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# 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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    class SpecimenParams(BaseModel):
        """Parameters for specimen generation."""

        end_date: date = Field(description="End date for specimen collection")
        length: int = Field(
            gt=0, description="Length of specimen genomes (must be positive)"
        )
        max_mass: float = Field(
            gt=0, description="Maximum mass for specimens (must be positive)"
        )
        min_mass: float = Field(
            gt=0,
            description="Minimum mass for specimens (must be positive and less than max_mass)",
        )
        mut_scale: float = Field(ge=0, description="Scale factor for mutation effect")
        mutations: int = Field(
            ge=0,
            description="Number of mutations in specimens (must be between 0 and length)",
        )
        number: int = Field(
            gt=0, description="Number of specimens to generate (must be positive)"
        )
        seed: int = Field(ge=0, description="Random seed for reproducibility")
        start_date: date = Field(description="Start date for specimen collection")

        model_config = {"extra": "forbid"}

        @model_validator(mode="after")
        def validate_fields(self):
            """Validate requirements on fields."""
            if self.min_mass >= self.max_mass:
                raise ValueError("max_mass must be greater than min_mass")
            if self.mutations > self.length:
                raise ValueError("mutations must be between 0 and length")
            if self.end_date < self.start_date:
                raise ValueError("end_date must be greater than or equal to start_date")
            return self

### `validate_fields()`

Validate requirements on fields.

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

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    @model_validator(mode="after")
    def validate_fields(self):
        """Validate requirements on fields."""
        if self.min_mass >= self.max_mass:
            raise ValueError("max_mass must be greater than min_mass")
        if self.mutations > self.length:
            raise ValueError("mutations must be between 0 and length")
        if self.end_date < self.start_date:
            raise ValueError("end_date must be greater than or equal to start_date")
        return self

## `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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    class Specimen(BaseModel):
        """A single specimen."""

        ident: str = Field(description="unique identifier")
        collected_on: date = Field(description="date when specimen was collected")
        genome: str = Field(description="bases in genome")
        mass: float = Field(gt=0, description="snail mass in grams")
        site: Point = Field(description="grid location where specimen was collected")

## `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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    class AllSpecimens(BaseModel):
        """A set of generated specimens."""

        individuals: list[Specimen] = Field(description="list of individual specimens")
        loci: list[int] = Field(description="locations where mutations can occur")
        params: SpecimenParams = Field(description="parameters used to generate this data")
        reference: str = Field(description="unmutated genome")
        susceptible_base: str = Field(description="mutant base that induces mass changes")
        susceptible_locus: int = Field(ge=0, description="location of mass change mutation")

        def to_csv(self) -> str:
            """Return a CSV string representation of the specimens data.

            Returns:
                A CSV-formatted string with people data (without parameters)
            """

            output = io.StringIO()
            writer = utils.csv_writer(output)
            writer.writerow(
                ["ident", "x", "y", "genome", "mass", "collected_on"]
            )
            for indiv in self.individuals:
                writer.writerow(
                    [
                        indiv.ident,
                        indiv.site.x,
                        indiv.site.y,
                        indiv.genome,
                        indiv.mass,
                        indiv.collected_on,
                    ]
                )
            return output.getvalue()

### `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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    def to_csv(self) -> str:
        """Return a CSV string representation of the specimens data.

        Returns:
            A CSV-formatted string with people data (without parameters)
        """

        output = io.StringIO()
        writer = utils.csv_writer(output)
        writer.writerow(
            ["ident", "x", "y", "genome", "mass", "collected_on"]
        )
        for indiv in self.individuals:
            writer.writerow(
                [
                    indiv.ident,
                    indiv.site.x,
                    indiv.site.y,
                    indiv.genome,
                    indiv.mass,
                    indiv.collected_on,
                ]
            )
        return output.getvalue()

## `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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    def specimens_generate(
        params: SpecimenParams, grid: Grid | None = None
    ) -> AllSpecimens:
        """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:
            params: SpecimenParams object
            grid: Grid object to place specimens on for mass mutation

        Returns:
            AllSpecimens object containing the generated specimens and parameters

        """
        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)]
        identifiers = _make_idents(params.number)
        collection_dates = _make_collection_dates(params)
        masses = _make_initial_masses(params, genomes, susc_loc, susc_base)

