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# Specimens

Generate snail specimens.

## `Point` `dataclass`

A 2D point with x and y coordinates.

Source code in `src/snailz/specimens.py`

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    @dataclass
    class Point:
        """A 2D point with x and y coordinates."""

        x: int | None = None
        y: int | None = None

## `Individual` `dataclass`

A single specimen with genome, mass, site location and unique identifier.

Source code in `src/snailz/specimens.py`

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    @dataclass
    class Individual:
        """A single specimen with genome, mass, site location and unique identifier."""

        genome: str
        ident: str
        mass: float
        site: Point

## `Specimens` `dataclass`

Keep track of generated specimens.

Source code in `src/snailz/specimens.py`

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    @dataclass
    class Specimens:
        """Keep track of generated specimens."""

        individuals: list[Individual]
        loci: list[int]
        params: dict[str, object]
        reference: str
        susceptible_base: str
        susceptible_locus: int

## `specimens_check(params)`

Check specimen generation parameters.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `dict[str, object]` | Dictionary containing specimen generation parameters | required

Raises:

Type | Description
--- | ---
`ValueError` | If parameters are missing, have wrong types, or have invalid values

Source code in `src/snailz/specimens.py`

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    def specimens_check(params: dict[str, object]) -> None:
        """Check specimen generation parameters.

        Parameters:
            params: Dictionary containing specimen generation parameters

        Raises:
            ValueError: If parameters are missing, have wrong types, or have invalid values
        """
        utils.check_keys_and_types(SPECIMENS_PARAMS, params)

        for name in ["length", "min_mass", "mutations", "number"]:
            utils.require(0 < params[name], f"{name} must be positive")
        utils.require(
            0 <= params["mutations"] <= params["length"],
            "mutations must be between 0 and length",
        )
        utils.require(
            params["min_mass"] < params["max_mass"],
            "max_mass must be greater than min_mass",
        )

## `specimens_generate(params)`

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.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `dict[str, object]` | Dictionary containing specimen generation parameters | required

Returns:

Type | Description
--- | ---
`Specimens` | Specimens object containing the generated specimens and parameters

Source code in `src/snailz/specimens.py`

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    def specimens_generate(params: dict[str, object]) -> Specimens:
        """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.

        Parameters:
            params: Dictionary containing specimen generation parameters

        Returns:
            Specimens object containing the generated specimens and parameters
        """
        specimens_check(params)
        loci = _make_loci(params)
        reference = _make_reference_genome(params)
        susc_loc = _choose_one(loci)
        susc_base = reference[susc_loc]
        genomes = [_make_genome(reference, loci) for i in range(params["number"])]
        masses = _make_masses(params, genomes, susc_loc, susc_base)

        # Generate unique identifiers
        identifiers = _make_idents(params["number"])

        individuals = [
            Individual(genome=g, mass=m, site=Point(), ident=i)
            for g, m, i in zip(genomes, masses, identifiers)
        ]

        return Specimens(
            individuals=individuals,
            loci=loci,
            params=params,
            reference=reference,
            susceptible_base=susc_base,
            susceptible_locus=susc_loc,
        )

## `specimens_to_csv(specimens, filename)`

Write specimens data as CSV.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`specimens` | `Specimens` | A Specimens object containing specimen data | required
`filename` | `str | None` | Path to output file, or None to write to standard output | required

Side effects

Either writes to the specified output file or prints to stdout

Source code in `src/snailz/specimens.py`

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    def specimens_to_csv(specimens: Specimens, filename: str | None) -> None:
        """Write specimens data as CSV.

        Parameters:
            specimens: A Specimens object containing specimen data
            filename: Path to output file, or None to write to standard output

        Side effects:
            Either writes to the specified output file or prints to stdout
        """
        stream = sys.stdout if filename is None else open(filename, "w", newline="")
        writer = csv.writer(stream)
        writer.writerow(["ident", "x", "y", "genome", "mass"])
        for indiv in specimens.individuals:
            writer.writerow(
                [indiv.ident, indiv.site.x, indiv.site.y, indiv.genome, indiv.mass]
            )
        if stream is not sys.stdout:
            stream.close()

## `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.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`grid` | `Grid` | A Grid object containing pollution values | required
`specimens` | `Specimens` | A Specimens 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`

Side effects

Modifies specimen masses in-place for susceptible individuals Updates site coordinates for all individuals

Source code in `src/snailz/specimens.py`

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    def mutate_masses(
        grid: Grid,
        specimens: Specimens,
        mut_scale: float,
        specific_index: int | None = None,
    ) -> 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.

