Domesticator first release

First release of Domesticator. This is the version that's been running on Digs for about 7 months now with no problems. Lots of not-ready stuff in here, but if you stick to the options that have help messages, you should be good?

Installation instructions:

Create the domesticator conda environment by cloning from the yml.
$ conda env create -f domesticator.yml

The yml file is not needed after this point so you may delete it.
Next, activate the domesticator environment
$ conda activate domesticator

Save the path to your executable
(domesticator) $ which python

Edit the first line of domesticator.py to be "#!/PATH/TO/python", replacing /PATH/TO/python with the output of $ which python

Edit the 6th line of domesticator.py to point to the domesticator database directory where it lives in your system

For installing ViennaRNA, cd to a directory you wish to install software to, then run
$ wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.14.tar.gz

Extract it
$ tar -xzf ViennaRNA-2.4.14.tar.gz

Compile it
$ cd ViennaRNA-2.4.14
$ sudo ./configure && sudo make && sudo make install

Change a filename
$ cd interfaces/Python3/RNA
$ mv _RNA.<some_random_string>.so _RNA.so

Create a symlink from ViennaRNA to your conda environment. Use full paths, not relative paths
$ ln -s path/to/install/software/ViennaRNA-2.4.14/interfaces/Python3/RNA /path/to/anaconda3/envs/domesticator/lib/python3.5/site-packages/

Finally, set the domesticator.py script to be executable if it isn't already
$ cd /PATH/TO/DOMESTICATOR
$ chmod +x domesticator.py

An example of how to run it:
$ /domesticator.py protein.fasta --avoid_restriction_sites NdeI XhoI --avoid_patterns AGGAGG TAAGGAG GCTGGTGG ATCTGTT GGRGGT MAGGTRAG YYYYNTAGG --species e_coli --avoid_kmers 9 --avoid_kmers_boost 10

Where protein.fasta contains the sequence of the protein you want to back translate in fasta format.

see domesticator.py --help for more details