Specimens
Generate specimens.
Specimen
Bases: MinimalSpecimen
A single specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
survey_id
|
str
|
survey identifier |
required |
species
|
int
|
species this snail belongs to |
required |
collected
|
date
|
date when specimen was collected |
required |
genome
|
str
|
bases in genome |
required |
is_mutant
|
bool
|
is this specimen a mutant? |
False
|
Source code in src/snailz/specimens.py
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|
AllSpecimens
Bases: BaseModel
A set of generated specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
loci
|
list[list[int]]
|
locations where mutations can occur |
required |
references
|
list[str]
|
unmutated genomes of each species |
required |
susc_base
|
str
|
mutant base that induces mass changes |
required |
susc_locus
|
int
|
location of mass change mutation |
required |
items
|
list[Specimen]
|
list of individual specimens |
required |
Source code in src/snailz/specimens.py
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|
to_csv(full=False)
Return a CSV string representation of the specimen data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
full
|
bool
|
include mutant and species information |
False
|
Returns:
Type | Description |
---|---|
str
|
A CSV-formatted string. |
Source code in src/snailz/specimens.py
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|
generate(params, surveys)
staticmethod
Generate a set of specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
specimen generation parameters |
required |
surveys
|
AllSurveys
|
surveys to generate specimens for |
required |
Returns:
Type | Description |
---|---|
AllSpecimens
|
A set of surveys. |
Source code in src/snailz/specimens.py
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_make_specimen(params, specimens, survey, ident)
Make a single specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
specimen parameters |
required |
survey
|
Survey
|
survey this specimen is from |
required |
ident
|
str
|
specimen identifier |
required |
Returns:
Type | Description |
---|---|
Specimen
|
A randomly-generated specimen. |
Source code in src/snailz/specimens.py
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|
_specimen_id_generator()
Specimen ID generation function.
Returns:
Type | Description |
---|---|
str
|
Candidate ID for a specimen. |
Source code in src/snailz/specimens.py
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