def run_command(self,
command,
script_name,
progress_update,
check_output=None):
"""
Runs a script. Must provide script_name (e.g. "script.py") and progress_update (e.g.
"BINARIZING DATABASE"). Optionally can provide list of output files whose existences are
checked to make sure command was successfully ran. We ALWAYS cd into the MODELLER's
directory before running a script, and we ALWAYS cd back into the original directory after
running a script.
"""
# first things first, we CD into MODELLER's directory
os.chdir(self.directory)
# run the command
self.progress.update(progress_update)
# try and execute the command
process = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
# if MODELLER script gave a traceback, it is caught here and everything is stopped
if process.returncode:
self.progress.end()
error = error.decode('utf-8').strip()
error = "\n" + "\n".join(error.split('\n'))
print(terminal.c(error, color='red'))
self.out["structure_exists"] = False
raise ModellerScriptError("The MODELLER script {} did not execute properly. Hopefully it is clear \
from the above error message. No structure is going to be modelled."\
.format(script_name))
# If we made it this far, the MODELLER script ran to completion. Now check outputs exist
if check_output:
for output in check_output:
utils.filesnpaths.is_file_exists(output)
# MODELLER outputs a log that we rename right here, right now
old_log_name = os.path.splitext(script_name)[0] + ".log"
new_log_name = "gene_{}_{}".format(self.corresponding_gene_call,
old_log_name)
os.rename(old_log_name, new_log_name)
# add to logs
self.logs[script_name] = new_log_name
self.run.info("Log of {}".format(script_name),
new_log_name,
progress=self.progress)
# last things last, we CD back into the starting directory
os.chdir(self.start_dir)
def run_command(self,
command,
script_name,
check_output=None,
rename_log=True):
"""Base routine for running MODELLER scripts
Parameters
==========
command : list of strs
E.g. ['mod921', 'test_script.py', 'input1', 'input2'] corresponds to the command line
"mod9.21 test_script.py input1 input2"
script_name : str
E.g. 'test_script.py'
check_output : list, None
Verify that this list of filepaths exist after the command is ran
rename_log : bool, True
MODELLER outputs a log that is renamed to reflect the command and gene used
"""
# first things first, we CD into MODELLER's directory
os.chdir(self.directory)
# try and execute the command
process = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
# if MODELLER script gave a traceback, it is caught here and everything is stopped
if process.returncode:
error = error.decode('utf-8').strip()
error = "\n" + "\n".join(error.split('\n'))
print(terminal.c(error, color='red'))
self.out["structure_exists"] = False
raise ModellerScriptError("The MODELLER script {} did not execute properly. Hopefully it is clear "
"from the above error message. No structure is going to be modelled."\
.format(script_name))
# If we made it this far, the MODELLER script ran to completion. Now check outputs exist
if check_output:
for output in check_output:
utils.filesnpaths.is_file_exists(output)
# MODELLER outputs a log that we rename right here, right now
old_log_name = os.path.splitext(script_name)[0] + ".log"
if rename_log:
new_log_name = "gene_{}_{}".format(self.corresponding_gene_call,
old_log_name)
os.rename(old_log_name, new_log_name)
else:
new_log_name = old_log_name
# add to logs
self.logs[script_name] = new_log_name
self.run.info("Log of {}".format(script_name), new_log_name)
# last things last, we CD back into the starting directory
os.chdir(self.start_dir)