VirtualMicrobes.mutate package

Submodules

VirtualMicrobes.mutate.Mutation module

class VirtualMicrobes.mutate.Mutation.ChromosomalMutation(chromosomes, genome)[source]

Bases: VirtualMicrobes.mutate.Mutation.Mutation

class VirtualMicrobes.mutate.Mutation.ChromosomeDeletion(chromosome, genome)[source]

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.ChromosomeDuplication(chromosome, genome)[source]

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Fission(chromosome, genome, pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)[source]
pos
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Fusion(chrom1, chrom2, genome, end1, end2)[source]

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

end1
end2
mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Insertion(chromosome, genome, stretch, insert_pos, is_external)[source]

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

Insertion of a stretch of exogenous genomic material

insert_pos
is_external
mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Inversion(chromosome, genome, start_pos, end_pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)[source]

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

reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Mutation(target, genomic_unit)[source]

Bases: object

Version:
Author:
applied
genomic_target
genomic_unit
mutate(time)[source]
post_mutation
reapply()[source]
rewind()[source]
Go back to the ancestral state by patching the mutated cell with the unmutated genomic state. It should make a check that the genomic element is a part of this cell.

:param virtual_cell.Cell mutant : On which cell do we play the reversal? :return : :author

time
uid = 0
exception VirtualMicrobes.mutate.Mutation.MutationAlreadyAppliedError(value="Cannot 'reapply' if already applied")[source]

Bases: VirtualMicrobes.mutate.Mutation.MutationError

exception VirtualMicrobes.mutate.Mutation.MutationError[source]

Bases: exceptions.Exception

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

Bases: exceptions.Exception

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

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

mutate(time)[source]
new_val
par
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.PointMutation(gene, chromosome, par, new_val, pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

mutate(time)[source]
new_val
par
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.SGDeletion(gene, chromosome, pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

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

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

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

Bases: VirtualMicrobes.mutate.Mutation.Mutation

mutate(time)[source]
pos
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.StretchDeletion(chromosome, genome, start_pos, end_pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.StretchMutation(chromosome, genome, start_pos=None, end_pos=None, stretch=None)[source]

Bases: VirtualMicrobes.mutate.Mutation.Mutation

end_pos
positive_positions()[source]
start_pos
stretch
class VirtualMicrobes.mutate.Mutation.TandemDuplication(chromosome, genome, start_pos, end_pos)[source]

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)[source]
reapply()[source]
rewind()[source]
class VirtualMicrobes.mutate.Mutation.Translocation(chromosome, genome, start_pos, end_pos, target_chrom, insert_pos, invert)[source]

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

insert_pos
invert
mutate(time)[source]
positive_positions()[source]
reapply()[source]
rewind()[source]

Module contents