Metadata-Version: 2.1
Name: plasmid-design
Version: 0.0.1
Summary: Automated plasmid design from speadsheet specification
Author: David Feldman
License: Copyright (c) 2022 David Feldman
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
Project-URL: Homepage, https://github.com/feldman4/plasmid-design
Project-URL: Bug Tracker, https://github.com/feldman4/plasmid-design/issues
Keywords: plasmid,vector,design,DNA
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE.txt

## 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](https://docs.google.com/spreadsheets/d/1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM/edit#gid=52604569).

```yaml
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}/`.

