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improve pathlib handling (fix #421) #423

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Merged
merged 1 commit into from
Feb 24, 2025
Merged

improve pathlib handling (fix #421) #423

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5 changes: 5 additions & 0 deletions pybedtools/bedtool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1460,6 +1460,11 @@ def handle_kwargs(self, prog:str, arg_order: Optional[list[str]] = None, **kwarg
"mapBed": ",",
}
stdin = None

# If anything in kwargs is a pathlib Path, convert to string here.
for k, v in kwargs.items():
if isinstance(v, pathlib.PurePath):
kwargs[k] = str(v)

# -----------------------------------------------------------------
# Decide how to send instream1 to BEDTools. If there's no implicit
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13 changes: 13 additions & 0 deletions pybedtools/test/test_pathlib.py
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Expand Up @@ -25,3 +25,16 @@ def test_pathlib_nonexistent_file():
path = pathlib.Path(fn)
with pytest.raises(FileNotFoundError):
pybedtools.BedTool(path)


def test_pathlib_on_methods():
# Above functions test the creation of BedTool from Path objects; here we
# test arbitrary methods to test that Path objs are converted to str when
# composing the relevant command.
fn_a = os.path.join(pybedtools.filenames.data_dir(), "a.bed")
fn_b = os.path.join(pybedtools.filenames.data_dir(), "b.bed")
p_a = pathlib.Path(fn_a)
p_b = pathlib.Path(fn_b)
bt = pybedtools.BedTool(fn_a)
res = bt.intersect(p_b)

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