VirtualMicrobes.mutate package

Submodules

VirtualMicrobes.mutate.Mutation module

class VirtualMicrobes.mutate.Mutation.ChromosomalMutation(chromosomes, genome)

Bases: VirtualMicrobes.mutate.Mutation.Mutation

class VirtualMicrobes.mutate.Mutation.ChromosomeDeletion(chromosome, genome)

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.ChromosomeDuplication(chromosome, genome)

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Fission(chromosome, genome, pos)

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

pos

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Fusion(chrom1, chrom2, genome, end1, end2)

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

end1

end2

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Insertion(chromosome, genome, stretch, insert_pos, is_external)

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

Insertion of a stretch of exogenous genomic material

insert_pos

is_external

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Inversion(chromosome, genome, start_pos, end_pos)

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)

The invert is in place, hence pre- and post- mutation will appear the same

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Mutation(target, genomic_unit)

Bases: object

Base class for mutations.

applied

indicates that the mutation has been applied

Type:boolean

genomic_target

Type:target of the mutation

post_mutation

Type:post mutation state of the genomic_target

genomic_unit

Type:contains the genomic_target

time

simulation time when first mutated

Type:int

applied

genomic_target

genomic_unit

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

post_mutation

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

time

uid = 0

exception VirtualMicrobes.mutate.Mutation.MutationAlreadyAppliedError(value="Cannot 'reapply' if already applied")

Bases: VirtualMicrobes.mutate.Mutation.MutationError

exception VirtualMicrobes.mutate.Mutation.MutationError

Bases: exceptions.Exception

exception VirtualMicrobes.mutate.Mutation.MutationNotAppliedError(value="Cannot 'rewind' if not already applied")

Bases: exceptions.Exception

class VirtualMicrobes.mutate.Mutation.OperatorInsertion(gene, chromosome, new_val, pos)

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

new_val

par

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.PointMutation(gene, chromosome, par, new_val, pos)

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

new_val

par

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.SGDeletion(gene, chromosome, pos)

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

class VirtualMicrobes.mutate.Mutation.SGDuplication(gene, chromosome, pos)

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

class VirtualMicrobes.mutate.Mutation.SingleGeneMutation(gene, chromosome, pos)

Bases: VirtualMicrobes.mutate.Mutation.Mutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

pos

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.StretchDeletion(chromosome, genome, start_pos, end_pos)

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.StretchMutation(chromosome, genome, start_pos=None, end_pos=None, stretch=None)

Bases: VirtualMicrobes.mutate.Mutation.Mutation

end_pos

positive_positions()

start_pos

stretch

class VirtualMicrobes.mutate.Mutation.TandemDuplication(chromosome, genome, start_pos, end_pos)

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

class VirtualMicrobes.mutate.Mutation.Translocation(chromosome, genome, start_pos, end_pos, target_chrom, insert_pos, invert)

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

insert_pos

invert

mutate(time)

Apply mutation.

Parameters:time (int) – simulation time

positive_positions()

reapply()

Reapply mutation after rewinding

rewind()

Go back to the ancestral state.

Module contents