| Name | plasmid-design JSON |
| Version |
0.0.4
JSON |
| download |
| home_page | |
| Summary | Automated plasmid design from speadsheet specification |
| upload_time | 2023-07-17 06:47:40 |
| maintainer | |
| docs_url | None |
| author | David Feldman |
| requires_python | >=3.7 |
| 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. |
| keywords |
plasmid
vector
design
dna
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## Installation
```bash
pip install plasmid_design
```
## Example
In a new directory, save the following to `config.yaml`, then run `plasmid_design run`. The `drive_key` below refers to [this spreadsheet](https://docs.google.com/spreadsheets/d/1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM/edit#gid=52604569).
```yaml
drive_key: &drive_key 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM
tables:
# vector definitions
templates:
table: drive_key:templates
# selects just these rows
gate: experiment == "example"
drive_key: *drive_key
# DNA and protein part definitions
parts:
table: drive_key:parts
drive_key: *drive_key
# these DNA features will automatically be annotated
features:
table: drive_key:features
drive_key: *drive_key
# these restriction sites will be avoided
restriction_enzymes:
table: drive_key:enzymes
# selects just these rows
gate: pT02_BsaI == "x"
drive_key: *drive_key
```
The `run` command prints estimated cost and complexity scores. The following files will be generated:
```bash
gene_order.fa # genes, ready to order
gene_order_idt_scores.csv # IDT gene synthesis complexity scores (different from gblock complexity)
parts.csv # snapshot of input table
templates.csv # snapshot of input table
features.csv # snapshot of input table
reverse_translations/restriction_enzymes.csv # snapshot of input table
reverse_translations/input.fa # amino acid parts that need reverse translation
reverse_translations/output.fa # corresponding DNA, generated by DNA Chisel
reverse_translations/idt_scores.csv # per-part IDT gene synthesis complexity scores, not meaningful for short parts
reverse_translations/dna_chisel/ # DNA Chisel logs
```
## 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 in the plasmid map 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.
Raw data
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"description": "## Installation\n```bash\npip install plasmid_design\n```\n\n## Example\nIn a new directory, save the following to `config.yaml`, then run `plasmid_design run`. The `drive_key` below refers to [this spreadsheet](https://docs.google.com/spreadsheets/d/1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM/edit#gid=52604569).\n\n```yaml\ndrive_key: &drive_key 1QWFQUlIJYERJ6zY-THD9uNagD2a_He7RUfcOeF2eEKM\ntables:\n # vector definitions\n templates: \n table: drive_key:templates\n # selects just these rows\n gate: experiment == \"example\"\n drive_key: *drive_key\n\n # DNA and protein part definitions\n parts: \n table: drive_key:parts\n drive_key: *drive_key\n \n # these DNA features will automatically be annotated\n features: \n table: drive_key:features\n drive_key: *drive_key\n \n # these restriction sites will be avoided\n restriction_enzymes: \n table: drive_key:enzymes\n # selects just these rows\n gate: pT02_BsaI == \"x\"\n drive_key: *drive_key\n```\n\nThe `run` command prints estimated cost and complexity scores. The following files will be generated:\n\n```bash\ngene_order.fa # genes, ready to order\ngene_order_idt_scores.csv # IDT gene synthesis complexity scores (different from gblock complexity)\nparts.csv # snapshot of input table\ntemplates.csv # snapshot of input table\nfeatures.csv # snapshot of input table\nreverse_translations/restriction_enzymes.csv # snapshot of input table\nreverse_translations/input.fa # amino acid parts that need reverse translation\nreverse_translations/output.fa # corresponding DNA, generated by DNA Chisel\nreverse_translations/idt_scores.csv # per-part IDT gene synthesis complexity scores, not meaningful for short parts\nreverse_translations/dna_chisel/ # DNA Chisel logs\n```\n\n## Configuration\nTables can be sourced in different ways.\n- local csv\n - `table: /path/to/csv`\n- private google sheets\n - `table: \"drive:{spreadsheet name}/{sheet name}\"`\n- public google sheets\n - `table: \"drive_key:{sheet_name}\"`\n - `drive_key: {drive_key}`\n\nFor 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}/`.\n\n## Changing the vector backbone\nThe DNA sequences upstream and downstream of the designed gene in the plasmid map 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.\n\n",
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