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The read and potentially the write methods of the IO registry may not be aware of how to interact with pathlib.Path:
read
write
pathlib.Path
(skdev-py310) 8:34:48 (dtmcdonald@there):scikit-bio@biom_format$ cat foo.fasta >a ATGC >b TTGC (skdev-py310) 8:34:53 (dtmcdonald@there):scikit-bio@biom_format$ python Python 3.10.13 (main, Sep 11 2023, 08:39:02) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import skbio, pathlib >>> list(skbio.read('foo.fasta', format='fasta')) [Sequence --------------------- Metadata: 'description': '' 'id': 'a' Stats: length: 4 --------------------- 0 ATGC, Sequence --------------------- Metadata: 'description': '' 'id': 'b' Stats: length: 4 --------------------- 0 TTGC] >>> list(skbio.read(pathlib.Path('foo.fasta'), format='fasta')) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/dtmcdonald/ResearchWork/software/scikit-bio/skbio/io/registry.py", line 1180, in read return io_registry.read(file, format=format, into=into, verify=verify, **kwargs) File "/Users/dtmcdonald/ResearchWork/software/scikit-bio/skbio/io/registry.py", line 495, in read return (x for x in itertools.chain([next(gen)], gen)) File "/Users/dtmcdonald/ResearchWork/software/scikit-bio/skbio/io/registry.py", line 518, in _read_gen with _resolve_file(file, **io_kwargs) as (file, _, _): File "/Users/dtmcdonald/miniconda3/envs/skdev-py310/lib/python3.10/contextlib.py", line 135, in __enter__ return next(self.gen) File "/Users/dtmcdonald/ResearchWork/software/scikit-bio/skbio/io/util.py", line 222, in _resolve_file file, source, is_binary_file = _resolve(file, **kwargs) File "/Users/dtmcdonald/ResearchWork/software/scikit-bio/skbio/io/util.py", line 77, in _resolve raise IOSourceError("Could not open source: %r (mode: %r)" % (file, mode)) skbio.io._exception.IOSourceError: Could not open source: PosixPath('foo.fasta') (mode: 'r') >>>
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The
read
and potentially thewrite
methods of the IO registry may not be aware of how to interact withpathlib.Path
:The text was updated successfully, but these errors were encountered: