def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.log.info("Loading GO tree from %s..." % go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s..." % \
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file, self.go_tree)
self.log.info("Processing domain architectures from %s..." % \
input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the label assignment application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.log.info("Loading GO tree from %s...", go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s...",
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file,
self.go_tree)
self.log.info("Processing domain architectures from %s...", input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.options.results_by_protein = self.__parse_bool(self.options.results_by_protein)
if not self.options.results_by_protein and not self.options.arch_file:
self.error("Either results by protein or by arch should be set")
self.log.info("Loading GO tree from %s..." % go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s..." % \
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file, self.go_tree)
self.log.info("Processing domain architectures from %s..." % \
input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
rbp = self.options.results_by_protein
self.options.results_by_protein = self.__parse_bool(rbp)
if not self.options.results_by_protein and not self.options.arch_file:
self.error("Either results by protein or by arch should be set")
self.log.info("Loading GO tree from %s...", go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s...",
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file,
self.go_tree)
self.log.info("Processing domain architectures from %s...", input_file)
return self.process_file(input_file)