snailz 0.2.0

Synthetic data generator for snail mutation survey

Snailz

These synthetic data generators model genomic analysis of snails in the Pacific Northwest that are growing to unusual size as a result of exposure to pollution.

• A grid is created to record the pollution levels at a sampling site.
• One or more specimens are collected from the grid. Each specimen has a genome and a mass.
• Laboratory staff design and perform assays of those genomes.
• Each assay is represented by a design file and an assay file.
• Assay files are mangled to create raw files with formatting glitches.

Usage

1. Create a fresh Python environment: uv venv
2. Activate that environment: source .venv/bin/activate
3. Install dependencies and editable version of package: uv pip install -e '.[dev]'
4. View available commands: doit list or snailz --help
5. Regenerate all data in ./tmp using parameters in ./params: doit all

Parameters

./params contains the parameter files used to control generation of the reference dataset.

• grid.json
  • depth: integer range of random values in cells
  • seed: RNG seed
  • size: width and height of (square) grid in cells
• people.json
  • locale: language and region to use for name generation
  • number: number of staff to create
  • seed: RNG seed
• specimens.json
  • length: genome length in characters
  • max_mass: maximum specimen mass
  • min_mass: minimum specimen mass
  • mut_scale: scaling factor for mutated specimens
  • mutations: number of mutations to introduce
  • number: number of specimens to create
  • seed: RNG seed
• assays.json
  • baseline: assay response for unmutated specimens
  • end_date: date of final assay
  • mutant: assay response for mutated specimens
  • noise: noise to add to control cells
  • plate_size: width and height of assay plate
  • seed: RNG seed
  • start_date: date of first assay

Note: there are no parameters for assay file mangling.

Data Dictionary

doit all creates these files in tmp using the sample parameters in params:

• assays/
  • NNNNNN_assay.csv: tidy, consistently-formatted CSV file with assay result.
  • NNNNNN_design.csv: tidy, consistently-formatted CSV file with assay design.
  • NNNNNN_raw.csv: CSV file derived from NNNNNN_assay.csv with randomly-introduced formatting errors.
• assays.csv: CSV file containing summary of assay metadata with columns.
  • ident: assay identifier (integer).
  • specimen_id: specimen identifier (text).
  • performed: assay date (date).
  • performed_by: person identifier (text).
• assays.json: all assay data in JSON format.
• grid.csv: CSV file containing pollution grid values.
  • This file is a matrix of values with no column IDs or row IDs.
• grid.json: grid data as JSON.
• people.csv: CSV file describing experimental staff members.
  • ident: person identifier (text)
  • personal: personal name (text)
  • family: family name (text)
• people.json: staff member data in JSON format.
• specimens.csv: CSV file containing details of snail specimens.
  • ident: specimen identifier (text)
  • x: X coordinate of collection cell (integer)
  • y: Y coordinate of collection cell (integer)
  • genome: base sequence (text)
  • mass: snail mass (real)
• specimens.json: specimen data in JSON format.