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 |
grid
|
str
|
sample grid ID |
''
|
x
|
int
|
sample X coordinate |
-1
|
y
|
int
|
sample Y coordinate |
-1
|
sampled
|
date
|
Date sample taken |
datetime.date(2025, 4, 1)
|
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.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
parameters |
required |
ref_genome
|
str
|
reference genome |
required |
is_mutant
|
bool
|
is this specimen a mutant? |
required |
susc_locus
|
int
|
susceptible locus in genome |
required |
susc_base
|
str
|
base indicating mutant |
required |
Returns:
Type | Description |
---|---|
Specimen
|
randomly-generated 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.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
parameters |
required |
num
|
int
|
number of specimens required |
required |
Returns:
Type | Description |
---|---|
AllSpecimens
|
collection of randomly-generated specimens. |
Source code in src/snailz/specimens.py
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|
to_csv(writer)
Save specimens as CSV.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
writer
|
stream
|
where to write |
required |
Source code in src/snailz/specimens.py
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|