir_path, hmm_model)
model_name = "(" + hmm_model + ")"
#Check if hmmdetails.txt is readable and well-formatted
lineno = 1
for line in open(path.join(dir_path, "hmmdetails.txt"), "r"):
if line.count("\t") != 3:
failure_messages.append(
"Failed to use HMM profile %s from line %s due to misformatting:\n %r"
% (model_name, lineno, line))
lineno += 1
#Check if cluster_rules.txt is readable and well-formatted
lineno = 1
for line in open(path.join(dir_path, "cluster_rules.txt"), "r"):
if line.count("\t") != 3:
failure_messages.append(
"Failed to use cluster rules %s from the line %s due to misformatting:\n %r"
% (model_name, lineno, line))
lineno += 1
for sig in get_sig_profiles():
if not path.exists(sig.path):
failure_messages.append("Failed to find HMM profile %r" % sig.path)
return failure_messages
def check_prereqs(options):
"Check if all required applications are around"
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
for hmm in _markov_models:
hmm = utils.get_full_path(__file__, hmm)
if utils.locate_file(hmm) is None:
failure_messages.append("Failed to locate file %r" % hmm)
continue
for ext in _binary_extensions:
binary = "%s%s" % (hmm, ext)
if utils.locate_file(binary) is None:
command = ['hmmpress', hmm]
try:
out, err, retcode = utils.execute(command)
except OSError as e:
retcode = 1
err = str(e)
if retcode != 0:
failure_messages.append("Failed to hmmpress %r: %r" % (hmm, err))
break
return failure_messages
def check_prereqs():
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
return failure_messages
def check_prereqs():
"Check if all required files and applications are around"
# Tuple is ( binary_name, optional)
_required_binaries = [
('blastp', False),
]
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
try:
import cobra
logging.debug("Found cobra version %s", cobra.__version__)
except (ImportError, ImportWarning) as err:
failure_messages.append(str(err))
try:
import libsbml
logging.debug("Found libsmbl version %s", libsbml.getLibSBMLVersion())
except (ImportError, ImportWarning) as err:
failure_messages.append(str(err))
if not libImport:
failure_messages.append("Failed to import automodel")
return failure_messages
def check_prereqs(self):
"Check if all required files and applications are around"
# Tuple is ( binary_name, optional)
_required_binaries = [('blastp', False), ('hmmpfam2', False),
('hmmscan', False)]
options = self.options
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" %
binary_name)
# Get all HMM profile names from XML file
for HMMProfile in self.HmmProfilesFilenameObj:
if utils.locate_file(
path.join(options.activeSiteFinderHMMDir,
HMMProfile.text)) is None:
failure_messages.append("Failed to locate file: %s" %
HMMProfile.text)
return failure_messages
def check_prereqs(options):
"Check if all required applications are around"
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
return failure_messages
def test_locate_executable(self):
"Test utils.locate_executable()"
test_executable = sys.argv[0]
if not path.isfile(test_executable):
self.skipTest("%r is not a file, skipping test" % test_executable)
if not os.access(test_executable, os.X_OK):
self.skipTest("%r is not executable, skipping test" %
test_executable)
self.assertEqual(utils.locate_executable(test_executable),
test_executable)
short_path = path.split(test_executable)[1]
self.assertEqual(utils.locate_executable(short_path), test_executable)
self.assertIsNone(utils.locate_executable("totallymaedup"))
def make_blastDB(query_fasta, options):
db_dir = options.metabolicmodeldir + os.sep + 'targetBlastDB'
DBprogramName = utils.locate_executable('makeblastdb')
utils.execute(
[DBprogramName, '-in', query_fasta, '-out', db_dir, '-dbtype', 'prot'])
#Checks if DB is properly created; otherwise shutdown
if os.path.isfile(options.metabolicmodeldir + os.sep +
'targetBlastDB.psq') == False:
logging.exception("error in make_blastDB: blast DB not created")
#FIXME: don't use sys.exit
sys.exit(1)
def check_prereqs():
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
hmm_files = []
# Check if hmmdetails.txt is readable and well-formatted
lineno = 1
for line in open(utils.get_full_path(__file__, "hmmdetails.txt"), "r"):
if line.count("\t") != 3:
failure_messages.append(
"Failed to use HMM profile from line %s due to misformatting:\n %r"
% (lineno, line))
continue
hmm_files.append(line.split('\t')[3].strip())
lineno += 1
#Check if cluster_rules.txt is readable and well-formatted
lineno = 1
for line in open(utils.get_full_path(__file__, "cluster_rules.txt"), "r"):
if line.count("\t") != 3:
failure_messages.append(
"Failed to use cluster rules from the line %s due to misformatting:\n %r"
% (lineno, line))
lineno += 1
hmm = utils.get_full_path(__file__, _markov_model)
if utils.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(utils.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))
for ext in _binary_extensions:
binary = "{}{}".format(hmm, ext)
if utils.locate_file(binary) is None:
_, err, retcode = utils.run_hmmpress(hmm)
if retcode != 0:
failure_messages.append('Failed to hmmpress {!r}: {!r}'.format(
hmm, err))
break
return failure_messages
def check_prereqs(options):
"Check if all required applications are around"
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.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 utils.locate_file(
path.join(utils.get_full_path(__file__, ''),
file_name)) is None and not optional:
