Testing for codon reassignment in bacteriophages
Pre-requisities
- anaconda or miniconda already installed
- python3
- Jupyter notebook or jupyter lab
- To setup Jupyter notebook or lab on the cluster: https://fame.flinders.edu.au/blog/2022/07/16/jupyter-deepthought2
- Artemis genome browser: http://sanger-pathogens.github.io/Artemis/Artemis/
Setting up the environment
```
conda create -n phicore
conda activate phicore
#install trnascan-se
conda install -c bioconda trnascan-se
mamba install -c anaconda seaborn
mamba install -c anaconda numpy
mamba install -c conda-forge matplotlib
mamba install -c conda-forge biopython
mamba install -c bioconda dna_features_viewer
mamba install -y ipykernel
#install phanotate dev version
git clone -b develop https://github.com/deprekate/PHANOTATE.git
cd PHANOTATE/
python3 -m venv env
source env/bin/activate
python setup.py install
```
Installing phicore
```
git clone https://github.com/npbhavya/Phicore.git
```
Deactivating environment
```
#deactivate the virtual environment
deactivate
#deactivate the conda environment
conda deactivate
```
Activating environment if already installed
```
conda activate phicore
cd PHANOTATE
source env/bin/activate
```
- Fasta files saved to "test-data"
- Genbank files saved to "genbank"
README.md added to both directories
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