# HG changeset patch # User luca_milaz # Date 1720033686 0 # Node ID 1bdc84fe4a881f6dfa4ab4030f96ac60b671158c # Parent d58974850ed09acd1d0ee532a3bc35248f342c42 Uploaded diff -r d58974850ed0 -r 1bdc84fe4a88 marea_2_0/flux_sampling.py --- a/marea_2_0/flux_sampling.py Wed Jul 03 18:59:46 2024 +0000 +++ b/marea_2_0/flux_sampling.py Wed Jul 03 19:08:06 2024 +0000 @@ -105,24 +105,24 @@ elif ARGS.output_format is utils.FileFormat.CSV: dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = False) -def OPTGP_sampler(model:cobra.Model, model_name:str, n_samples:int=1000, thinning:int=100, n_batches:int=1, seed:int=0)-> None: + - if not os.path.exists(ARGS.output_folder + "OPTGP/"): - os.makedirs(ARGS.output_folder + "OPTGP/") +def OPTGP_sampler(model:cobra.Model, model_name:str, n_samples:int=1000, thinning:int=100, n_batches:int=1, seed:int=0)-> None: for i in range(0, n_batches): optgp = OptGPSampler(model, thinning, seed) samples = optgp.sample(n_samples) - samples.to_csv(ARGS.output_folder + "OPTGP/" + ARGS.model_name + '_'+ str(i)+'.csv') - i+=1 + samples.to_csv(ARGS.output_folder + model_name + '_'+ str(i)+'_OPTGP.csv', index=False) seed+=1 samplesTotal = pd.DataFrame() for i in range(0, n_batches): - samples_batch = pd.read_csv(ARGS.output_folder + "OPTGP/" + ARGS.model_name + '_'+ str(i)+'.csv') + samples_batch = pd.read_csv(ARGS.output_folder + model_name + '_'+ str(i)+'_OPTGP.csv') samplesTotal = pd.concat([samplesTotal, samples_batch], ignore_index = True) - write_to_file(samplesTotal, ARGS.output_folder + "OPTGP/" + ARGS.model_name) + + write_to_file(samplesTotal, model_name) + for i in range(0, n_batches): - os.remove(ARGS.output_folder + "OPTGP/" + ARGS.model_name + '_'+ str(i)+'.csv') + os.remove(ARGS.output_folder + model_name + '_'+ str(i)+'_OPTGP.csv') pass @@ -142,17 +142,17 @@ ARGS.out_log) CBS_backend.randomObjectiveFunctionSampling_cobrapy(model, n_samples, df_coefficients.iloc[:,i*n_samples:(i+1)*n_samples], samples) - samples.to_csv(ARGS.output_folder + model_name + '_'+ str(i)+'.csv', index=False) + samples.to_csv(ARGS.output_folder + model_name + '_'+ str(i)+'_CBS.csv', index=False) samplesTotal = pd.DataFrame() for i in range(0, n_batches): - samples_batch = pd.read_csv(ARGS.output_folder + model_name + '_'+ str(i)+'.csv') + samples_batch = pd.read_csv(ARGS.output_folder + model_name + '_'+ str(i)+'_CBS.csv') samplesTotal = pd.concat([samplesTotal, samples_batch], ignore_index = True) write_to_file(samplesTotal, model_name) for i in range(0, n_batches): - os.remove(ARGS.output_folder + model_name + '_'+ str(i)+'.csv') + os.remove(ARGS.output_folder + model_name + '_'+ str(i)+'_CBS.csv') pass