Specimens - Snailz Docs

Skip to content

# Specimens

Generate snail specimens.

## `SpecimenParams`

Bases: `BaseModel`

Parameters for specimen generation.

- 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

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

    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    28
    29
    30
    31
    32
    33
    34
    35
    36
    37
    38
    39
    40
    41
    42
    43
    44
    45
    46
    47
    48
    49
    50
    51
    class SpecimenParams(BaseModel):
        """Parameters for specimen generation.

        - 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
        """

        length: int = Field(gt=0)
        max_mass: float = Field(gt=0)
        min_mass: float = Field(gt=0)
        mut_scale: float = Field()
        mutations: int = Field(ge=0)
        number: int = Field(gt=0)
        seed: int = Field()

        @model_validator(mode="after")
        def validate_mass_range(self):
            """Validate that max_mass is greater than min_mass."""
            if self.min_mass >= self.max_mass:
                raise ValueError("max_mass must be greater than min_mass")
            return self

        @model_validator(mode="after")
        def validate_mutations_range(self):
            """Validate that mutations is not greater than genome length."""
            if self.mutations > self.length:
                raise ValueError("mutations must be between 0 and length")
            return self

        model_config = {"extra": "forbid"}

### `validate_mass_range()`

Validate that max_mass is greater than min_mass.

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

    37
    38
    39
    40
    41
    42
    @model_validator(mode="after")
    def validate_mass_range(self):
        """Validate that max_mass is greater than min_mass."""
        if self.min_mass >= self.max_mass:
            raise ValueError("max_mass must be greater than min_mass")
        return self

### `validate_mutations_range()`

Validate that mutations is not greater than genome length.

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

    44
    45
    46
    47
    48
    49
    @model_validator(mode="after")
    def validate_mutations_range(self):
        """Validate that mutations is not greater than genome length."""
        if self.mutations > self.length:
            raise ValueError("mutations must be between 0 and length")
        return self

## `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`

    54
    55
    56
    57
    58
    59
    60
    61
    62
    class Point(BaseModel):
        """A 2D point with x and y coordinates.

        - x: X coordinate in grid
        - y: Y coordinate in grid
        """

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

## `Individual`

Bases: `BaseModel`

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

- genome: bases in genome
- ident: unique identifier
- mass: snail mass in grams
- site: grid location where specimen was collected

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

    65
    66
    67
    68
    69
    70
    71
    72
    73
    74
    75
    76
    77
    class Individual(BaseModel):
        """A single specimen with unique identifier, genome, mass, and site location.

        - genome: bases in genome
        - ident: unique identifier
        - mass: snail mass in grams
        - site: grid location where specimen was collected
        """

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

## `Specimens`

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`

     80
     81
     82
     83
     84
     85
     86
     87
     88
     89
     90
     91
     92
     93
     94
     95
     96
     97
     98
     99
    100
    101
    102
    103
    104
    105
    106
    107
    108
    109
    110
    111
    112
    113
    114
    115
    116
    class Specimens(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
        """

        individuals: list[Individual]
        loci: list[int]
        params: SpecimenParams
        reference: str
        susceptible_base: str
        susceptible_locus: int

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

            Returns:
                A CSV-formatted string containing specimen data with fields:
                - ident: specimen identifier
                - x: X coordinate in grid
                - y: Y coordinate in grid
                - genome: bases in genome
                - mass: snail mass in grams
            """
            output = io.StringIO()
            writer = csv.writer(output, **utils.CSV_SETTINGS)
            writer.writerow(["ident", "x", "y", "genome", "mass"])
            for indiv in self.individuals:
                writer.writerow(
                    [indiv.ident, indiv.site.x, indiv.site.y, indiv.genome, indiv.mass]
                )
            return output.getvalue()

### `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` | ident: specimen identifier
`str` | x: X coordinate in grid
`str` | y: Y coordinate in grid
`str` | genome: bases in genome
`str` | mass: snail mass in grams

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

     98
     99
    100
    101
    102
    103
    104
    105
    106
    107
    108
    109
    110
    111
    112
    113
    114
    115
    116
    def to_csv(self) -> str:
        """Return a CSV string representation of the specimens data.

        Returns:
            A CSV-formatted string containing specimen data with fields:
            - ident: specimen identifier
            - x: X coordinate in grid
            - y: Y coordinate in grid
            - genome: bases in genome
            - mass: snail mass in grams
        """
        output = io.StringIO()
        writer = csv.writer(output, **utils.CSV_SETTINGS)
        writer.writerow(["ident", "x", "y", "genome", "mass"])
        for indiv in self.individuals:
            writer.writerow(
                [indiv.ident, indiv.site.x, indiv.site.y, indiv.genome, indiv.mass]
            )
        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. 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` | Grid object to place specimens on for mass mutation | `None`

Returns:

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

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

    119
    120
    121
    122
    123
    124
    125
    126
    127
    128
    129
    130
    131
    132
    133
    134
    135
    136
    137
    138
    139
    140
    141
    142
    143
    144
    145
    146
    147
    148
    149
    150
    151
    152
    153
    154
    155
    156
    157
    158
    159
    160
    161
    def specimens_generate(params: SpecimenParams, grid: Grid = None) -> 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.  Specimen masses are only mutated if a
        grid is provided.

        Parameters:
            params: SpecimenParams object
            grid: Grid object to place specimens on for mass mutation

        Returns:
            Specimens 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)]
        masses = _make_masses(params, genomes, susc_loc, susc_base)
        identifiers = _make_idents(params.number)

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

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

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

        return result

## `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` | `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`

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

    164
    165
    166
    167
    168
    169
    170
    171
    172
    173
    174
    175
    176
    177
    178
    179
    180
    181
    182
    183
    184
    185
    186
    187
    188
    189
    190
    191
    192
    193
    194
    195
    196
    197
    198
    199
    200
    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.  Modifies specimen masses
        in-place for susceptible individuals; updates site coordinates for
        all individuals.

        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
        """
        grid_size = len(grid.grid)
        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 i in individuals:
            x = random.randrange(grid_size)
            y = random.randrange(grid_size)
            i.site.x = x
            i.site.y = y
            if grid.grid[x][y] > 0 and i.genome[susc_locus] == susc_base:
                i.mass = mutate_mass(i.mass, mut_scale, grid.grid[x][y])

## `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`

    203
    204
    205
    206
    207
    208
    209
    210
    211
    212
    213
    214
    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)

## `_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`

    217
    218
    219
    220
    221
    222
    223
    224
    225
    226
    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`

    229
    230
    231
    232
    233
    234
    235
    236
    237
    238
    239
    240
    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`

    243
    244
    245
    246
    247
    248
    249
    250
    251
    252
    253
    254
    255
    256
    257
    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`

    260
    261
    262
    263
    264
    265
    266
    267
    268
    269
    270
    271
    272
    273
    274
    275
    276
    277
    278
    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_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`

    281
    282
    283
    284
    285
    286
    287
    288
    289
    290
    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_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`

    293
    294
    295
    296
    297
    298
    299
    300
    301
    302
    303
    304
    305
    306
    307
    308
    309
    310
    311
    312
    313
    314
    def _make_masses(
        params: SpecimenParams,
        genomes: list[str],
        susceptible_locus: int,
        susceptible_base: str,
    ) -> list[float]:
        """Generate random masses for 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 randomly generated mass values between min_mass and max_mass,
            rounded to PRECISION decimal places
        """
        return [
            round(random.uniform(params.min_mass, params.max_mass), utils.PRECISION)
            for _ in genomes
        ]

## `_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`

    317
    318
    319
    320
    321
    322
    323
    324
    325
    326
    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))