CANDO
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help needed : UnpicklingError: pickle data was truncated
UnpicklingError: pickle data was truncated
Dear Sir, I want to run the following code: (https://github.com/lamawmouk/Tox21_FeatureSelection_SMOTEENN_RF/tree/main/Featuregeneration_using_CANDO)/Feature_generation_trainset.ipynb ............................. import csv with open('train_smile_toxnum.csv','r') as csvin, open('train_smile.tsv', 'w') as tsvout: csvin = csv.reader(csvin) tsvout = csv.writer(tsvout, delimiter='\t')
for row in csvin:
tsvout.writerow(row)
import cando as cnd ncpus=3 cnd.add_cmpds("train_smile.tsv", file_type='smi', fp='rd_ecfp4', vect="int", cmpd_dir=".", v="tox21_train") cnd.generate_matrix(v="tox21_train", lib_path='.', fp="rd_ecfp4", vect="int", dist="dice", org='homo_sapien', bs='coach', c_cutoff=0.0, p_cutoff=0.0, percentile_cutoff=0.0, i_score="dCxP", out_file='homo_sapien-tox21_train.tsv', out_path="", nr_ligs=True, approved_only=False, lig_name=False, ncpus=ncpus)
But the following error is encountered. How to resolve this?
Error message: Generating CANDO matrix... Traceback (most recent call last):
File "", line 10, in lig_name=False, ncpus=ncpus)
File "/home/mazharul/anaconda3/lib/python3.7/site-packages/cando/cando.py", line 4242, in generate_matrix l_fps = pickle.load(f)
UnpicklingError: pickle data was truncated