将大型fasta拆分为多个文件，无法使用GI编号命名

Question

首先，我应该说我是Python和Biopython的新手。我想分一大块。将文件（具有多个条目）快速转换为单个文件，每个文件具有一个条目。我在BiopythonWiki/Cookbook网站上找到了以下大部分代码，并对其进行了一些修改。我的问题是，这个生成器将它们命名为“1.fasta”、“2.fasta”等，我需要用一些标识符（如GI编号）来命名它们。

 def batch_iterator(iterator, batch_size) :
    """Returns lists of length batch_size.

    This can be used on any iterator, for example to batch up
    SeqRecord objects from Bio.SeqIO.parse(...), or to batch
    Alignment objects from Bio.AlignIO.parse(...), or simply
    lines from a file handle.

    This is a generator function, and it returns lists of the
    entries from the supplied iterator.  Each list will have
    batch_size entries, although the final list may be shorter.
    """
    entry = True #Make sure we loop once
    while entry :
        batch = []
        while len(batch) < batch_size :
            try :
                entry = next(iterator)
            except StopIteration :
                entry = None
            if entry is None :
                #End of file
                break
            batch.append(entry)
        if batch :
            yield batch

from Bio import SeqIO
infile = input('Which .fasta file would you like to open? ')
record_iter = SeqIO.parse(open(infile), "fasta")
for i, batch in enumerate(batch_iterator(record_iter, 1)) :
    outfile = "c:\python32\myfiles\%i.fasta" % (i+1)
    handle = open(outfile, "w")
    count = SeqIO.write(batch, handle, "fasta")
    handle.close()

如果我尝试替换：

outfile = "c:\python32\myfiles\%i.fasta" % (i+1)

与：

outfile = "c:\python32\myfiles\%s.fasta" % (record_iter.id)

因此，它将命名类似于SeqIO中seq_record.id的东西，它会给出以下错误：

    Traceback (most recent call last):
  File "C:\Python32\myscripts\generator.py", line 33, in [HTML]
    outfile = "c:\python32\myfiles\%s.fasta" % (record_iter.id)
AttributeError: 'generator' object has no attribute 'id'

虽然生成器函数没有属性'id'，但我能以某种方式绕过它吗？这个剧本对我来说太复杂了吗？！？谢了查尔斯

Answer 1

因为一次只需要一条记录，所以可以放弃批处理迭代器包装器和枚举：

for seq_record in record_iter:

然后你需要的是每个记录的id属性，而不是整个迭代器：

for seq_record in record_iter:
    outfile = "c:\python32\myfiles\{0}.fasta".format(seq_record.id)
    handle = open(outfile, "w")
    count = SeqIO.write(seq_record, handle, "fasta")
    handle.close()

为供参考，生成器错误是由于您试图从对象记录\u iter获取属性idrecord\u iter不是一条记录，而是一组记录，它们作为Python生成器保存，这有点像一个正在进行的列表，因此您不必一次读取整个文件，而且内存使用效率更高。关于生成器的更多信息：您可以使用Python生成器函数做什么，http://docs.python.org/tutorial/classes.html#generators ,