| import pickle
|
| import random
|
| import os |
| from _bootstrap import use_project_root |
|
|
| use_project_root() |
| random.seed(123) |
|
|
| CDR_kmer = 3
|
| Ag_kmer = 3
|
|
|
| def sequence2tokens(seq, kmer):
|
| tokens = []
|
| for i in range(len(seq) - (kmer-1)):
|
| tokens.append(seq[i:i + kmer])
|
| return tokens
|
|
|
| def CDR_Ag_create_tsv(CDR_Ag_pairs, mode, CDR_kmer, Ag_kmer, CDR_TSV, Ag_TSV):
|
|
|
| f1 = open(CDR_TSV, "w")
|
| f2 = open(Ag_TSV, "w")
|
|
|
| for pair in CDR_Ag_pairs:
|
| ID = pair[0]
|
| CDR_seq = pair[2]
|
| Ag_seq = pair[3]
|
| label = pair[4]
|
| CDR_number = pair[5]
|
|
|
| label_str = str(label)
|
| CDR_number_str = str(CDR_number)
|
| CDR = str(CDR_seq).lower()
|
| CDR_tokens = ""
|
| tokens = sequence2tokens(CDR, CDR_kmer)
|
| for token in tokens:
|
| CDR_tokens = CDR_tokens + token + " "
|
| res = mode + "\t" + ID + "\t" + label_str + "\t" + CDR_tokens + "\t" + CDR_number_str
|
| f1.write(res + "\n")
|
|
|
| Ag = str(Ag_seq).lower()
|
| Ag_tokens = ""
|
| tokens = sequence2tokens(Ag, Ag_kmer)
|
| for token in tokens:
|
| Ag_tokens = Ag_tokens + token + " "
|
| res = mode + "\t" + ID + "\t" + label_str + "\t" + Ag_tokens + "\t" + CDR_number_str
|
| f2.write(res + "\n")
|
|
|
| def CDR_Ag_createTrainValTestTSV():
|
| with open('conf/data/asPICKLE/train_CDR_antigen.pickle', 'rb') as binary_reader:
|
| train_CDR_antigen = pickle.load(binary_reader)
|
|
|
| with open('conf/data/asPICKLE/val_CDR_antigen.pickle', 'rb') as binary_reader:
|
| val_CDR_antigen = pickle.load(binary_reader)
|
|
|
| with open('conf/data/asPICKLE/test_CDR_antigen.pickle', 'rb') as binary_reader:
|
| test_CDR_antigen = pickle.load(binary_reader)
|
|
|
|
|
| CDR_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/CDR_tr.tsv"
|
| Ag_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/Ag_tr.tsv"
|
| CDR_Ag_create_tsv(train_CDR_antigen, "train", CDR_kmer, Ag_kmer, CDR_TSV, Ag_TSV)
|
|
|
|
|
| CDR_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/CDR_val.tsv"
|
| Ag_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/Ag_val.tsv"
|
| CDR_Ag_create_tsv(val_CDR_antigen, "val", CDR_kmer, Ag_kmer, CDR_TSV, Ag_TSV)
|
|
|
|
|
| CDR_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/CDR_te.tsv"
|
| Ag_TSV = "conf/data/asTSV/cdr_kmer" + str(CDR_kmer) + "_ag_kmer" + str(Ag_kmer) + "/Ag_te.tsv"
|
| CDR_Ag_create_tsv(test_CDR_antigen, "test", CDR_kmer, Ag_kmer, CDR_TSV, Ag_TSV)
|
|
|
| if not os.path.exists('./conf/data/asTSV'):
|
| os.makedirs('./conf/data/asTSV')
|
|
|
| CDR_Ag_createTrainValTestTSV()
|
| print("hello") |
|
|
