COD_FISH

This repository contains the code for running COD_FISH, the smFISH probe designer.

Running the package

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.

Running with python

To run it using python, this repository can be downloaded using

git clone https://github.com/ryandikdan/COD_FISH

Then we recommend making a virtual environment so that required dependencies don't conflict

python -m venv .venv

Activate the virtual environment (varies per OS)

# Windows Powershell
.\.venv\Scripts\Activate.ps1
# Windows Command Prompt
.venv\Scripts\activate.bat
# Mac or linux
source ./venv/bin/activate

You should see an indicator that you're using this environment. Then install the dependencies in this virtual environment by running

pip install -r requirements.txt

After this, you should be able to run the GUI via

python gui_COD_FISH.py

To run via the command line you can use

python COD_FISH.py

To leave the virtual environment you can simply run

deactivate

Next steps

• 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