File size: 1,284 Bytes
bf928ee | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | import pickle
from _bootstrap import use_project_root
use_project_root()
with open('conf/data/asPICKLE/data_filter.pickle', 'rb') as binary_reader:
data_filter = pickle.load(binary_reader)
# extract the complexes with antibody identity 98% from data_filter
# 1. read the nanobody_seqs_98.fasta to get the PDB id of the complexes
fasta_file_path = 'conf/data/asFASTA/nanobody_seqs_98.fasta'
PDB = ''
PDBs = []
with open(fasta_file_path, 'r') as file:
lines = file.readlines()
for line in lines:
if line[0] == '>':
PDB = line[1:]
PDB = PDB.strip()
PDBs.append(PDB)
file.close()
data_filter_nano_identiy98 = []
for item in data_filter:
if item[0] in PDBs:
data_filter_nano_identiy98.append(item)
# Save data_filter_nano_identiy98 as pickle file
with open('conf/data/asPICKLE/data_filter_nano_identiy98.pickle', 'wb') as binary_writer:
pickle.dump(data_filter_nano_identiy98, binary_writer)
# write the antigen sequences as FASTA file
antigen_seqs_fasta = open("conf/data/asFASTA/antigen_seqs_after_nanobody_identiy98.fasta", "w")
for item in data_filter_nano_identiy98:
antigen_seqs_fasta.write(">" + item[0] + " \n")
antigen_seqs_fasta.write(item[17] + " \n")
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