def main():
if len(sys.argv) not in [5, 6]:
print 'Usage:python %s data_type objective_function run_num go/no_go go_num <if go>' % sys.argv[0]
exit()
# Sort out command line arguments.
data_type, objective_function, run_num, network = sys.argv[1:5]
assert data_type == 'mouse' or data_type.isdigit()
assert objective_function in ['oclode', 'schaeffer', 'wlogv']
assert run_num.isdigit()
assert network in ['go', 'no_go']
if data_type.isdigit():
data_type = file_operations.get_tcga_disease_list()[int(data_type)]
# Construct the results folders if it's the first time.
results_folder = './results/%s_results/' % data_type
if not os.path.exists(results_folder):
os.makedirs(results_folder)
obj_func_folder = results_folder + 'wlogv/'
if not os.path.exists(obj_func_folder):
os.makedirs(obj_func_folder)
os.makedirs(obj_func_folder + 'clus_info_no_go/')
os.makedirs(obj_func_folder + 'clus_info_go/')
os.makedirs(obj_func_folder + 'cluster_enrichment_terms_go/')
os.makedirs(obj_func_folder + 'cluster_enrichment_terms_no_go/')
os.makedirs(obj_func_folder + 'cluster_eval_no_go/')
os.makedirs(obj_func_folder + 'clusters_go/')
os.makedirs(obj_func_folder + 'cluster_eval_go/')
os.makedirs(obj_func_folder + 'clusters_no_go/')
plot_folder = results_folder + 'comparison_plots/'
if not os.path.exists(plot_folder):
os.makedirs(plot_folder)
config_dct = file_operations.read_config_file(data_type)[run_num]
temp = config_dct['temp']
num_clusters = config_dct['num_clusters']
# Get the binary associated with the desired objective function.
if objective_function == 'oclode':
binary = '''./OCLODE/makedir/OCLODE_efficient'''
elif objective_function == 'schaeffer':
binary = './SchaefferScore/makedir/SchaefferImplementNotWeighted'
else:
binary = './WlogV/makedir/WlogVImplement'
# Build the command.
command = '%s %s 1 0 "./data/%s_data/orth.txt" 1 ' % (binary, num_clusters,
data_type)
command += '"./data/%s_data/networks_%s/network_%s_%s' % (data_type, network,
network, run_num)
if network == 'go':
go_num = sys.argv[5]
command += '_%s' % go_num
command += '.txt" -t %s 2>log > "./results/%s_results/%s/clusters_%s/clusters_%s_%s' % (
temp, data_type, objective_function, network, network, run_num)
if network == 'go':
command += '_%s' % go_num
command += '.txt"'
# Execute the command in the shell.
print command
subprocess.call(command, shell=True)
