This project simplifies the process of building multiplexed-plasmids and packaging them up into a single annoated genbank file that can be easily used on benchling or another workbench. Although this task is commonly perfomred by hand in a browser or desktop application, performing senstive tasks like this with python allows us to be eaxct with our changes and to verify the changes.

The script accepts the following input parameters:

• --backbone-file: Required. The path to the GenBank file of the plasmid backbone to build from.
• --target-dir: Required. The path to the directory containing the list of target genes to replace.
• --replacement-dir: Required. The path to the directory containing the list of replacement genes to use.
• --crispr-file: Required. The path to the GenBank file containing the desired multiplexed-CRISPR variant.
• --output-file: Required. The path to the final plasmid.

To use the script, navigate to the directory containing the script and run the following command:

python3 main.py --backbone-file ./genes/backbone.gb --target-dir ./genes/targets/ --replacement-dir ./genes/replacements/ --crispr-file ./genes/crispr.gb --output-file plasmid_1.gb

This command assumes CRISPR is being used for a 1:1 replacment of a list of genes. To do this the code above will modify the plasmid GenBank file located at genes/backbone.gb and will add pair the replacements with targets based off of the alphabetical sort order of both directories.

Commands can be saved within a .sh file and re-run to re-build a specific plasmid when needed. A team should be able to build any number of therapies or tests out of the same directory. The code will take in fasta or genebank files.