Specimens
Generate snail specimens.
SpecimenParams
Bases: BaseModel
Parameters for specimen generation.
- end_date: End date for specimen collection
- length: Length of specimen genomes (must be positive)
- max_mass: Maximum mass for specimens (must be positive)
- min_mass: Minimum mass for specimens (must be positive and less than max_mass)
- mut_scale: Scale factor for mutation effect
- mutations: Number of mutations in specimens (must be between 0 and length)
- number: Number of specimens to generate (must be positive)
- seed: Random seed for reproducibility
- start_date: Start date for specimen collection
- end_date: End date for specimen collection
Source code in src/snailz/specimens.py
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validate_fields()
Validate requirements on fields.
Source code in src/snailz/specimens.py
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Point
Bases: BaseModel
A 2D point with x and y coordinates.
- x: X coordinate in grid
- y: Y coordinate in grid
Source code in src/snailz/specimens.py
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Specimen
Bases: BaseModel
A single specimen with unique identifier, genome, mass, site location, and collection date.
- ident: unique identifier
- collected_on: date when specimen was collected
- genome: bases in genome
- mass: snail mass in grams
- site: grid location where specimen was collected
- territory: share of the grid that belongs to this specimen
Source code in src/snailz/specimens.py
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AllSpecimens
Bases: BaseModel
A set of generated specimens.
- individuals: list of individual specimens
- loci: locations where mutations can occur
- params: parameters used to generate this data
- reference: unmutated genome
- susceptible_base: mutant base that induces mass changes
- susceptible_locus: location of mass change mutation
Source code in src/snailz/specimens.py
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to_csv()
Return a CSV string representation of the specimens data.
Returns:
Type | Description |
---|---|
str
|
A CSV-formatted string containing specimen data with fields: |
str
|
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str
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str
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str
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str
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str
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str
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Source code in src/snailz/specimens.py
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specimens_generate(params, grid=None)
Generate specimens with random genomes and masses.
Each genome is a string of bases of the same length. One locus is randomly chosen as "significant", and a specific mutation there predisposes the snail to mass changes. Other mutations are added randomly at other loci. Specimen masses are only mutated if a grid is provided.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
SpecimenParams object |
required |
grid
|
Grid | None
|
Grid object to place specimens on for mass mutation |
None
|
Returns:
Type | Description |
---|---|
AllSpecimens
|
AllSpecimens object containing the generated specimens and parameters |
Source code in src/snailz/specimens.py
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calculate_ranges(size, specimens)
Calculate the territory of each specimen.
Source code in src/snailz/specimens.py
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mutate_masses(grid, specimens, mut_scale, specific_index=None)
Mutate mass based on grid values and genetic susceptibility.
For each specimen, choose a random cell from the grid and modify the mass if the cell's value is non-zero and the genome is susceptible. Records the chosen site coordinates for each specimen regardless of whether mutation occurs. Modifies specimen masses in-place for susceptible individuals; updates site coordinates for all individuals.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
grid
|
Grid
|
A Grid object containing pollution values |
required |
specimens
|
AllSpecimens
|
A AllSpecimens object with individuals to potentially mutate |
required |
mut_scale
|
float
|
Scaling factor for mutation effect |
required |
specific_index
|
int | None
|
Optional index to mutate only a specific specimen |
None
|
Source code in src/snailz/specimens.py
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mutate_mass(original, mut_scale, cell_value)
Mutate a single specimen's mass.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
original
|
float
|
The original mass value |
required |
mut_scale
|
float
|
Scaling factor for mutation effect |
required |
cell_value
|
int
|
The grid cell value affecting the mutation |
required |
Returns:
Type | Description |
---|---|
float
|
The mutated mass value, rounded to PRECISION decimal places |
Source code in src/snailz/specimens.py
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_choose_one(values)
Choose a single random item from a collection.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
values
|
list[int]
|
A sequence to choose from |
required |
Returns:
Type | Description |
---|---|
int
|
A randomly selected item from the values sequence |
Source code in src/snailz/specimens.py
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_choose_other(values, exclude)
Choose a value at random except for the excluded values.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
values
|
str
|
A collection to choose from |
required |
exclude
|
str
|
Value or collection of values to exclude from the choice |
required |
Returns:
Type | Description |
---|---|
str
|
A randomly selected item from values that isn't in exclude |
Source code in src/snailz/specimens.py
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_make_genome(reference, loci)
Make an individual genome by mutating the reference genome.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
reference
|
str
|
Reference genome string to base the new genome on |
required |
loci
|
list[int]
|
List of positions that can be mutated |
required |
Returns:
Type | Description |
---|---|
str
|
A new genome string with random mutations at some loci |
Source code in src/snailz/specimens.py
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_make_idents(count)
Create unique specimen identifiers.
Each identifier is a 6-character string: - First two characters are the same uppercase letters for all specimens - Remaining four chararacters are random uppercase letters and digits
Parameters:
Name | Type | Description | Default |
---|---|---|---|
count
|
int
|
Number of identifiers to generate |
required |
Returns:
Type | Description |
---|---|
list[str]
|
List of unique specimen identifiers |
Source code in src/snailz/specimens.py
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_make_locations(size, num)
Generate non-adjacent locations for specimens or fail.
Source code in src/snailz/specimens.py
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_make_loci(params)
Make a list of mutable loci positions.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
SpecimenParams with length and mutations attributes |
required |
Returns:
Type | Description |
---|---|
list[int]
|
A list of unique randomly selected positions that can be mutated |
Source code in src/snailz/specimens.py
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_make_masses(params, genomes, susceptible_locus, susceptible_base)
Generate random masses for specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
SpecimenParams with min_mass and max_mass attributes |
required |
genomes
|
list[str]
|
List of genome strings |
required |
susceptible_locus
|
int
|
Position that determines susceptibility |
required |
susceptible_base
|
str
|
Base that makes a specimen susceptible |
required |
Returns:
Type | Description |
---|---|
list[float]
|
List of randomly generated mass values between min_mass and max_mass, |
list[float]
|
rounded to PRECISION decimal places |
Source code in src/snailz/specimens.py
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_make_collection_dates(params)
Generate random collection dates for specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
SpecimenParams with start_date, end_date, and number attributes |
required |
Returns:
Type | Description |
---|---|
list[date]
|
List of randomly generated collection dates between start_date and end_date |
Source code in src/snailz/specimens.py
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_make_reference_genome(params)
Make a random reference genome.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
SpecimenParams with length attribute |
required |
Returns:
Type | Description |
---|---|
str
|
A randomly generated genome string of the specified length |
Source code in src/snailz/specimens.py
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