Spaces:
Running
on
Zero
Running
on
Zero
File size: 2,494 Bytes
7968cb0 |
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 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 |
# read in the predictions.txt file
# take the sequence from there
import argparse
import os
import biotite.structure.io.pdb as pdb
from biotite.structure import get_residues
def compare_sequences(pdb_code):
# Read the predicted sequence from predictions.txt
with open('predict_example/predictions.txt', 'r') as f:
predictions = f.readlines()
# Extract the sequence (skip the header line that starts with '>')
predicted_seqs = {}
current_pdb = None
for line in predictions:
if line.startswith('>'):
current_pdb = line.strip()[1:] # Remove the '>' character
elif current_pdb and line.strip():
predicted_seqs[current_pdb] = line.strip()
# Use the provided pdb_code to get the corresponding sequence
predicted_seq = predicted_seqs.get(pdb_code, "")
# Read the PDB file
pdb_file = f'predict_example/{pdb_code}.pdb'
with open(pdb_file, 'r') as f:
structure = pdb.PDBFile.read(f)
atoms = pdb.get_structure(structure)
# Get residue names from the structure
residues = get_residues(atoms)[1]
# Convert three-letter codes to one-letter codes
aa_dict = {
'ALA': 'A', 'CYS': 'C', 'ASP': 'D', 'GLU': 'E', 'PHE': 'F',
'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LYS': 'K', 'LEU': 'L',
'MET': 'M', 'ASN': 'N', 'PRO': 'P', 'GLN': 'Q', 'ARG': 'R',
'SER': 'S', 'THR': 'T', 'VAL': 'V', 'TRP': 'W', 'TYR': 'Y'
}
pdb_seq = ''.join([aa_dict.get(res, 'X') for res in residues])
# Compare the two sequences
match_count = sum(1 for a, b in zip(predicted_seq, pdb_seq) if a == b)
total_length = max(len(predicted_seq), len(pdb_seq))
percent_identity = (match_count / min(len(predicted_seq), len(pdb_seq))) * 100
# Print the result
print(f"Predicted sequence: {predicted_seq}")
print(f"PDB sequence: {pdb_seq}")
print(f"Sequence length - Predicted: {len(predicted_seq)}, PDB: {len(pdb_seq)}")
print(f"Matching residues: {match_count}/{min(len(predicted_seq), len(pdb_seq))}")
print(f"Percent identity: {percent_identity:.2f}%")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Compare predicted sequence with PDB sequence')
parser.add_argument('--pdb_code', type=str, help='PDB code (e.g., 1ah7_A)')
args = parser.parse_args()
compare_sequences(args.pdb_code)
|