我的氨基酸序列正样本存储在一个txt文件,负样本存储在另一个txt文件,我需要先对氨基酸序列度热编码得到每个氨基酸二维数组,再输入支持向量机中训练和验证,该怎么写python代码呢
时间: 2024-10-09 18:01:43 浏览: 27
你可以按照以下步骤编写Python代码来实现这个过程,这里我们使用`sklearn.preprocessing`库来进行热编码,以及`sklearn.model_selection`库来进行训练集和测试集的划分:
```python
import numpy as np
import pandas as pd
from sklearn.feature_extraction.text import CountVectorizer
from sklearn.preprocessing import LabelEncoder
from sklearn.svm import SVC
from sklearn.model_selection import train_test_split
# 定义读取两个txt文件并将内容存储到DataFrame
def read_data(pos_file, neg_file):
pos_data = pd.read_csv(pos_file, sep='\t', header=None, names=['sequence'])
neg_data = pd.read_csv(neg_file, sep='\t', header=None, names=['sequence'])
return pos_data.append(neg_data)
# 加载数据并编码
def encode_sequences(data):
vectorizer = CountVectorizer(analyzer='char') # 对氨基酸序列进行字符级计数
encoded_data = vectorizer.fit_transform(data['sequence'])
# 将标签转换为整数
label_encoder = LabelEncoder()
labels = label_encoder.fit_transform(data['label']) # 假设标签为'positive'或'negative'
return encoded_data, labels, vectorizer, label_encoder
# 主程序
if __name__ == "__main__":
pos_file = 'positive_sequences.txt'
neg_file = 'negative_sequences.txt'
data = read_data(pos_file, neg_file)
# 度热编码并拆分数据集
encoded_data, labels, _, _ = encode_sequences(data)
X_train, X_test, y_train, y_test = train_test_split(encoded_data, labels, test_size=0.2, random_state=42)
# 训练支持向量机
model = SVC(kernel='linear')
model.fit(X_train, y_train)
# 验证模型
predictions = model.predict(X_test)
accuracy = accuracy_score(y_test, predictions)
print(f"Accuracy: {accuracy}")
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