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mamba create -yqn test conda-forge::python=3.9 bioconda::pybedtools=0.9.0 conda-forge::numpy=1.19
## Preparing transaction: ...working... done## Verifying transaction: ...working... done## Executing transaction: ...working... done
conda run -n test python -c "import numpy as np, pybedtools; pybedtools.BedTool([['chr1', np.int64(1), np.int64(2)]])"## Traceback (most recent call last):## File "<string>", line 1, in <module>## File "/home/ec2-user/mambaforge3/envs/test/lib/python3.9/site-packages/pybedtools/bedtool.py", line 589, in __init__## fn = BedTool(iter(fn)).saveas().fn## File "/home/ec2-user/mambaforge3/envs/test/lib/python3.9/site-packages/pybedtools/bedtool.py", line 923, in decorated## result = method(self, *args, **kwargs)## File "/home/ec2-user/mambaforge3/envs/test/lib/python3.9/site-packages/pybedtools/bedtool.py", line 3362, in saveas## fn = self._collapse(## File "/home/ec2-user/mambaforge3/envs/test/lib/python3.9/site-packages/pybedtools/bedtool.py", line 1422, in _collapse## for i in iterable:## File "pybedtools/cbedtools.pyx", line 793, in pybedtools.cbedtools.IntervalIterator.__next__## File "pybedtools/cbedtools.pyx", line 657, in pybedtools.cbedtools.create_interval_from_list## File "pybedtools/cbedtools.pyx", line 579, in pybedtools.cbedtools.isdigit## AttributeError: 'numpy.int64' object has no attribute 'isdigit'## ## ERROR conda.cli.main_run:execute(47): `conda run python -c import numpy as np,pybedtools; pybedtools.BedTool([['chr1', np.int64(1), np.int64(2)]])` failed. (See above for error)
The following minimal example raises an exception
The reason appears to be that numpy integer types are not correctly handled https://github.com/daler/pybedtools/blob/master/pybedtools/cbedtools.pyx#L576
I ran into the same problem as #362 and I think this is the root cause.
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