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 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]])
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]])