def create_conf_file(self): self.conf_file = [] if self.mode == "gfam" or self.mode == "uniprot": from gfam.scripts.master import GFamMasterScript script = GFamMasterScript() conf_file = os.path.join(self.directory, "gfam.conf") if os.path.isfile(conf_file): os.remove(conf_file) self.conf_file.append(conf_file) script.run(args=["init", "-s", "-c", conf_file]) if self.mode == "uniprot": self._fill_config_file(conf_file, self.params_gfam) else: self._fill_config_file(conf_file) if self.mode == "consat" or self.mode == "uniprot"\ or self.mode == "uniprot_consat": from gfam.scripts.master_consat import ConSATMasterScript script = ConSATMasterScript() conf_file = os.path.join(self.directory, "consat.conf") if os.path.isfile(conf_file): os.remove(conf_file) self.conf_file.append(conf_file) script.run(args=["init", "-s", "-c", conf_file]) self._fill_config_file(conf_file) if self.mode == "uniprot": self._fill_config_file(conf_file, self.params_consat) else: self._fill_config_file(conf_file)
def run_calculation(self): if self.mode == "gfam": self.log.info("Running GFam on users' sequences") from gfam.scripts.master import GFamMasterScript script = GFamMasterScript() script.run(args=["run", "-c", self.conf_file[0]]) elif self.mode == "consat": self.log.info("Running ConSAT on users' sequences") from gfam.scripts.master_consat import ConSATMasterScript script = ConSATMasterScript() script.run(args=["run", "-c", self.conf_file[0]]) elif self.mode == "uniprot_consat": self.log.info("Running ConSAT on UniProt") from gfam.scripts.master_consat import ConSATMasterScript script = ConSATMasterScript() script.run(args=["run", "-c", self.conf_file[0]]) else: self.log.info("Running GFam on UniProtKB") from gfam.scripts.master import GFamMasterScript script = GFamMasterScript() script.run(args=["run", "-c", self.conf_file[0]]) self.log.info("Running ConSAT on UniProtKB") from gfam.scripts.master_consat import ConSATMasterScript script2 = ConSATMasterScript() script2.run(args=["run", "-c", self.conf_file[1]])