解析 GFF 文件抛出 TypeError

如何解决解析 GFF 文件抛出 TypeError

我正在尝试使用 Biopython 解析一个 gif 文件,并且正在使用其 website 中的示例代码。这是代码:

from BCBio import GFF

in_file = "infile.gff"

in_handle = open(in_file)
for rec in GFF.parse(in_handle):
        print(rec)
        in_handle.close()

当我运行代码时出现以下错误:

Traceback (most recent call last):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py",line 47,in __init__
    self.stream = open(source,"r" + mode)
TypeError: expected str,bytes or os.PathLike object,not FakeHandle

During handling of the above exception,another exception occurred:

Traceback (most recent call last):
  File "get_genes_dpt.py",line 37,in <module>
    for rec in GFF.parse(in_handle):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py",line 746,in parse
    target_lines):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py",line 322,in parse_in_parts
    for results in self.parse_simple(gff_files,limit_info,target_lines):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py",line 343,in parse_simple
    for results in self._gff_process(gff_files,line 637,in _gff_process
    for out in self._lines_to_out_info(line_gen,line 699,in _lines_to_out_info
    fasta_recs = self._parse_fasta(FakeHandle(line_iter))
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py",line 560,in _parse_fasta
    return list(SeqIO.parse(in_handle,"fasta"))
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/__init__.py",line 607,in parse
    return iterator_generator(handle)
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py",line 183,in __init__
    super().__init__(source,mode="t",fmt="Fasta")
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py",line 51,in __init__
    if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given

我不确定如何修复错误,因为我似乎传递的是 str 而不是 FakeHandle。我正在使用 conda 运行 biopython 1.78。

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