Question

我正在尝试应用biopython代码来分割大型fasta文件。代码如上：

def batch_iterator():
    entry=True # to make sure the loop run once
    while entry:
        batch=[]
        while len(batch) < batch_size:
            try:
                entry=iterator.next()
            except StopIteration:
                entry=None
            if entry is None:
                #end of file
                break
            batch.append(entry)
        if batch:
            yield batch
record_iter=SeqIO.parse(open('/home/to/file/sorted_sequence.fa', 'fasta')
for i, batch in enumerate (batch_iterator(record_iter, 93)):
    filename='gene_%i.fasta' % (i + 1)
    with open('/home/path/files/', filename, 'w') as ouput_handle:
        count=SeqIO.write(batch, ouput_handle, 'fasta')
    print ('Wrote %i records to %s' % (count, filename))

在这一行： 对于i，枚举中的批处理（batch_iterator（record_iter，93））：给了我 SyntaxError：语法无效。但我看不出错误，有人能帮我找到它吗，拜托？我从这个http://biopython.org/wiki/Split_large_file中获取了代码感谢。

Answer 1

此行中缺少括号

record_iter = SeqIO.parse(open('/home/to/file/sorted_sequence.fa', 'fasta')

尝试添加一个

record_iter = SeqIO.parse(open('/home/to/file/sorted_sequence.fa'), 'fasta')

biopython脚本给出错误＆＃39;无效的语法＆＃39;

1 个答案: