Assays
Generate snail assays.
AssayParams
Bases: BaseModel
Parameters for assay generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
baseline
|
float
|
Baseline reading value (must be positive) |
required |
degrade
|
float
|
Rate at which sample responses decrease per day after first day (0-1) |
required |
delay
|
int
|
Maximum number of days between specimen collection and assay (must be positive) |
required |
mutant
|
float
|
Mutant reading value (must be positive) |
required |
noise
|
float
|
Noise level for readings (must be positive) |
required |
oops
|
float
|
Factor to multiply response values by for one random person (0 means no adjustment) |
required |
plate_size
|
int
|
Size of assay plate (must be positive) |
required |
seed
|
int
|
Random seed for reproducibility |
required |
Source code in src/snailz/assays.py
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Assay
Bases: BaseModel
A single assay.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
performed
|
date
|
date assay was performed |
required |
ident
|
str
|
unique identifier |
required |
specimen_id
|
str
|
which specimen |
required |
person_id
|
str
|
who did the assay |
required |
readings
|
list[list[float]]
|
grid of assay readings |
required |
treatments
|
list[list[str]]
|
grid of samples or controls |
required |
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. |
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.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
items
|
list[Assay]
|
actual assays |
required |
params
|
AssayParams
|
parameters used in generation |
required |
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 |
Source code in src/snailz/assays.py
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assays_generate(params, people, specimens)
Generate an assay for each specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
AssayParams object containing assay generation parameters |
required |
people
|
AllPersons
|
People object with staff members |
required |
specimens
|
AllSpecimens
|
Specimens object with individual specimens to generate assays for |
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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