Welcome to Circular Genome Tools’s documentation!

Readme File

Circular genome tools (cgt)

A sage package for working with circular genomes represented by signed or unsigned permutations. It includes tools for converting between representations as well as visualisations using matplotlib.

To install and use this package, paste the following command in your terminal

sage -pip install cgt

and use import cgt in a sage script or environment.

If you would like to contribute to cgt, please see ``CONTRIBUTING.md` <CONTRIBUTING.md>`_ for how to get set up.

If you use this software in your work, please cite it use the citation function on the github page or see ``CITATION.cff` <CITATION.cff>`_

Note: you will need to at least have Sage version 9.0 installed. If you aren’t sure how to do this, see the installation instructions in ``INSTALL.md` <INSTALL.md>`_.

Contents:

• cgt package
  • cgt.distances module
    • MFPT()
    • dict_to_distance_matrix()
    • discrete_MFPT()
    • distance()
    • distance_between()
    • distance_matrix()
    • fast_MFPT()
    • first_nonzero_value()
    • genomes_for_dist_matrix()
    • get_distance_function()
    • likelihood_function()
    • maximise()
    • min_distance()
    • min_distance_using_irreps()
    • mle()
    • mles()
    • prob_to_reach_in_steps_func()
    • probability_to_reach_in_steps()
  • cgt.enums module
    • ALGEBRA
      • ALGEBRA.genome
      • ALGEBRA.genome_class
      • ALGEBRA.group
    • CLASSES
      • CLASSES.conjugacy_classes
      • CLASSES.cosets
      • CLASSES.double_cosets
    • DATA
      • DATA.eig_data
      • DATA.eigval_lists
      • DATA.eigval_sets
      • DATA.eigval_sets_old
      • DATA.eigvec_lists
      • DATA.eigvec_mat_inv
      • DATA.irreps_z
      • DATA.irreps_z_np
      • DATA.irreps_zs
      • DATA.partial_traces
      • DATA.projections
      • DATA.reg_rep_of_zs
    • DISPLAY
      • DISPLAY.arrows
      • DISPLAY.cycles
      • DISPLAY.one_row
    • DISTANCE
      • DISTANCE.DMFPT
      • DISTANCE.MFPT
      • DISTANCE.MLE
      • DISTANCE.discrete_MFPT
      • DISTANCE.discrete_mean_first_passage_time
      • DISTANCE.maximum_likelihood_distance
      • DISTANCE.maximum_likelihood_estimate
      • DISTANCE.mean_first_passage_time
      • DISTANCE.min
      • DISTANCE.min_weighted
      • DISTANCE.minimum
      • DISTANCE.minimum_distance
      • DISTANCE.minimum_weighted
    • FORMAT
      • FORMAT.dictionary
      • FORMAT.equiv_classes
      • FORMAT.formal_sum
      • FORMAT.only_reps
    • IRREP_TYPE
      • IRREP_TYPE.orthogonal
      • IRREP_TYPE.seminormal
      • IRREP_TYPE.specht
      • IRREP_TYPE.speck
    • MODEL
      • MODEL.all_inversions
      • MODEL.all_inversions_larger_less_likely
      • MODEL.all_transpositions
      • MODEL.one_region_inversions
      • MODEL.one_region_moves
      • MODEL.one_region_moves_without_inversions
      • MODEL.three_region_transpositions
      • MODEL.two_region_adjacent_transpositions
      • MODEL.two_region_inversions
      • MODEL.two_region_revrevs
      • MODEL.two_region_transpositions
      • MODEL.two_region_transpositions_without_inversions
    • SET
      • SET.one_row
      • SET.signed_cycles
      • SET.unsigned_cycles
      • SET.wreath
      • SET.wreath_s2
    • SYMMETRY
      • SYMMETRY.C_2
      • SYMMETRY.D_n
      • SYMMETRY.S_2
      • SYMMETRY.circular
      • SYMMETRY.dihedral
      • SYMMETRY.flip
      • SYMMETRY.linear
      • SYMMETRY.reflection
    • TYPE
      • TYPE.pos_to_signed_reg
      • TYPE.reg_to_signed_pos
      • TYPE.signed_pos_to_reg
      • TYPE.signed_reg_to_pos
