Automated plasmid design from speadsheet specification
Project description
Installation
pip install plasmid_design
Example
In a new directory, save the following to config.yaml
, then run plasmid_design run
. The configuration below refers to this spreadsheet.
tables:
# vector definitions
templates:
table: drive_key:templates
# selects just these rows
gate: experiment == "example"
drive_key: 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM
# DNA and protein part definitions
parts:
table: drive_key:parts
drive_key: 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM
# these DNA features will automatically be annotated
features:
table: drive_key:features
drive_key: 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM
# these restriction sites will be avoided
restriction_enzymes:
table: drive_key:enzymes
# selects just these rows
gate: pT02_BsaI == "x"
drive_key: 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM
The run
command prints estimated cost and complexity scores. the following files will be generated.
Configuration
Tables can be sourced in different ways.
- local csv
table: /path/to/csv
- private google sheets
table: "drive:{spreadsheet name}/{sheet name}"
- public google sheets
table: "drive_key:{sheet_name}"
drive_key: {drive_key}
For the public option, first enable link access in google sheets, then copy drive_key
from the URL: https://docs.google.com/spreadsheets/d/{drive_key}/
.
Changing the vector backbone
The DNA sequences upstream and downstream of the designed gene are identified by having "up" or "down" in the part name. To change the vector backbone, define new upstream and downstream DNA parts, then change the template column in the templates sheet accordingly.
Project details
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