VirtualMicrobes.mutate package

Subpackages

• VirtualMicrobes.mutate.test package
  • Submodules
  • VirtualMicrobes.mutate.test.TestMutate module
  • Module contents

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)

reapply()

rewind()

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

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)

reapply()

rewind()

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

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

mutate(time)

pos

reapply()

rewind()

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

Bases: VirtualMicrobes.mutate.Mutation.ChromosomalMutation

end1

end2

mutate(time)

reapply()

rewind()

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)

reapply()

rewind()

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()

rewind()

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

Bases: object

Version: Author:

applied

genomic_target

genomic_unit

mutate(time)

post_mutation

reapply()

rewind()

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")

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)

new_val

par

reapply()

rewind()

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

Bases: VirtualMicrobes.mutate.Mutation.SingleGeneMutation

mutate(time)

new_val

par

reapply()

rewind()

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)

pos

reapply()

rewind()

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

Bases: VirtualMicrobes.mutate.Mutation.StretchMutation

mutate(time)

reapply()

rewind()

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)

reapply()

rewind()

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)

positive_positions()

reapply()

rewind()

Module contents