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

        result = AllSpecimens(
            individuals=individuals,
            loci=loci,
            params=params,
            reference=reference,
            susceptible_base=susc_base,
            susceptible_locus=susc_loc,
        )

        if grid is not None:
            _place_specimens_on_grid(grid, result)
            _adjust_masses_by_location(grid, result, params.mut_scale)

        return result

## `_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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    def _adjust_masses_by_location(
        grid: Grid,
        specimens: AllSpecimens,
        mut_scale: float,
        specific_index: int | None = None,
    ) -> 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:
            grid: A Grid object containing pollution values
            specimens: An AllSpecimens object with individuals to potentially adjust
            mut_scale: Scaling factor for mutation effect
            specific_index: Optional index to adjust only a specific specimen
        """
        susc_locus = specimens.susceptible_locus
        susc_base = specimens.susceptible_base

        if specific_index is None:
            individuals = specimens.individuals
        else:
            individuals = [specimens.individuals[specific_index]]

        for indiv in individuals:
            assert indiv.site.x is not None and indiv.site.y is not None, "Specimens must be placed on grid first"
            x, y = indiv.site.x, indiv.site.y
            if grid.grid[x][y] > 0 and indiv.genome[susc_locus] == susc_base:
                indiv.mass = _mutate_mass(indiv.mass, mut_scale, grid.grid[x][y])

## `_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_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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    def _make_collection_dates(params: SpecimenParams) -> list[date]:
        """Generate random collection dates for specimens.

        Parameters:
            params: SpecimenParams with start_date, end_date, and number attributes

        Returns:
            List of randomly generated collection dates between start_date and end_date
        """
        start_ordinal = params.start_date.toordinal()
        end_ordinal = params.end_date.toordinal()
        return [
            date.fromordinal(random.randint(start_ordinal, end_ordinal))
            for _ in range(params.number)
        ]

## `_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: - 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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    def _make_idents(count: int) -> list[str]:
        """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:
            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_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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    def _make_initial_masses(
        params: SpecimenParams,
        genomes: list[str],
        susceptible_locus: int,
        susceptible_base: str,
    ) -> list[float]:
        """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:
            params: SpecimenParams with min_mass and max_mass attributes
            genomes: List of genome strings
            susceptible_locus: Position that determines susceptibility
            susceptible_base: Base that makes a specimen susceptible

        Returns:
            List of generated mass values between min_mass and max_mass,
            rounded to PRECISION decimal places
        """
        # Calculate mass range midpoint
        midpoint = (params.max_mass + params.min_mass) / 2

        # Create masses based on susceptibility
        masses = []
        for genome in genomes:
            if genome[susceptible_locus] == susceptible_base:
                # Susceptible specimens get higher mass range
                mass = round(
                    random.uniform(midpoint, params.max_mass),
                    utils.PRECISION
                )
            else:
                # Non-susceptible specimens get lower mass range
                mass = round(
                    random.uniform(params.min_mass, midpoint),
                    utils.PRECISION
                )
            masses.append(mass)

        return masses

## `_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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    def _make_locations(size: int, num: int) -> list[tuple[int, int]]:
        """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:
            size: Size of the grid (assuming square grid)
            num: Number of locations to generate

        Returns:
            List of (x, y) coordinate tuples

        Raises:
            ValueError: If there are not enough cells to place all specimens
        """
        if num > size * size:
            utils.fail(f"Cannot place {num} specimens on a {size}x{size} grid")

        # Create all possible grid locations
        all_locations = [(x, y) for x in range(size) for y in range(size)]

        # Select locations randomly without replacement
        chosen_locations = random.sample(all_locations, num)

        return chosen_locations

## `_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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    def _make_loci(params: SpecimenParams) -> list[int]:
        """Make a list of mutable loci positions.

        Parameters:
            params: SpecimenParams with length and mutations attributes

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

## `_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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    def _make_reference_genome(params: SpecimenParams) -> str:
        """Make a random reference genome.

        Parameters:
            params: SpecimenParams with length attribute

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

## `_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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    def _mutate_mass(original: float, mut_scale: float, cell_value: int) -> float:
        """Mutate a single specimen's 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)

## `_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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    def _place_specimens_on_grid(
        grid: Grid,
        specimens: AllSpecimens,
    ) -> None:
        """Place specimens randomly on the grid, ensuring no two share the same cell.

        Updates the site coordinates for each specimen.

        Parameters:
            grid: A Grid object containing pollution values
            specimens: An AllSpecimens object with individuals to place on the grid
        """
        grid_size = len(grid.grid)
        locations = _make_locations(grid_size, len(specimens.individuals))

        for indiv, (x, y) in zip(specimens.individuals, locations):
            indiv.site.x = x
            indiv.site.y = y