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PyBedTools 0.12 intersect doesn't work with Python 3.13 #425

@PlatonB

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@PlatonB
python
Python 3.13.5 | packaged by conda-forge | (main, Jun 16 2025, 08:27:50) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pybedtools import BedTool
>>> import pybedtools
>>> pybedtools.__version__
'0.12.0'
>>> vcf_bt_obj = BedTool(fn='/users/home/bykadorovpa/software/platinum-metrics/temp_platon/deno_f_clnd.vcf')
>>> vcf_bt_obj.intersect(b='/users/home/bykadorovpa/software/platinum-metrics/temp_platon/Simple_Repeats.bed')
Traceback (most recent call last):
  File "<python-input-4>", line 1, in <module>
    vcf_bt_obj.intersect(b='/users/home/bykadorovpa/software/platinum-metrics/temp_platon/Simple_Repeats.bed')
    ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/users/home/bykadorovpa/miniconda3/lib/python3.13/site-packages/pybedtools/bedtool.py", line 454, in decorated
    result = method(self, *args, **kwargs)
  File "/users/home/bykadorovpa/miniconda3/lib/python3.13/site-packages/pybedtools/bedtool.py", line 250, in not_implemented_func
    raise NotImplementedError(help_str)
NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled.  Please install a more recent version of BEDTools and re-import to use this method.
>>>

Works ok with Python 3.12.

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