我想为一组 DNA 序列生成一个热编码。例如,序列 ACGTCCA 可以以转置方式表示如下。但是下面的代码将以水平方式生成一种热编码,我更喜欢垂直形式的编码。谁能帮我?
ACGTCCA
1000001 - A
0100110 - C
0010000 - G
0001000 - T
示例代码:
from sklearn.preprocessing import OneHotEncoder
import itertools
# two example sequences
seqs = ["ACGTCCA","CGGATTG"]
# split sequences to tokens
tokens_seqs = [seq.split("\\") for seq in seqs]
# convert list of of token-lists to one flat list of tokens
# and then create a dictionary that maps word to id of word,
# like {A: 1, B: 2} here
all_tokens = itertools.chain.from_iterable(tokens_seqs)
word_to_id = {token: idx for idx, token in enumerate(set(all_tokens))}
# convert token lists to token-id lists, e.g. [[1, 2], [2, 2]] here
token_ids = [[word_to_id[token] for token in tokens_seq] for tokens_seq in tokens_seqs]
# convert list of token-id lists to one-hot representation
vec = OneHotEncoder(n_values=len(word_to_id))
X = vec.fit_transform(token_ids)
print X.toarray()
但是,代码给了我输出:
[[ 0. 1.]
[ 1. 0.]]
预期输出:
[[1. 0. 0. 0. 0. 0. 1. 0. 1. 0. 0. 1. 1. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0.]
[0. 0. 0. 1. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 0. 1. 0. 0. 0. 0. 1. 1. 0.]]