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)
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(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():
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 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 _execute_tool(self, analysisResource, fileName=None, stdin_data=None):
"Perform the external program execution"
cmdlineList = []
# Assemble commad line list
# extract program name from XML
executeObj = analysisResource.find('./Execute')
cmdlineList.append(executeObj.attrib['program'])
# Cycle through parameters in XML
for parameter in list(analysisResource.findall('./Execute/parameters/parameter')):
if 'prefix' in parameter.attrib:
cmdlineList.append(parameter.attrib['prefix'])
cmdlineList.append(parameter.text)
# Get database name
database = analysisResource.find('./Execute/database')
if 'prefix' in database.attrib:
cmdlineList.append(database.attrib['prefix'])
# Add searchpath
cmdlineList.append(utils.locate_file(path.join(self.options.activeSiteFinderHMMDir, database.text)))
if fileName:
# Get (optional) input file prefix (e.g. -query in blast)
if 'inputfile_prefix' in executeObj.attrib:
cmdlineList.append(executeObj.attrib['inputfile_prefix'])
cmdlineList.append(fileName)
if stdin_data:
# Get (optional) prefix for stdin (e.g. "-" for hmmpfam / hmmscan
if 'STDINprefix' in executeObj.attrib:
cmdlineList.append(executeObj.attrib['STDINprefix'])
logging.debug("ASF: %s; external program call:\n%s", analysisResource.attrib['name'], " ".join(cmdlineList))
try:
if fileName:
logging.debug("Executing tool with file input")
out, _, retcode = utils.execute(cmdlineList)
else:
logging.debug("Executing tools with STDIN input")
out, _, retcode = utils.execute(cmdlineList, input=stdin_data)
except OSError:
logging.warn('OS error on execution of: %s', " ".join(cmdlineList))
return []
if retcode != 0:
logging.warn('%s returned %s', cmdlineList[0], retcode)
return []
res_stream = StringIO(out)
logging.debug('External program output: %s', res_stream)
# Get Biopython parser information from XML
biopython_parser = analysisResource.find('./Execute/BioPythonParser')
try:
results = list(SearchIO.parse(res_stream, biopython_parser.text))
except Exception as e:
logging.warn('Error parsing results for active site finder analysis: %s ; no hits will be reported', e)
results = []
return results
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
def test_locate_file(self):
"Test utils.locate_file()"
self.assertEqual(__file__, utils.locate_file(__file__))
self.assertIsNone(utils.locate_file('totallymadeup'))