We use Pipenv to manage dependencies.
pip install --user pipenvgit clone https://github.com/JetBrains-Research/Genegram
cd Genegram
pipenv install --ignore-pipfileRun the following command with arguments.
python -m genegram| Argument | Required | Description |
|---|---|---|
| -i, --inp | True | Path to the FASTA file |
| -o, --out | True | Path to the folder where the Connectivity Tables will be saved |
| -m, --model | False | Type of the model to be used: main -- The default model, the best on average mps -- Multiplet prediction model pks -- Pseudoknots prediction model |
| -l, --log | False | Type of the logging level to be used: INFO -- Confirmation that things are working as expected WARNING -- An indication that something unexpected happened, the software is still working as expected ERROR -- Due to a more serious problem, the software has not been able to perform some function CRITICAL -- A serious error, indicating that the program itself may be unable to continue running DEBUG -- Detailed information, typically of interest only when diagnosing problems |
We recommend you use a pre-commit hook, which runs black when you type git commit.
pipenv install --dev
pre-commit installpre-commit run --all-files --color always --verbose
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