cellranger：如何将 gtf 文件转换为字符串

Question

我正在使用 cellranger mkref 并遇到一个奇怪的 python GTF (custome gtf) 问题：

Traceback (most recent call last):
  File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 750, in validate_gtf
    subprocess.check_output(cmd, stderr=subprocess.STDOUT)
  File "/home/user/cellranger-6.0.1/external/anaconda/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/home/user/cellranger-6.0.1/external/anaconda/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['gtf_to_gene_index', '/home/user/cellranger-6.0.1/indexes', '/home/user/cellranger-6.0.1/indexes/tmp74f_vsxg.json']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/cellranger-6.0.1/bin/rna/mkref", line 139, in <module>
    main()
  File "/home/user/cellranger-6.0.1/bin/rna/mkref", line 130, in main
    reference_builder.build_gex_reference()
  File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 613, in build_gex_reference
    self.validate_gtf()
  File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 753, in validate_gtf
    raise GexReferenceError("Error detected in GTF file: " + exc.output) from exc
TypeError: can only concatenate str (not "bytes") to str

此外，我有类似的 gtf 文件，cellranger 可以毫无问题地接受它。我比较了这些文件（此外，我从第二个文件制作的第一个文件）：

文件 1：text/plain; charset=us-ascii 文件 2：text/plain; charset=us-ascii

此外，我检查了 cat -vE，文件是相同的

如何更改文件？提前致谢！

Answer 1

我遇到了同样的问题。问题出在我的 GTF 文件中的重复 ID。删除这些重复项解决了这个问题。请参阅关于 Cellranger GitHub 的讨论：https://github.com/10XGenomics/cellranger/issues/125

cellranger：如何将 gtf 文件转换为字符串

cellranger: how to convert a gtf file to string

python

bash

bioinformatics