Setup (You only have to do this once!)

If you don’t have python installed, or if you aren’t sure, visit our setup guide to install things. You’ll only have to do this once!

Running a python script on your local machine

Once you have python installed:

1. Find a result table that interests you, and download the generated code.
   • Let’s try the results for the HumanMine Pax6 Targets list
2. Click on the Generate Python Code button at the top right of your results table.
3. Save the file on your computer (and pay attention to where you’ve saved it, so you can go there in the next step). I’ve saved mine to the location ~/Downloads/query.py
4. Now it’s time to run the script! Open up a terminal. In Linux, this is often accomplished by pressing CTRL+ALT+T, or on a Mac press CMD+Space and type “terminal”, then press enter.
5. Navigate to the directory where your downloaded script is located. If you saved it to your downloads folder, the command might be cd ~/Downloads/.
   • cd stands for change directory - we’re telling the computer to change directory into the downloads folder.
6. Okay, nearly there! Two things left to do: we need to make the script executable, and then we can run it!
7. Making it executable: type chmod +x query.py.
   • Breakdown: chmod is the unix command to change file permissions, +x means “please make this file executable”, and query.py is the name of the generated code script we downloaded. If you changed the file name when you downloaded it, make sure to substitute the correct name in the command!
   • You can try the next step without making the script executable to see what happens if you like. It’ll probably give you an error.
8. Right, time to run the script: type ./query.py. You should see the results of your query printed to the screen! If it looks a little odd, make the terminal wider and run it again the same way.
   • ./some-file-name-here - the ./ means “execute this script, please”.

Local python scripts - some tips

• Better reproducibility & tweakability - The nice bit about running analyses like this is they’re easy to tweak or reproduce in the future. Want the same query, but for a different organism or different gene? Open the downloaded script in a text editor and change that gene name, then save and re-run the results. Ta-da!
• Saving results to a text file If you want to save your results to a text file, add > results.txt to the end of the command. It’ll now look something like this: ./query.py > results.txt. You won’t see the results in the terminal this time, but your query results should now be in the downloads folder, inside the file named results.txt!
  • Breakdown: > means “please output results to”, and results.txt could be any file name you like - you’re just asking your script to save results to a file with the name you specified.