  • cgt.examples module
    • example()
  • cgt.genome module
    • Genome
  • cgt.models module
    • Model
      • Model.named_model_with_relative_probs()
      • Model.reg_rep_of_zs()
      • Model.s_element()
  • cgt.position_paradigm module
    • Framework
    • GenomeFramework
    • PositionParadigmFramework
      • PositionParadigmFramework.canonical_double_cosets()
      • PositionParadigmFramework.canonical_instance()
      • PositionParadigmFramework.coefficient_in()
      • PositionParadigmFramework.collect_genome_terms()
      • PositionParadigmFramework.cycles()
      • PositionParadigmFramework.draw_instance()
      • PositionParadigmFramework.fast_canonical_instance_generator()
      • PositionParadigmFramework.fast_reg_rep_of_zs()
      • PositionParadigmFramework.genome()
      • PositionParadigmFramework.genome_canonical_instances()
      • PositionParadigmFramework.genome_canonical_instances_generator()
      • PositionParadigmFramework.genome_conjugacy_classes()
      • PositionParadigmFramework.genome_equivalence_classes()
      • PositionParadigmFramework.genome_group()
      • PositionParadigmFramework.genomes()
      • PositionParadigmFramework.group_algebra()
      • PositionParadigmFramework.identity_instance()
      • PositionParadigmFramework.instances()
      • PositionParadigmFramework.irreps()
      • PositionParadigmFramework.num_genomes()
      • PositionParadigmFramework.one_row()
      • PositionParadigmFramework.random_genome()
      • PositionParadigmFramework.random_instance()
      • PositionParadigmFramework.reg_rep_of_zs()
      • PositionParadigmFramework.regular_representation()
      • PositionParadigmFramework.standard_reflection()
      • PositionParadigmFramework.standard_rotation()
      • PositionParadigmFramework.symmetry_element()
      • PositionParadigmFramework.symmetry_group()
  • cgt.rearrangements module
    • all_adjacent_transpositions_representatives()
    • all_inversion_instances()
    • all_inversions_representatives()
    • all_transposition_instances()
    • c_perm()
    • conjugacy_class()
    • cut_positions()
    • double_coset()
    • fast_all_inversion_reps()
    • inversion()
    • permutation_with_cuts()
    • representatives()
    • segment_length()
    • segment_midpoint()
    • signed_inversion()
    • single_coset()
    • transposition()
  • cgt.structures module
    • HyperoctahedralGroup()
    • set_plus_minus()
  • cgt.visualisation module
    • draw_genome_instance()
  • cgt.simulations module
    • draw_branch_length()
    • draw_genome()
    • draw_rearrangement()
    • draw_tree()
    • evolve_on_tree()
    • grow_tree()
    • newick_to_tree()
    • set_node()
  • cgt.hyperoctahedral module
    • HyperoctahedralGroup
      • HyperoctahedralGroup.Phi()
      • HyperoctahedralGroup.character_for_tuple()
      • HyperoctahedralGroup.element_in_little_subgroup()
      • HyperoctahedralGroup.hyperoctahedral_twist()
      • HyperoctahedralGroup.irrep()
      • HyperoctahedralGroup.little_subgroup()
      • HyperoctahedralGroup.little_subgroup_pairs()
      • HyperoctahedralGroup.little_subgroups()
      • HyperoctahedralGroup.orbit_representative()
      • HyperoctahedralGroup.representation_little_subgroup()
      • HyperoctahedralGroup.right_transversal()
      • HyperoctahedralGroup.right_transversal_of_little_subgroup()
      • HyperoctahedralGroup.semidirect_product_with_hyperoctahedral_twist()
    • HyperoctahedralGroupRepresentations()
  • cgt.sorting module
  • cgt.pickle_manager module
    • retrieve_irrep_of_z()
  • cgt.constants module

Indices and tables

• Index

• Module Index