HLA 결합력 변화 비교 #

import pandas as pd
import numpy as np

with open('/data/home/ysh980101/2411/data-mhc/patient_id.txt', 'r') as file:
    patients = [line.strip() for line in file]
len(patients)

388 #387+reference

hotspot = "c315"
dfs = []

for pid in patients:
    file_path = f"/data/home/ysh980101/2411/data-mhc/{hotspot}/{pid}/binding_affinities_HLA-I.csv"
    df = pd.read_csv(file_path)
    
    df.rename(columns={'Affinity': f'{pid}'}, inplace=True)
    df.rename(columns={'Peptide': f'Peptide_{pid}'}, inplace=True)
    
    if pid == 'reference':
        dfs.append(df)
    else:
        dfs.append(df[[f'{pid}']])
        #dfs.append(df[[f'{pid}', f'Peptide_{pid}']])

res_df = pd.concat(dfs, axis=1)
res_df = res_df.set_index('Allele')
res_df

res_df.iloc[:, 1:] = res_df.iloc[:, 1:].subtract(res_df['reference'], axis=0)
res_df

res_df.to_csv(f"/data/home/ysh980101/2411/data/{hotspot}/aff-table.csv")

hotspot = "c315"
peptide_df_list = []

for patient in patients:
    peptide_df = pd.read_csv(f"/data/home/ysh980101/2411/data-mhc/{hotspot}/{patient}/peptides_HLA-I.csv")
    peptide_df = peptide_df[~peptide_df['Peptide'].str.contains('[-*]', regex=True, na=False)]
    
    patient_name = patient 
    
    peptide_df = peptide_df[['Peptide']]  
    peptide_df.columns = [patient_name]  
    
    peptide_df_list.append(peptide_df)

merged_df = pd.concat(peptide_df_list, axis = 1)
merged_df.index = f"{hotspot}." + merged_df.index.astype(str)
merged_df

merged_df.to_csv(f"/data/home/ysh980101/2412/result/epitope_{hotspot}.csv")