plasmid-design 0.0.1

Automated plasmid design from speadsheet specification

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

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}/.