Source code for miniworld.utils.kalign_mapping

import torch



def kalign_mapping(kalign_output):
    with open(kalign_output, 'r') as f:
        lines = f.readlines()

    query_seq = lines[1].strip()
    target_seq = lines[3].strip()

    map = {}
    query_idx = 0
    target_idx = 0
    for query_aa, target_aa in zip(query_seq, target_seq):
        if query_aa != '-' and target_aa != '-':
            map[query_idx] = target_idx
        if query_aa != '-':
            query_idx += 1
        if target_aa != '-':
            target_idx += 1

    query_map_idx = map.keys()
    target_map_idx = map.values()

    query_map_idx = torch.tensor(list(query_map_idx))
    target_map_idx = torch.tensor(list(target_map_idx))

    return query_map_idx, target_map_idx


if __name__ == "__main__":
    path = '/home/casp16/run/TS.human/H0217/MiniWorld/kalign/s1.out'

    query_idx, target_idx = kalign_mapping(path)