deepbgc info crash - same as Issue #39

[jfoldi81]

@prihoda Hello! I am running into this same issue now adn have not been able to resolve it by downgrading my biopython. Tensorflow did not recognize version 1.12.0 as a possibility so I am not sure how to test that route. This is the same issue as #39. Please let me know if you need any other information!

`(deepbgc) jonathanfoldi@Jonathans-MacBook-Pro ~ % pip install biopython==1.76
Collecting biopython==1.76
  Using cached biopython-1.76-cp37-cp37m-macosx_10_6_intel.whl (2.4 MB)
Requirement already satisfied: numpy in ./anaconda3/envs/deepbgc/lib/python3.7/site-packages (from biopython==1.76) (1.16.1)
ERROR: deepbgc 0.1.31 has requirement biopython>=1.78, but you'll have biopython 1.76 which is incompatible.
Installing collected packages: biopython
  Attempting uninstall: biopython
    Found existing installation: biopython 1.81
    Uninstalling biopython-1.81:
      Successfully uninstalled biopython-1.81
Successfully installed biopython-1.76
(deepbgc) jonathanfoldi@Jonathans-MacBook-Pro ~ % deepbgc info
Traceback (most recent call last):
  File "/Users/jonathanfoldi/Library/Python/3.9/bin/deepbgc", line 5, in <module>
    from deepbgc.main import main
  File "/Users/jonathanfoldi/Library/Python/3.9/lib/python/site-packages/deepbgc/__init__.py", line 2, in <module>
    from .pipeline import DeepBGCClassifier, DeepBGCDetector, HmmscanPfamRecordAnnotator, DeepBGCAnnotator, ProdigalProteinRecordAnnotator
  File "/Users/jonathanfoldi/Library/Python/3.9/lib/python/site-packages/deepbgc/pipeline/__init__.py", line 1, in <module>
    from .classifier import DeepBGCClassifier
  File "/Users/jonathanfoldi/Library/Python/3.9/lib/python/site-packages/deepbgc/pipeline/classifier.py", line 4, in <module>
    from deepbgc import util
  File "/Users/jonathanfoldi/Library/Python/3.9/lib/python/site-packages/deepbgc/util.py", line 18, in <module>
    from Bio.Alphabet import SingleLetterAlphabet, generic_dna
  File "/Users/jonathanfoldi/Library/Python/3.9/lib/python/site-packages/Bio/Alphabet/__init__.py", line 20, in <module>
    raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
(deepbgc) jonathanfoldi@Jonathans-MacBook-Pro ~ % conda list
# packages in environment at /Users/jonathanfoldi/anaconda3/envs/deepbgc:
#
# Name                    Version                   Build  Channel
absl-py                   2.1.0                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
argparse                  1.4.0                    pypi_0    pypi
astor                     0.8.1                    pypi_0    pypi
biopython                 1.76                     pypi_0    pypi
c-ares                    1.26.0               h10d778d_0    conda-forge
ca-certificates           2024.2.2             hf0a4a13_0    conda-forge
cycler                    0.11.0                   pypi_0    pypi
deepbgc                   0.1.31                   pypi_0    pypi
gast                      0.2.2                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpc-cpp                  1.48.1               h966d1d5_1    conda-forge
grpcio                    1.48.1           py37hed26be4_1    conda-forge
h5py                      3.8.0                    pypi_0    pypi
hmmer                     3.4                  h7133b54_0    bioconda
importlib-metadata        6.7.0                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
keras                     2.2.4                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
libabseil                 20220623.0      cxx17_h28b99d4_6    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libprotobuf               3.21.12              h7d26f99_2    conda-forge
libsqlite                 3.45.1               h091b4b1_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
markdown                  3.4.4                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                2.2.3                    pypi_0    pypi
ncurses                   6.4                  h463b476_2    conda-forge
numpy                     1.16.1                   pypi_0    pypi
openssl                   3.2.1                hd75f5a5_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
pandas                    0.24.1                   pypi_0    pypi
pip                       20.0.2                   py37_1    conda-forge
prodigal                  2.6.3                h2413b67_7    bioconda
protobuf                  3.20.3                   pypi_0    pypi
pyparsing                 3.1.1                    pypi_0    pypi
python                    3.7.12          hf3644f1_100_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.7                     4_cp37m    conda-forge
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
re2                       2022.06.01           h9a09cb3_1    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
scikit-learn              0.21.3                   pypi_0    pypi
scipy                     1.2.0                    pypi_0    pypi
setuptools                68.0.0                   pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
sqlite                    3.45.1               hf2abe2d_0    conda-forge
tensorboard               1.15.0                   pypi_0    pypi
tensorflow                1.15.4                   pypi_0    pypi
tensorflow-estimator      1.15.1                   pypi_0    pypi
termcolor                 2.3.0                    pypi_0    pypi
tk                        8.6.13               h5083fa2_1    conda-forge
typing-extensions         4.7.1                    pypi_0    pypi
werkzeug                  2.2.3                    pypi_0    pypi
wheel                     0.34.2                   py37_0    conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xz                        5.2.6                h775f41a_0    conda-forge
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               h8a1eda9_5    conda-forge`