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Running
on
Zero
File size: 1,860 Bytes
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import os
import yaml
import pandas as pd
def extract_rmsf_labels(file_path):
with open(file_path, 'r') as f:
lines = f.readlines()
protein_id = file_path.split('/')[-2].split('_')[:-1]
protein_id = '.'.join(protein_id)
rmsf_values = []
for line in lines[1:]:
parts = line.strip().split('\t')
rmsf_r1 = float(parts[1])
rmsf_r2 = float(parts[2])
rmsf_r3 = float(parts[3])
avg_rmsf = (rmsf_r1 + rmsf_r2 + rmsf_r3) / 3
rmsf_values.append(avg_rmsf)
return protein_id, rmsf_values
def extract_bfactor_labels(file_path):
bfactor = pd.read_csv(file_path, delimiter='\t')['Bfactor']
protein_id = file_path.split('/')[-2].split('_')[:-1]
protein_id = '.'.join(protein_id)
return protein_id, bfactor
def extract_plddt_labels(file_path):
plddt = pd.read_csv(file_path, delimiter='\t')['pLDDT']
protein_id = file_path.split('/')[-2].split('_')[:-1]
protein_id = '.'.join(protein_id)
return protein_id, plddt
if __name__ == "__main__":
config = yaml.load(open('configs/data_config.yaml'), Loader=yaml.FullLoader)
in_path = config['atlas_out_dir']
out_path = config['atlas_labels_path']
rmsf_data = {}
for folder in os.listdir(in_path):
folder_path = os.path.join(in_path, folder)
if os.path.isdir(folder_path):
for file in os.listdir(folder_path):
if file.endswith("_RMSF.tsv"):
file_path = os.path.join(folder_path, file)
protein_id, rmsf_labels = extract_rmsf_labels(file_path)
rmsf_data[protein_id] = rmsf_labels
with open(out_path, 'w') as out_file:
for protein_id, values in rmsf_data.items():
out_file.write(f"{protein_id}: {', '.join(map(str, values))}\n")
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