def create_inputs(options, outpath, found_sequences):
errors = []
# Create subdirectories
job_inputs = []
for (pdb_id, chain, file_name), sequence in sorted(found_sequences.iteritems()):
created_new_subdirectory = False
subdir_path = os.path.join(outpath, "%s%s" % (pdb_id, chain))
try:
if os.path.exists(subdir_path):
if options.overwrite:
colorprinter.warning("Path %s exists. Removing all files in that path as per the override option." % subdir_path)
shutil.rmtree(subdir_path)
created_new_subdirectory = True
else:
errors.append('The directory %s already exists.' % subdir_path) # uncomment this if we want to turn on the _001, _002, etc. directories
count = 1
while count < 1000:
subdir_path = os.path.join(outpath, "%s%s_%.3i" % (pdb_id, chain, count))
if not os.path.exists(subdir_path):
break
count += 1
if count == 1000:
errors.append("The directory %s contains too many previous results. Please clean up the old results or choose a new output directory." % outpath)
sys.exit(ERRCODE_OLDRESULTS)
os.makedirs(subdir_path, 0755)
# Create a FASTA file for the sequence in the output directory
fasta_file = os.path.join(subdir_path, "%s%s.fasta" % (pdb_id, chain))
colorprinter.message("Creating a new FASTA file %s." % fasta_file)
assert(not(os.path.exists(fasta_file)))
write_file(fasta_file, '\n'.join(sequence) + '\n', 'w') # The file must terminate in a newline for the Perl script to work
job_inputs.append(JobInput(fasta_file, pdb_id, chain))
except:
if created_new_subdirectory and os.path.exists(subdir_path):
shutil.rmtree(subdir_path)
errors.append('An error occurred creating the input for %s%s.' % (pdb_id, chain))
job_inputs = []
break
return job_inputs, errors
def main():
this_dir = os.path.dirname(os.path.realpath(__file__))
make_fragments_script_path = os.path.join(this_dir, make_fragments_script)
errors = [] #check_configuration_paths()
if errors:
colorprinter.error("There is an error in the configuration files:")
for e in errors:
print("")
flname = e[0]
es = e[1]
colorprinter.warning(flname)
for e in es:
colorprinter.error(e)
sys.exit(ERRCODE_CONFIG)
options = parse_args()
if options["outpath"] and options['job_inputs']:
job_script = None
try:
cluster_job = ClusterEngine.FragmentsJob(make_fragments_script_path, options, test_mode = test_mode)
job_script = cluster_job.script
except JobInitializationException, e:
colorprinter.error(str(e))
sys.exit(ERRCODE_ARGUMENTS)
submission_script = os.path.join(options["outpath"], 'submission_script.py')
write_file(submission_script, job_script, 'w')
try:
send_mail = options['sendmail']
username = None
if send_mail:
username = get_username()
(jobid, output) = ClusterEngine.submit(submission_script, options["outpath"], send_mail = send_mail, username = username )
except Exception, e:
colorprinter.error("An exception occurred during submission to the cluster.")
colorprinter.error(str(e))
colorprinter.error(traceback.format_exc())
sys.exit(ERRCODE_CLUSTER)
