Assays
Generate snail assays.
AssayParams
Bases: BaseModel
Parameters for assay generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
baseline
|
float
|
Baseline reading value |
2.0
|
degrade
|
float
|
Rate at which sample responses decrease per day after first day (0..1) |
0.05
|
delay
|
int
|
Maximum number of days between specimen collection and assay |
5
|
mutant
|
float
|
Mutant reading value (must be positive) |
5.0
|
noise
|
float
|
Noise level for readings (must be positive) |
0.2
|
plate_size
|
int
|
Size of assay plate (must be positive) |
4
|
image_noise
|
int
|
Plate image noise (grayscale 0-255) |
32
|
Source code in src/snailz/assays.py
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|
validate_fields()
Validate requirements on fields.
Source code in src/snailz/assays.py
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Assay
Bases: BaseModel
A single assay.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ident
|
str
|
unique identifier |
required |
specimen
|
str
|
which specimen |
required |
person
|
str
|
who did the assay |
required |
performed
|
date
|
date assay was performed |
required |
readings
|
Grid[float]
|
assay readings |
required |
treatments
|
Grid[str]
|
samples or controls |
required |
Source code in src/snailz/assays.py
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|
to_csv(kind)
Return a CSV string representation of the assay data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
kind
|
str
|
Either "readings" or "treatments" |
required |
Returns:
Type | Description |
---|---|
str
|
A CSV-formatted string with the assay data. |
Raises:
Type | Description |
---|---|
ValueError
|
If 'kind' is not "readings" or "treatments" |
Source code in src/snailz/assays.py
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|
AllAssays
Bases: BaseModel
All generated assays.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
items
|
list[Assay]
|
actual assays |
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, persons, specimens)
Generate an assay for each specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
assay generation parameters |
required |
persons
|
AllPersons
|
all staff members |
required |
specimens
|
AllSpecimens
|
specimens to generate assays for |
required |
Returns:
Type | Description |
---|---|
AllAssays
|
Assay list object |
Source code in src/snailz/assays.py
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|
_calc_degradation(params, collected, assayed)
Calculate degradation based on days since collection.
Source code in src/snailz/assays.py
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_make_readings(params, specimen, performed, treatments)
Make a single assay.
Source code in src/snailz/assays.py
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|
_make_treatments(params)
Generate random treatments.
Source code in src/snailz/assays.py
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|