seq_import = function("prodigal_outdir.fna"){ Error: unexpected string constant in "seq_import = function("prodigal_outdir.fna""

这个错误提示是因为在定义函数时，函数名后面的括号中应该列出函数的参数，而不是直接写入参数的值。可以将函数名后面的括号中的参数名改为 `file_name`，然后在函数内部使用这个参数名来读取文件，例如：

seq_import = function(file_name){
  seq_data = read.fasta(file_name)
  # 这里可以对读取到的序列数据进行处理
  return(seq_data)
}

# 调用函数
seq_data = seq_import("prodigal_outdir.fna")

在调用函数时，需要将要读取的文件名作为参数传递给函数。

相关问题

class Net(nn.Module): def __init__(self,input_size,hidden_size,num_layers,output_size,batch_size,seq_length) -> None: super(Net,self).__init__() self.input_size=input_size self.hidden_size=hidden_size self.num_layers=num_layers self.output_size=output_size self.batch_size=batch_size self.seq_length=seq_length self.num_directions=1 # 单向LSTM self.lstm=nn.LSTM(input_size=input_size,hidden_size=hidden_size,num_layers=num_layers,batch_first=True) # LSTM层 self.fc=nn.Linear(hidden_size,output_size) # 全连接层 def forward(self,x): # e.g. x(10,3,100) 三个句子，十个单词，一百维的向量,nn.LSTM(input_size=100,hidden_size=20,num_layers=4) # out.shape=(10,3,20) h/c.shape=(4,b,20) batch_size, seq_len = x.size()[0], x.size()[1] # x.shape=(604,3,3) h_0 = torch.randn(self.num_directions * self.num_layers, x.size(0), self.hidden_size) c_0 = torch.randn(self.num_directions * self.num_layers, x.size(0), self.hidden_size) # output(batch_size, seq_len, num_directions * hidden_size) output, _ = self.lstm(x, (h_0, c_0)) # output(5, 30, 64) pred = self.fc(output) # (5, 30, 1) pred = pred[:, -1, :] # (5, 1) return pred改成python代码

这段代码是一个简单的使用 PyTorch 实现的 LSTM 模型。下面是将其转化为 Python 代码的版本：

import torch
import torch.nn as nn

class Net(nn.Module):
    def __init__(self, input_size, hidden_size, num_layers, output_size, batch_size, seq_length):
        super(Net, self).__init__()
        self.input_size = input_size
        self.hidden_size = hidden_size
        self.num_layers = num_layers
        self.output_size = output_size
        self.batch_size = batch_size
        self.seq_length = seq_length
        self.num_directions = 1  # 单向LSTM

        # LSTM层
        self.lstm = nn.LSTM(input_size=input_size, hidden_size=hidden_size, num_layers=num_layers, batch_first=True)

        # 全连接层
        self.fc = nn.Linear(hidden_size, output_size)

    def forward(self, x):
        # x.shape=(10,3,100)，三个句子，十个单词，一百维的向量
        # out.shape=(10,3,20)，h/c.shape=(4,b,20)
        batch_size, seq_len = x.size()[0], x.size()[1]
        h_0 = torch.randn(self.num_directions * self.num_layers, x.size(0), self.hidden_size)
        c_0 = torch.randn(self.num_directions * self.num_layers, x.size(0), self.hidden_size)
        output, _ = self.lstm(x, (h_0, c_0))  # output(batch_size, seq_len, num_directions * hidden_size)
        pred = self.fc(output)  # (5, 30, 1)
        pred = pred[:, -1, :]  # (5, 1)

        return pred

下面的这段python代码，哪里有错误，修改一下：import numpy as np import matplotlib.pyplot as plt import pandas as pd import torch import torch.nn as nn from torch.autograd import Variable from sklearn.preprocessing import MinMaxScaler training_set = pd.read_csv('CX2-36_1971.csv') training_set = training_set.iloc[:, 1:2].values def sliding_windows(data, seq_length): x = [] y = [] for i in range(len(data) - seq_length): _x = data[i:(i + seq_length)] _y = data[i + seq_length] x.append(_x) y.append(_y) return np.array(x), np.array(y) sc = MinMaxScaler() training_data = sc.fit_transform(training_set) seq_length = 1 x, y = sliding_windows(training_data, seq_length) train_size = int(len(y) * 0.8) test_size = len(y) - train_size dataX = Variable(torch.Tensor(np.array(x))) dataY = Variable(torch.Tensor(np.array(y))) trainX = Variable(torch.Tensor(np.array(x[1:train_size]))) trainY = Variable(torch.Tensor(np.array(y[1:train_size]))) testX = Variable(torch.Tensor(np.array(x[train_size:len(x)]))) testY = Variable(torch.Tensor(np.array(y[train_size:len(y)]))) class LSTM(nn.Module): def __init__(self, num_classes, input_size, hidden_size, num_layers): super(LSTM, self).__init__() self.num_classes = num_classes self.num_layers = num_layers self.input_size = input_size self.hidden_size = hidden_size self.seq_length = seq_length self.lstm = nn.LSTM(input_size=input_size, hidden_size=hidden_size, num_layers=num_layers, batch_first=True) self.fc = nn.Linear(hidden_size, num_classes) def forward(self, x): h_0 = Variable(torch.zeros( self.num_layers, x.size(0), self.hidden_size)) c_0 = Variable(torch.zeros( self.num_layers, x.size(0), self.hidden_size)) # Propagate input through LSTM ula, (h_out, _) = self.lstm(x, (h_0, c_0)) h_out = h_out.view(-1, self.hidden_size) out = self.fc(h_out) return out num_epochs = 2000 learning_rate = 0.001 input_size = 1 hidden_size = 2 num_layers = 1 num_classes = 1 lstm = LSTM(num_classes, input_size, hidden_size, num_layers) criterion = torch.nn.MSELoss() # mean-squared error for regression optimizer = torch.optim.Adam(lstm.parameters(), lr=learning_rate) # optimizer = torch.optim.SGD(lstm.parameters(), lr=learning_rate) runn = 10 Y_predict = np.zeros((runn, len(dataY))) # Train the model for i in range(runn): print('Run: ' + str(i + 1)) for epoch in range(num_epochs): outputs = lstm(trainX) optimizer.zero_grad() # obtain the loss function loss = criterion(outputs, trainY) loss.backward() optimizer.step() if epoch % 100 == 0: print("Epoch: %d, loss: %1.5f" % (epoch, loss.item())) lstm.eval() train_predict = lstm(dataX) data_predict = train_predict.data.numpy() dataY_plot = dataY.data.numpy() data_predict = sc.inverse_transform(data_predict) dataY_plot = sc.inverse_transform(dataY_plot) Y_predict[i,:] = np.transpose(np.array(data_predict)) Y_Predict = np.mean(np.array(Y_predict)) Y_Predict_T = np.transpose(np.array(Y_Predict))

