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Allowing R samples to have 0 S mutations #14

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Merged
viktoria023 merged 2 commits into from
Feb 12, 2025
Merged

Allowing R samples to have 0 S mutations #14

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f17ccd2
allowing 0 S mutations for R samples
ddissanayake1 Feb 12, 2025
e4b304d
formated
ddissanayake1 Feb 12, 2025
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25 changes: 18 additions & 7 deletions src/sbmlsim/Batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,7 @@ def generate(
number_susceptible,
selected_susceptible_mutations,
) = self._get_susceptible_mutations(
n_sus, remaining_aa_positions, sample_gene
n_sus, remaining_aa_positions, sample_gene, sample_label=label
)
else:
selected_susceptible_mutations = []
Expand Down Expand Up @@ -342,7 +342,9 @@ def _get_resistant_mutations(self, n_res, distribution, sample_gene):
number_resistant,
selected_resistant_mutations,
selected_resistant_positions,
) = self._get_defined_mutations(label="R", n=n_res, distribution=distribution)
) = self._get_defined_mutations(
label="R", n=n_res, sample_label="R", distribution=distribution
)

# Get amino acid positions that are not altered by selected resistant mutations
remaining_aa_positions = [
Expand All @@ -354,7 +356,9 @@ def _get_resistant_mutations(self, n_res, distribution, sample_gene):

return number_resistant, selected_resistant_mutations, remaining_aa_positions

def _get_susceptible_mutations(self, n_sus, remaining_aa_positions, sample_gene):
def _get_susceptible_mutations(
self, n_sus, remaining_aa_positions, sample_gene, sample_label
):
# choose susceptible mutations for a sample

if self.define_susceptibles:
Expand All @@ -366,6 +370,7 @@ def _get_susceptible_mutations(self, n_sus, remaining_aa_positions, sample_gene)
label="S",
n=n_sus,
distribution="poisson",
sample_label=sample_label,
remaining_aa_positions=remaining_aa_positions,
)

Expand Down Expand Up @@ -434,9 +439,13 @@ def _get_susceptible_mutations(self, n_sus, remaining_aa_positions, sample_gene)
return number_susceptible, selected_susceptible_mutations

def _get_defined_mutations(
self, label, n, distribution, remaining_aa_positions=None
self, label, n, distribution, sample_label, remaining_aa_positions=None
):

assert not (
label == "R" and sample_label == "S"
), "Cannot have resistant mutations in a susceptible sample"

if label == "R":
mutation_positions = self.resistant_positions
mutations = self.resistant_mutations
Expand All @@ -457,12 +466,14 @@ def _get_defined_mutations(
while True:
number_mutations = numpy.random.poisson(n)
if label == "R":
if number_mutations > 0 and number_mutations <= len(
if 0 < number_mutations <= len(mutation_positions):
break
if label == "S":
if sample_label == "S" and 0 < number_mutations <= len(
mutation_positions
):
break
if label == "S":
if number_mutations > 0 and number_mutations <= len(
if sample_label == "R" and number_mutations <= len(
mutation_positions
):
break
Expand Down