def g_execute(blast_options, outputoptions):
"""A function that takes in and executes options from the gui widgets"""
# variables
mp.freeze_support()
ts = time.time()
fomatted_time = datetime.datetime.fromtimestamp(ts).strftime("%Y-%m-%d %H:%M:%S")
print "Process Started {0}".format(fomatted_time)
processors = outputoptions["num_procs"]
pool = mp.Pool(processes=processors)
file_name = outputoptions["pre_split_up_input"]
path = outputoptions["tmp_data_directory"]
if not os.path.exists(path):
msg = "{0} is not found, creating directory...".format(path)
os.makedirs(os.path.abspath(path))
print msg
if not os.path.exists(os.getcwd() + "/internal_data"):
print "Copying internal data to current directory {0} to {1}".format(
outputoptions["internal_data_directory"], os.getcwd() + "/internal_data"
)
shutil.copytree(outputoptions["internal_data_directory"], os.getcwd() + "/internal_data")
raw_input()
# split fasta file up
all_fasta = split_fasta.split_fasta(processors, path, file_name, suffix=".tmp_fasta")
glob_path = os.path.join(path, os.path.basename(file_name).split(".fasta")[0] + "*.tmp_fasta")
print "Splitting up file {0} into {1}".format(file_name, path)
split_up_starting_files = glob.glob(glob_path)
# output options
zip_bool = outputoptions["zip_bool"]
output_file = outputoptions["final_outfile"]
# manager_dict
_manager_list = []
_manager_dict = {}
for i, _file in enumerate(split_up_starting_files, start=1): # the full file name
_manager_dict["executable"] = outputoptions["executable"]
_manager_dict["non_split"] = file_name
_manager_dict["split_file"] = _file
_manager_dict["zip_bool"] = zip_bool
_manager_dict["all_fasta"] = all_fasta
_manager_dict["blast_options"] = blast_options # all the blast options
_manager_dict["output_type"] = outputoptions["output_type"]
_manager_dict["output_file"] = output_file
_manager_dict["output_options"] = outputoptions["output_options"]
_manager_dict["temporary_path"] = path
_manager_dict["proc_number"] = i
_manager_list.append(_manager_dict)
_manager_dict = {}
# run_protocol
# for i in _manager_list:
# run_mp_and_delete(i)
pool.map(run_mp_and_delete, _manager_list)
concat(_manager_list[0])
print "Process is done"
print "Took {0}".format(time.time() - ts)
def execute(argument_class):
'''A function that takes in and executes options from the gui widgets'''
# variables
ts = datetime.time()
#fomatted_time = datetime.datetime.fromtimestamp(float(ts)).strftime('%Y-%m-%d %H:%M:%S')
print "Process Started {0}".format(ts)
# query, path and internal database
query_name = argument_class.get_query()
tmp_path = argument_class.get_tmp_dir()
processors = argument_class.get_procs()
internal_data = argument_class.get_internal_directory()
# output options
zip_bool = argument_class.get_zip_bool()
json_bool = argument_class.get_json_bool()
concat_bool = argument_class.get_concat_bool()
output_prefix = argument_class.get_output_prefix()
output_options = argument_class.get_output_options()
# blast options - all the options specific to blast executable
executable = argument_class.get_command()
blast_options = argument_class.get_blast_options()
# species
species = argument_class.get_organism()
#germ_properties_files
germ_properties = argument_class.get_germ_file()
# split fasta file up
print "Splitting up file {0} into {1}".format(os.path.abspath(query_name), tmp_path)
split_fasta.split_fasta(processors, tmp_path, query_name, suffix=".tmp_fasta")
glob_path = os.path.join(tmp_path, os.path.basename(query_name).split('.')[0] + "*.tmp_fasta")
# now grab all the temporary files in the temporary directory
split_up_starting_files = glob.glob(glob_path)
# manager_dict and list, holds all our values so we can pass them to varias processors
_manager_list = []
_manager_dict = {}
for i, _file in enumerate(split_up_starting_files, start=1): # the full file name
_manager_dict['executable'] = executable
_manager_dict['non_split'] = query_name
_manager_dict['split_file'] = _file
_manager_dict['zip_bool'] = zip_bool
_manager_dict['json_bool'] = json_bool
_manager_dict['concat_bool'] = concat_bool
_manager_dict['output_prefix'] = output_prefix
_manager_dict['tmp_path'] = tmp_path
_manager_dict['internal_data'] = internal_data
_manager_dict['blast_options'] = blast_options
_manager_dict['output_options'] = output_options
_manager_dict['species'] = species
_manager_dict['proc_number'] = i
_manager_dict['germ_properties'] = germ_properties
_manager_list.append(_manager_dict)
_manager_dict = {}
# run_protocol
for i in _manager_list:
run_mp_and_delete(i)
#pool = mp.Pool(processes=processors)
#pool.map(run_mp_and_delete, _manager_list)
concat(_manager_list[0])
print "Process is done"
print "Took {0}".format(datetime.time() - ts)
os.removedirs(_manager_dict['tmp_path'])
