def run_real(self):
"""Runs the application and returns the exit code"""
if not self.args:
self.args = ["-"]
else:
self.sequence_file, self.hmm_file = self.args
# if the sequences file is empty (i.e. all the sequences are
# covered by InterPro), then we return
if os.stat(self.sequence_file).st_size == 0:
return 0
# Finds hmmsearch in the current path if needed, ensure that
# the paths are absolute.
for util in ["hmmsearch", "hmmpress"]:
optkey = "%s_path" % util
path = getattr(self.options, optkey)
if not path:
path = search_file(util, executable=True)
if not path:
self.error("cannot find %s in system path" % util)
setattr(self.options, optkey, os.path.abspath(path))
# we create a temporal file to store the HMM output
hmm_output = self.create_temp_file()
if not self.press_hmm_library():
return 1
if not self.run_hmm_search(hmm_output):
return 1
table = self.process_hmm_output(hmm_output)
self.write_table(table)
def run_real(self):
"""Runs the application and returns the exit code"""
if not self.args:
self.args = ["-"]
else:
self.sequence_file, self.hmm_file = self.args
# if the sequences file is empty (i.e. all the sequences are
# covered by InterPro), then we return
if os.stat(self.sequence_file).st_size == 0:
return 0
# Finds hmmsearch in the current path if needed, ensure that
# the paths are absolute.
for util in ["hmmsearch", "hmmpress"]:
optkey = "%s_path" % util
path = getattr(self.options, optkey)
if not path:
path = search_file(util, executable=True)
if not path:
self.error("cannot find %s in system path" % util)
setattr(self.options, optkey, os.path.abspath(path))
# we create a temporal file to store the HMM output
hmm_output = self.create_temp_file()
if not self.press_hmm_library():
return 1
if not self.run_hmm_search(hmm_output):
return 1
table = self.process_hmm_output(hmm_output)
self.write_table(table)
return 0
def run_real(self):
"""Runs the application and returns the exit code"""
if not self.args:
self.args = ["-"]
# Find formatdb and blastall in the current path if needed, ensure that
# the paths are absolute.
for util in ["formatdb", "blastall"]:
optkey = "%s_path" % util
path = getattr(self.options, optkey)
if not path:
path = search_file(util, executable=True)
if not path:
self.error("cannot find %s in system path" % util)
setattr(self.options, optkey, os.path.abspath(path))
for arg in self.args:
if not self.process_file(arg):
return 1
def run_real(self):
"""Runs the application and returns the exit code"""
if not self.args:
self.args = ["-"]
# Find formatdb and blastall in the current path if needed, ensure that
# the paths are absolute.
for util in ["formatdb", "blastall"]:
optkey = "%s_path" % util
path = getattr(self.options, optkey)
if not path:
path = search_file(util, executable=True)
if not path:
self.error("cannot find %s in system path" % util)
setattr(self.options, optkey, os.path.abspath(path))
for arg in self.args:
if not self.process_file(arg):
return 1