在这段代码中，可能存在以下错误：

1. 缺少必要的库或模块。

2. training_set 的文件路径是否正确。

3. training_set 的数据处理是否正确。

4. LSTM 模型的定义是否正确。

5. 训练和预测的代码是否正确。

下面是修改后的代码：

import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import torch
import torch.nn as nn
from torch.autograd import Variable
from sklearn.preprocessing import MinMaxScaler

# 读取数据
training_set = pd.read_csv('CX2-36_1971.csv')
training_set = training_set.iloc[:, 1:2].values

# 定义数据处理函数
def sliding_windows(data, seq_length):
    x = []
    y = []
    
    for i in range(len(data) - seq_length):
        _x = data[i:(i + seq_length)]
        _y = data[i + seq_length]
        x.append(_x)
        y.append(_y)
    
    return np.array(x), np.array(y)

# 对数据进行归一化处理
sc = MinMaxScaler()
training_data = sc.fit_transform(training_set)

# 定义窗口长度
seq_length = 1

# 对数据进行窗口划分
x, y = sliding_windows(training_data, seq_length)

# 划分训练集和测试集
train_size = int(len(y) * 0.8)
test_size = len(y) - train_size

dataX = Variable(torch.Tensor(np.array(x)))
dataY = Variable(torch.Tensor(np.array(y)))

trainX = Variable(torch.Tensor(np.array(x[1:train_size])))
trainY = Variable(torch.Tensor(np.array(y[1:train_size])))

testX = Variable(torch.Tensor(np.array(x[train_size:len(x)])))
testY = Variable(torch.Tensor(np.array(y[train_size:len(y)])))

# 定义 LSTM 模型
class LSTM(nn.Module):
    def __init__(self, num_classes, input_size, hidden_size, num_layers):
        super(LSTM, self).__init__()
        
        self.num_classes = num_classes
        self.num_layers = num_layers
        self.input_size = input_size
        self.hidden_size = hidden_size
        self.seq_length = seq_length
        
        self.lstm = nn.LSTM(input_size=input_size, hidden_size=hidden_size,
                            num_layers=num_layers, batch_first=True)
        
        self.fc = nn.Linear(hidden_size, num_classes)
    
    def forward(self, x):
        h_0 = Variable(torch.zeros(
            self.num_layers, x.size(0), self.hidden_size))
        
        c_0 = Variable(torch.zeros(
            self.num_layers, x.size(0), self.hidden_size))
        
        # Propagate input through LSTM
        ula, (h_out, _) = self.lstm(x, (h_0, c_0))
        
        h_out = h_out.view(-1, self.hidden_size)
        
        out = self.fc(h_out)
        
        return out

# 定义训练参数
num_epochs = 2000
learning_rate = 0.001
input_size = 1
hidden_size = 2
num_layers = 1
num_classes = 1

# 实例化 LSTM 模型
lstm = LSTM(num_classes, input_size, hidden_size, num_layers)

# 定义损失函数和优化器
criterion = torch.nn.MSELoss()
optimizer = torch.optim.Adam(lstm.parameters(), lr=learning_rate)

# 训练模型
runn = 10
Y_predict = np.zeros((runn, len(dataY)))

for i in range(runn):
    print('Run: ' + str(i + 1))
    for epoch in range(num_epochs):
        outputs = lstm(trainX)
        optimizer.zero_grad()
        loss = criterion(outputs, trainY)
        loss.backward()
        optimizer.step()
        
        if epoch % 100 == 0:
            print("Epoch: %d, loss: %1.5f" % (epoch, loss.item()))
    
    lstm.eval()
    train_predict = lstm(dataX)
    data_predict = train_predict.data.numpy()
    dataY_plot = dataY.data.numpy()
    
    # 对结果进行反归一化
    data_predict = sc.inverse_transform(data_predict)
    dataY_plot = sc.inverse_transform(dataY_plot)
    
    Y_predict[i,:] = np.transpose(np.array(data_predict))

Y_Predict = np.mean(Y_predict, axis=0)
Y_Predict_T = np.transpose(np.array(Y_Predict))