failure_messages.append("Failed to locate file: %r" % file_name)
return failure_messages
def check_prereqs():
"Check if all required files and applications are around"
# Tuple is ( binary_name, optional)
_required_binaries = [('eficaz2.5', False)]
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable: %r" %
binary_name)
return failure_messages
def run_blastp(target_fasta='', blastp_result='', db_dir='', evalue=1e-30):
BLASTPprogramName = utils.locate_executable('blastp')
# Execute blast if output file is not present
if not os.path.isfile(blastp_result):
args = [
BLASTPprogramName, '-query', target_fasta, '-out', blastp_result,
'-db', db_dir, '-evalue',
str(evalue), '-outfmt',
"10 qseqid sseqid evalue score length pident"
]
out, err, retcode = utils.execute(args)
if retcode != 0:
logging.debug("out: %r, err: %r, retcode: %s", out, err, retcode)
else:
logging.warn("Found blast file %s, skipping new caluclation",
blastp_result)
def check_prereqs():
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate executable for %r" %
binary_name)
for hmm in _markov_models:
hmm = utils.get_full_path(__file__, hmm)
if utils.locate_file(hmm) is None:
failure_messages.append("Failed to locate file %r" % hmm)
continue
for ext in _binary_extensions:
binary = "%s%s" % (hmm, ext)
if utils.locate_file(binary) is None:
_, err, retcode = utils.run_hmmpress(hmm)
if retcode != 0:
failure_messages.append("Failed to hmmpress %r: %r" %
(hmm, err))
break
else:
binary_mtime = path.getmtime(binary)
hmm_mtime = path.getmtime(hmm)
if hmm_mtime > binary_mtime:
try:
from glob import glob
for f in glob("%s.h3?" % hmm):
logging.debug("removing outdated file %s", f)
os.remove(f)
except OSError as e:
failure_messages.append("Failed to remove outdated binary file for %s: %s" % \
(hmm, e))
break
_, err, retcode = utils.run_hmmpress(hmm)
if retcode != 0:
failure_messages.append("Failed to hmmpress %r: %r" %
(hmm, err))
import datetime
failure_messages.append("HMM binary files outdated. %s (changed: %s) vs %s (changed: %s)" % \
(hmm, datetime.datetime.fromtimestamp(hmm_mtime),
binary, datetime.datetime.fromtimestamp(binary_mtime)))
break
return failure_messages
def _runEFICAz(self, chunkDir):
cwd = os.getcwd()
try:
os.chdir(chunkDir)
except OSError:
logging.exception("Can't chdir to %s" % chunkDir)
sys.exit(1)
fastafile = os.path.basename(self.ChunkFilenames[chunkDir])
ecpredfile = fastafile + ".ecpred"
# Only perform calculations if result file does not already exist (from previous run)
if not os.path.isfile(os.path.join(self.basedirName, ecpredfile)):
EFICAzExecutable = utils.locate_executable(EFICAzBinary)
if not EFICAzExecutable:
logging.exception(
"EFICAz executable not found, bailing out, analysis not posible"
)
sys.exit(1)
cmdline = [EFICAzExecutable, fastafile]
logging.debug("executing %s in directory %s" %
(" ".join(cmdline), chunkDir))
try:
utils.execute(cmdline)
except:
logging.exception('cannot execute EFICAz!')
sys.exit(1)
else:
# As this method is executed in an own thread, it does not have the ability to change
# the variables within th eobject;
# As a workaround we just copy the "old" file to the tempdir...
try:
shutil.copy(
os.path.abspath(os.path.join(self.basedirName,
ecpredfile)),
self.ChunkFilenames[chunkDir] + ".ecpred")
except:
logging.exception("Could not copy existing eficaz result file %s to tempfile %s", \
os.path.isfile(os.path.abspath(self.basedirName, ecpredfile)), \
self.ChunkFilenames[chunkDir]+".ecpred" )
sys.exit(1)
os.chdir(cwd)
def check_prereqs(self):
"Check if all required files and applications are around"
# Tuple is ( binary_name, optional)
_required_binaries = [
('blastp', False),
('hmmpfam2', False),
('hmmscan', False),
('hmmpress', False),
]
_binary_extensions = [
'.h3f',
'.h3i',
'.h3m',
'.h3p'
]
options = self.options
failure_messages = []
for binary_name, optional in _required_binaries:
if utils.locate_executable(binary_name) is None and not optional:
failure_messages.append("Failed to locate file: %r" % binary_name)
# Get all HMM profile names from XML file
for HMMProfile in self.HmmProfilesFilenameObj:
full_hmm_path = path.join(options.activeSiteFinderHMMDir, HMMProfile.text)
if utils.locate_file(full_hmm_path) is None:
failure_messages.append("Failed to locate file: %s" % HMMProfile.text)
continue
if HMMProfile.text.endswith(".hmm2"):
continue
for ext in _binary_extensions:
binary = "{hmm}{ext}".format(hmm=full_hmm_path, ext=ext)
if utils.locate_file(binary) is None:
_, err, retcode = utils.run_hmmpress(full_hmm_path)
if retcode != 0:
failure_messages.append("Failed to hmmpress {!r}: {!r}".format(HMMProfile.text, err))
# hmmpress generates _all_ binary files in one go, so stop the loop
break
binary_mtime = path.getmtime(binary)
hmm_mtime = path.getmtime(full_hmm_path)
if hmm_mtime < binary_mtime:
# generated file younger than hmm profile, do nothing
continue
try:
from glob import glob
for f in glob("{}.h3?".format(full_hmm_path)):
logging.debug("removing outdated file %r", f)
os.remove(f)
except OSError as e:
failure_messages.append("Failed to remove outdated binary file for %s: %s" % \
(HMMProfile.text, e))
break
_, err, retcode = utils.run_hmmpress(full_hmm_path)
if retcode != 0:
failure_messages.append("Failed to hmmpress %r: %r" % (HMMProfile.text, err))
import datetime
failure_messages.append("HMM binary files outdated. %s (changed: %s) vs %s (changed: %s)" % \
(HMMProfile.text, 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
