You can run install.sh to install compile the library dynamically. Either using GCC or Clang.
The script accepts two flas -i and -c. -c can either be clang or gcc. -i does not have a value but if you pass it, then clean directive won't run.
The script will echo your options.
Run it like this:
bash ./install.sh -i -c gcc
or
bash ./install.sh -c clang
Or simply
bash ./install.sh
Remember that a shebang has been added to the script. It won't run with sh. you will have to run it with bash. Either that or do this ONCE:
sudo chmod +x ./install.sh
Then run it with no issue. Script needs sudo at some point so this will fix it.
To build the Python FFI using cffi you'll need cffi. Create a new virtual env using python3 -m venv env and then enter source env/bin/activate. You are now in the venv. Install pip3 install cffi. Then run:
python3 ffi.py
To run the script you'll need biopython. Install it in the same venv. Then run the script and pass the FASTA file like so:
python3 fastcompare.py <file>
A resulting JSON file will be created. Currently the JSON file does not map to the seqs and headers. It just shows seq #n (at index #n in the array in the JSON file) is a duplicate of #k, #k being the value of the array at and index. Sor for example of test.fa_out.json looks like this:
[-1, 0, -1, -1, -1]
``
That means sequence 2 in the file is a duplicate of sequence 1 in the file. If a sequence is not a duplicate, then the its value at the index in the array will be `-1`. Mappings will SOON be added!