        Parameters:
            grid: A Grid object containing pollution values
            specimens: A Specimens object with individuals to potentially mutate
            mut_scale: Scaling factor for mutation effect
            specific_index: Optional index to mutate only a specific specimen

        Side effects:
            Modifies specimen masses in-place for susceptible individuals
            Updates site coordinates for all individuals
        """
        grid_size = len(grid.grid)
        susc_locus = specimens.susceptible_locus
        susc_base = specimens.susceptible_base

        if specific_index is not None:
            indices = [specific_index]
        else:
            indices = range(len(specimens.individuals))

        for i in indices:
            individual = specimens.individuals[i]
            x = random.randrange(grid_size)
            y = random.randrange(grid_size)

            individual.site.x = x
            individual.site.y = y

            if grid.grid[x][y] > 0 and individual.genome[susc_locus] == susc_base:
                individual.mass = mutate_mass(individual.mass, mut_scale, grid.grid[x][y])

## `mutate_mass(original, mut_scale, cell_value)`

Mutate a single 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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    def mutate_mass(original: float, mut_scale: float, cell_value: int) -> float:
        """Mutate a single mass.

        Parameters:
            original: The original mass value
            mut_scale: Scaling factor for mutation effect
            cell_value: The grid cell value affecting the mutation

        Returns:
            The mutated mass value, rounded to PRECISION decimal places
        """
        return round(original * (1 + (mut_scale * cell_value)), utils.PRECISION)

## `_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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    def _choose_one(values: list[int]) -> int:
        """Choose a single random item from a collection.

        Parameters:
            values: A sequence to choose from

        Returns:
            A randomly selected item from the values sequence
        """
        return random.choices(values, k=1)[0]

## `_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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    def _choose_other(values: str, exclude: str) -> str:
        """Choose a value at random except for the excluded values.

        Parameters:
            values: A collection to choose from
            exclude: Value or collection of values to exclude from the choice

        Returns:
            A randomly selected item from values that isn't in exclude
        """
        candidates = list(sorted(set(values) - set(exclude)))
        return candidates[random.randrange(len(candidates))]

## `_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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    def _make_genome(reference: str, loci: list[int]) -> str:
        """Make an individual genome by mutating the reference genome.

        Parameters:
            reference: Reference genome string to base the new genome on
            loci: List of positions that can be mutated

        Returns:
            A new genome string with random mutations at some loci
        """
        result = list(reference)
        num_mutations = random.randint(1, len(loci))
        for loc in random.sample(range(len(loci)), num_mutations):
            result[loc] = _choose_other(BASES, reference[loc])
        return "".join(result)

## `_make_idents(count)`

Create unique specimen identifiers.

Each identifier is a 6-character string where: - First two chars are the same uppercase letters for all specimens - Remaining four chars are random uppercase letters and digits, unique for each specimen

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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    def _make_idents(count: int) -> list[str]:
        """Create unique specimen identifiers.

        Each identifier is a 6-character string where:
        - First two chars are the same uppercase letters for all specimens
        - Remaining four chars are random uppercase letters and digits, unique for each specimen

        Parameters:
            count: Number of identifiers to generate

        Returns:
            List of unique specimen identifiers
        """
        prefix = "".join(random.choices(string.ascii_uppercase, k=2))
        chars = string.ascii_uppercase + string.digits
        gen = utils.UniqueIdGenerator(
            "specimens", lambda: f"{prefix}{''.join(random.choices(chars, k=4))}"
        )
        return [gen.next() for _ in range(count)]

## `_make_loci(params)`

Make a list of mutable loci positions.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `dict[str, object]` | Dictionary with 'length' (genome length) and 'mutations' (number of mutable positions) | required

Returns:

Type | Description
--- | ---
`list[int]` | A list of randomly selected positions that can be mutated

Source code in `src/snailz/specimens.py`

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    def _make_loci(params: dict[str, object]) -> list[int]:
        """Make a list of mutable loci positions.

        Parameters:
            params: Dictionary with 'length' (genome length) and 'mutations' (number of mutable positions)

        Returns:
            A list of randomly selected positions that can be mutated
        """
        return random.sample(list(range(params["length"])), params["mutations"])

## `_make_masses(params, genomes, susceptible_locus, susceptible_base)`

Generate random masses for specimens.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `dict[str, object]` | Dictionary with 'min_mass' and 'max_mass' parameters | 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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    def _make_masses(
        params: dict[str, object],
        genomes: list[str],
        susceptible_locus: int,
        susceptible_base: str,
    ) -> list[float]:
        """Generate random masses for specimens.

        Parameters:
            params: Dictionary with 'min_mass' and 'max_mass' parameters
            genomes: List of genome strings
            susceptible_locus: Position that determines susceptibility
            susceptible_base: Base that makes a specimen susceptible

        Returns:
            List of randomly generated mass values between min_mass and max_mass,
            rounded to PRECISION decimal places
        """
        min_mass = params["min_mass"]
        max_mass = params["max_mass"]
        return [round(random.uniform(min_mass, max_mass), utils.PRECISION) for _ in genomes]

## `_make_reference_genome(params)`

Make a random reference genome.

Parameters:

Name | Type | Description | Default
--- | --- | --- | ---
`params` | `dict[str, object]` | Dictionary with 'length' parameter for the genome length | 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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    def _make_reference_genome(params: dict[str, object]) -> str:
        """Make a random reference genome.

        Parameters:
            params: Dictionary with 'length' parameter for the genome length

        Returns:
            A randomly generated genome string of the specified length
        """
        return "".join(random.choices(BASES, k=params["length"]))