tre_to_csv

Install

1. Install compiler to compile biopython

   sudo yum install gcc gcc-c++
   

2. Install latest development for biopython (v1.69)

   pip install git+https://github.com/biopython/biopython.git
   

Usage

Traditional way

python tre_to_csv.py <input.tre>

Another way using docker

This removes the need to worry about dependencies and will always run the same way regardless of computer

1. Only once do you have to build the docker image

   docker build -t local/biopython .
   

2. Then you can execute the code using docker

   docker run -it -v $PWD:/here -w /here local/biopython python tre_to_csv.py examples/test.tre
   

Output

output will go to standard output

Examples

python tre_to_csv.py examples/test.tre

Taxnames

Make sure not to have dashes in your taxnames or it will break at this time due to biopython/biopython#1022