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clauswilke / pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates
http://pinetree.readthedocs.io
MIT License
11 stars 5 forks source link

Support for multiple genomes #17

Open jeffreybarrick opened 3 years ago

jeffreybarrick commented 3 years ago

We would like to do some simulations with a separate plasmid and/or genome in a cell that is being infected by the phage. Is this possible already? (Can you call register_genome() twice and it will include both?)

If not, it seems like it could be faked by appending the sequences and making sure that there is a perfect terminator between them, but it would be easier for us to set up if they were separate.

It might also be helpful to have a copy_number parameter for each genome (=DNA molecule) that would scale all of the promoter rates on that piece of DNA, in case that was a parameter that we wanted to adjust for a plasmid.

jeffreybarrick commented 3 years ago

Did some tests with adding multiple of the same phage genome. This appears to work! – so maybe there is nothing here to do. If this is true, it would be great if someone could add a note to the documentation saying this is possible.