Assays
Generate snail assays.
AssayParams
Bases: BaseModel
Parameters for assay generation.
- baseline: Baseline reading value (must be positive)
- end_date: End date for assay generation
- mutant: Mutant reading value (must be positive)
- noise: Noise level for readings (must be positive)
- plate_size: Size of assay plate (must be positive)
- seed: Random seed for reproducibility
- start_date: Start date for assay generation (must not be after end_date)
Source code in src/snailz/assays.py
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validate_date_range()
Validate that start_date is not after end_date.
Source code in src/snailz/assays.py
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Assay
Bases: BaseModel
A single assay.
- performed: date assay was performed
- ident: unique identifier
- specimen_id: which specimen
- person_id: who did the assay
- readings: grid of assay readings
- treatments: grid of samples or controls
Source code in src/snailz/assays.py
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to_csv(data_type)
Return a CSV string representation of the assay data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data_type
|
str
|
Type of data to output, either "readings" or "treatments" |
required |
Returns:
Type | Description |
---|---|
str
|
A CSV-formatted string with the assay data in the format: |
str
|
id, |
str
|
specimen, |
str
|
performed, |
str
|
performed_by, |
str
|
,A,B,C,... |
str
|
1,,,... |
str
|
2,,,... |
str
|
... |
str
|
The CSV output uses Unix line endings (LF). |
Raises:
Type | Description |
---|---|
ValueError
|
If data_type is not "readings" or "treatments" |
Source code in src/snailz/assays.py
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AllAssays
Bases: BaseModel
Keep track of generated assays.
- items: actual assays
- params: parameters used in generation
Source code in src/snailz/assays.py
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to_csv()
Return a CSV string representation of the assay summary data.
Returns:
Type | Description |
---|---|
str
|
A CSV-formatted string containing a summary of all assays with fields: |
str
|
|
str
|
|
str
|
|
str
|
|
str
|
The CSV output uses Unix line endings (LF). |
Source code in src/snailz/assays.py
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assays_generate(params, specimens, people)
Generate an assay for each specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
AssayParams object containing assay generation parameters |
required |
specimens
|
AllSpecimens
|
Specimens object with individual specimens to generate assays for |
required |
people
|
AllPersons
|
People object with staff members |
required |
Returns:
Type | Description |
---|---|
AllAssays
|
Assays object containing generated assays and parameters |
Source code in src/snailz/assays.py
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assays_to_csv(input, output)
Write assays to standard output or files.
Source code in src/snailz/assays.py
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