时间戳

首页 > 解决方案 > 解析 GFF 文件抛出 TypeError

python - 解析 GFF 文件抛出 TypeError

问题描述

我正在尝试使用 Biopython 解析 gif 文件，并且正在使用他们网站上的示例代码。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, limit_info, target_lines):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 637, in _gff_process
    for out in self._lines_to_out_info(line_gen, limit_info, target_lines):
  File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", 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

我不确定如何解决该错误，因为我似乎传递的是 astr而不是 a FakeHandle。我正在使用 conda 运行 biopython 1.78。

标签： pythonbiopython

解决方案

推荐阅读