ctokheim / deepdegron Goto Github PK

$ git clone https://github.com/ctokheim/deepDegron
$ cd deepDegron
$ conda env create -f environment.yml  # install dependencies
$ conda activate deepDegron  # activate environment
$ pyensembl install --release 75 --species human  # download human hg19 reference data
$ pyensembl install --release 95 --species human  # download human hg38 reference data
$ python setup.py install  # install deepDegron

$ deepdegron score -i tests/data/gata3_mutations.txt -c models/cterm/neural_network_pos_specific.pickle,models/cterm/neural_network_bag_of_amino_acids.pickle -o GATA3_delta_degron_potential.txt

Traceback (most recent call last):
  File "/opt/conda/envs/deepDegron/bin/deepdegron", line 33, in <module>
    sys.exit(load_entry_point('deepDegron==1.1.0', 'console_scripts', 'deepdegron')())
  File "/opt/conda/envs/deepDegron/lib/python3.7/site-packages/deepDegron-1.1.0-py3.7.egg/deepDegron/deep_degron.py", line 170, in cli_main
    main(opts)
  File "/opt/conda/envs/deepDegron/lib/python3.7/site-packages/deepDegron-1.1.0-py3.7.egg/deepDegron/deep_degron.py", line 154, in main
    import deepDegron.score_mutations as score
  File "/opt/conda/envs/deepDegron/lib/python3.7/site-packages/deepDegron-1.1.0-py3.7.egg/deepDegron/score_mutations.py", line 18, in <module>
    import varcode
  File "/opt/conda/envs/deepDegron/lib/python3.7/site-packages/varcode/__init__.py", line 16, in <module>
    from .variant import Variant
  File "/opt/conda/envs/deepDegron/lib/python3.7/site-packages/varcode/variant.py", line 31, in <module>
    from pyensembl.biotypes import is_coding_biotype
ModuleNotFoundError: No module named 'pyensembl.biotypes'