README.md

Phicore

Testing for codon reassignment in bacteriophages

Installation

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
```

Test data

• Fasta files saved to "test-data"
• Genbank files saved to "genbank"

README.md added to both directories