deepbgc info crash - same as Issue #39
jfoldi81 opened this issue · comments
@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`