https://github.com/therook/multiplexedplasmidbuilder
To combine and modify genbank files to construct multiplexed CRISPR plasmids.
https://github.com/therook/multiplexedplasmidbuilder
biohacking biology biopython crispr python
Last synced: 3 months ago
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To combine and modify genbank files to construct multiplexed CRISPR plasmids.
- Host: GitHub
- URL: https://github.com/therook/multiplexedplasmidbuilder
- Owner: TheRook
- License: gpl-2.0
- Created: 2023-02-20T20:40:18.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-02-20T21:27:26.000Z (over 2 years ago)
- Last Synced: 2025-01-09T04:46:18.057Z (5 months ago)
- Topics: biohacking, biology, biopython, crispr, python
- Language: Python
- Homepage:
- Size: 18.6 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## Construct a Multiplexed Plasmid
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.
### CLI Input
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.
### Example Usage
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.
### Reproduceablity / Flexablity
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.