Including other REs for Radinitio

[Alex S]

Hello, I'm working on an in silico digest of a specific organism, and I'm using Radinitio because we are planning on utilizing RADseq after. 

Would it be possible to include other restriction enzymes in the options? Or at least have a way to input my own. 

[Angel Rivera-Colón]

Hi Alex,

Thanks for checking out RADinitio.

Which restriction enzyme are you interested in using? Also, adding new enzymes is possible in the Python API. You can see general examples of the API in the manual (https://catchenlab.life.illinois.edu/radinitio/manual/#python). To add a new enzyme you can include the following before specifying your library parameters (step #4 in the example):

import radinitio as ri

# New enzyme info

new_enz_name = 'SalI'

new_enz_cut = 'G/TCGAC'  # The '/' specifies the cut position and overhangs

# Add the new enzyme

ri.known_enzymes[new_enz_name.lower()] = (new_enz_name, new_enz_cut)

# Rebuild the name list and lookup set
ri.known_enz_names = [ri.known_enzymes[e][0] for e in sorted(ri.known_enzymes)]
ri.known_enz_set   = set(e.lower() for e in ri.known_enz_names)

# Use it in the library

lib_opts = ri.LibraryOptions(library_type='sdRAD', renz_1='SalI', ...)

Let me know if this works. Also, let me know the enzyme info. I can try to add it and make a quick release.

Thanks,

Angel