| import pandas as pd |
| import argparse |
| import json |
|
|
| def parse_args(): |
| parser = argparse.ArgumentParser( |
| description="Generate json records for test file with only sequences" |
| ) |
| parser.add_argument( |
| "--in_file", |
| help="Path to csv file", |
| required=True, |
| ) |
| |
| parser.add_argument("--out_file", help="output file for json records") |
|
|
| args = parser.parse_args() |
| return args |
|
|
| args = parse_args() |
| df = pd.read_csv(args.data_file) |
| assert('pdbpath' in df.columns) |
| assert('sequence' in df.columns) |
|
|
| import json |
| dic_full = {} |
| for ind, row in df.iterrows(): |
| dic = {} |
| dic['name'] = row.pdbpath |
| dic['seq'] = row.sequence |
| dic_full[row.pdbpath] = dic |
|
|
| f = open(args.out_file,'w') |
| f.write(json.dumps(dic_full)) |
| f.close() |
