Specimens
Generate snail specimens.
This module handles the generation of snail specimens with the following process: 1. Generate genomes with random mutations 2. Assign initial masses based on whether they have the significant mutation 3. Place specimens randomly on the grid (no two snails in the same cell) 4. Adjust masses based on whether their location is polluted or not
SpecimenParams
Bases: BaseModel
Parameters for specimen generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
end_date
|
date
|
End date for specimen collection |
required |
length
|
int
|
Length of specimen genomes (must be positive) |
required |
max_mass
|
float
|
Maximum mass for specimens (must be positive) |
required |
min_mass
|
float
|
Minimum mass for specimens (must be positive and less than max_mass) |
required |
mut_scale
|
float
|
Scale factor for mutation effect |
required |
mutations
|
int
|
Number of mutations in specimens (must be between 0 and length) |
required |
number
|
int
|
Number of specimens to generate (must be positive) |
required |
seed
|
int
|
Random seed for reproducibility |
required |
start_date
|
date
|
Start date for specimen collection |
required |
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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Specimen
Bases: BaseModel
A single specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ident
|
str
|
unique identifier |
required |
collected_on
|
date
|
date when specimen was collected |
required |
genome
|
str
|
bases in genome |
required |
mass
|
float
|
snail mass in grams |
required |
site
|
Point
|
grid location where specimen was collected |
required |
Source code in src/snailz/specimens.py
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AllSpecimens
Bases: BaseModel
A set of generated specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
individuals
|
list[Specimen]
|
list of individual specimens |
required |
loci
|
list[int]
|
locations where mutations can occur |
required |
params
|
SpecimenParams
|
parameters used to generate this data |
required |
reference
|
str
|
unmutated genome |
required |
susceptible_base
|
str
|
mutant base that induces mass changes |
required |
susceptible_locus
|
int
|
location of mass change mutation |
required |
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 with people data (without parameters) |
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.
The process follows these steps: 1. Generate genomes with random mutations 2. Assign initial masses based on whether they have the significant mutation 3. Place specimens randomly on the grid (no two snails in the same cell) 4. Adjust masses based on location 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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_adjust_masses_by_location(grid, specimens, mut_scale, specific_index=None)
Adjust mass based on grid values and genetic susceptibility.
For each specimen, if the cell value is non-zero and the genome is susceptible, modify the mass. Specimens must already have site coordinates assigned by _place_specimens_on_grid().
Parameters:
Name | Type | Description | Default |
---|---|---|---|
grid
|
Grid
|
A Grid object containing pollution values |
required |
specimens
|
AllSpecimens
|
An AllSpecimens object with individuals to potentially adjust |
required |
mut_scale
|
float
|
Scaling factor for mutation effect |
required |
specific_index
|
int | None
|
Optional index to adjust only a specific specimen |
None
|
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_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_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_initial_masses(params, genomes, susceptible_locus, susceptible_base)
Generate initial masses for specimens based on significant mutation.
Specimens with the susceptible base at the susceptible locus are given a higher initial mass range compared to non-susceptible 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 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_locations(size, num)
Generate non-overlapping locations for specimens.
Selects random locations from the grid, ensuring no two specimens are placed in the same cell. This implements the requirement that no two snails may be placed in the same cell.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
size
|
int
|
Size of the grid (assuming square grid) |
required |
num
|
int
|
Number of locations to generate |
required |
Returns:
Type | Description |
---|---|
list[tuple[int, int]]
|
List of (x, y) coordinate tuples |
Raises:
Type | Description |
---|---|
ValueError
|
If there are not enough cells to place all specimens |
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_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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_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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_place_specimens_on_grid(grid, specimens)
Place specimens randomly on the grid, ensuring no two share the same cell.
Updates the site coordinates for each specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
grid
|
Grid
|
A Grid object containing pollution values |
required |
specimens
|
AllSpecimens
|
An AllSpecimens object with individuals to place on the grid |
required |
Source code in src/snailz/specimens.py
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