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DataGenerator crashes when no "pssm_source" is provided #240

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DarioMarzella opened this issue Aug 6, 2021 · 0 comments
Open

DataGenerator crashes when no "pssm_source" is provided #240

DarioMarzella opened this issue Aug 6, 2021 · 0 comments
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@DarioMarzella
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Describe the bug
DataGenerator crashes when no "pssm_source" is provided

Environment:

  • OS system:Linux

To Reproduce
Steps/commands to reproduce the behaviour:

  1. Create a DataGenerator object, do not specify "pssm_souce" in it
  2. Run the script

Actual Results or Error Info

Traceback (most recent call last):
File "/srv/home2/dariom/deeprank_edesolv/./Edesolv/generate_dataset.py", line 55, in
database.create_database(prog_bar=False)
File "/srv/home2/dariom/deeprank_edesolv/deeprank/generate/DataGenerator.py", line 253, in create_database
self.f5.attrs['pssm_source'] = os.path.abspath(
File "/home/dariom/anaconda3/envs/3D-EP/lib/python3.9/posixpath.py", line 374, in abspath
path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not NoneType

Additional Context
The problem is raised in deeprank/generate/DataGenerator.py, line 253.
Can be fixed by simply adding the following line:

if self.pssm_source is not None:

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