This repository contains the code for running COD_FISH, the smFISH probe designer. To run on windows or mac, we recommend downloading the respective released zip file from https://github.com/ryandikdan/COD_FISH/releases (windows or mac), unzip it, and then double click the gui_COD_FISH.exe (windows) or gui_COD_FISH (mac) file and it should open the GUI and a terminal for progress. To run it using python, this repository must be downloaded into a directory (and other packages must be installed ie pip install tqdm primer3-py psutil ensembl_rest) and running the command python gui_COD_FISH.py will open up the GUI or the python COD_FISH.py command will run the command line version of the program.
- Troubleshoot apps and problems across windows and macintosh
- Make work on M1 and x86 macs
- Shrink the size of the releases (pyinstaller optimization)
- Make dynamic programming probe set selection
- Add more selection criteria (RBP, folding, etc)
- Rewrite how the program moves around probe sequences and scores (make a class)
- Upload cute logo
- Update to python 3.11