Specimens
Specimen
Bases: BaseModel
Store a single specimen specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
id
|
str
|
unique ID |
required |
genome
|
str
|
genome |
required |
is_mutant
|
bool
|
is this a mutant? |
required |
mass
|
float
|
mass (g) |
required |
Source code in src/snailz/specimens.py
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generate(params, ref_genome, is_mutant, susc_locus, susc_base)
staticmethod
Generate a single specimen.
Source code in src/snailz/specimens.py
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AllSpecimens
Bases: BaseModel
Store a set of specimens.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
generation parameters |
required |
ref_genome
|
str
|
reference genome |
required |
susc_locus
|
int
|
susceptible locus |
required |
susc_base
|
str
|
susceptible mutation |
required |
samples
|
list[Specimen]
|
specimens |
required |
Source code in src/snailz/specimens.py
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generate(params, num)
staticmethod
Generate specimens.
Source code in src/snailz/specimens.py
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to_csv(writer)
Save specimens as CSV.
Source code in src/snailz/specimens.py
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