phylogenie 2.1.4__py3-none-any.whl → 3.1.7__py3-none-any.whl

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Files changed (40) hide show
  1. phylogenie/__init__.py +60 -14
  2. phylogenie/draw.py +690 -0
  3. phylogenie/generators/alisim.py +12 -12
  4. phylogenie/generators/configs.py +26 -4
  5. phylogenie/generators/dataset.py +3 -3
  6. phylogenie/generators/factories.py +38 -12
  7. phylogenie/generators/trees.py +48 -47
  8. phylogenie/io/__init__.py +3 -0
  9. phylogenie/io/fasta.py +34 -0
  10. phylogenie/main.py +27 -10
  11. phylogenie/mixins.py +33 -0
  12. phylogenie/skyline/matrix.py +11 -7
  13. phylogenie/skyline/parameter.py +12 -4
  14. phylogenie/skyline/vector.py +12 -6
  15. phylogenie/treesimulator/__init__.py +36 -3
  16. phylogenie/treesimulator/events/__init__.py +5 -5
  17. phylogenie/treesimulator/events/base.py +39 -0
  18. phylogenie/treesimulator/events/contact_tracing.py +38 -23
  19. phylogenie/treesimulator/events/core.py +21 -12
  20. phylogenie/treesimulator/events/mutations.py +46 -46
  21. phylogenie/treesimulator/features.py +49 -0
  22. phylogenie/treesimulator/gillespie.py +59 -55
  23. phylogenie/treesimulator/io/__init__.py +4 -0
  24. phylogenie/treesimulator/io/newick.py +104 -0
  25. phylogenie/treesimulator/io/nexus.py +50 -0
  26. phylogenie/treesimulator/model.py +25 -49
  27. phylogenie/treesimulator/tree.py +196 -0
  28. phylogenie/treesimulator/utils.py +108 -0
  29. phylogenie/typings.py +3 -3
  30. {phylogenie-2.1.4.dist-info → phylogenie-3.1.7.dist-info}/METADATA +13 -15
  31. phylogenie-3.1.7.dist-info/RECORD +41 -0
  32. {phylogenie-2.1.4.dist-info → phylogenie-3.1.7.dist-info}/WHEEL +2 -1
  33. phylogenie-3.1.7.dist-info/entry_points.txt +2 -0
  34. phylogenie-3.1.7.dist-info/top_level.txt +1 -0
  35. phylogenie/io.py +0 -107
  36. phylogenie/tree.py +0 -92
  37. phylogenie/utils.py +0 -17
  38. phylogenie-2.1.4.dist-info/RECORD +0 -32
  39. phylogenie-2.1.4.dist-info/entry_points.txt +0 -3
  40. {phylogenie-2.1.4.dist-info → phylogenie-3.1.7.dist-info/licenses}/LICENSE.txt +0 -0
phylogenie/__init__.py CHANGED
@@ -1,3 +1,11 @@
1
+ from phylogenie.draw import (
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+ draw_colored_dated_tree_categorical,
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+ draw_colored_dated_tree_continuous,
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+ draw_colored_tree_categorical,
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+ draw_colored_tree_continuous,
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+ draw_dated_tree,
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+ draw_tree,
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+ )
1
9
  from phylogenie.generators import (
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  AliSimDatasetGenerator,
3
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  BDEITreeDatasetGenerator,
@@ -10,8 +18,8 @@ from phylogenie.generators import (
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  FBDTreeDatasetGenerator,
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  TreeDatasetGeneratorConfig,
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  )
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- from phylogenie.io import dump_newick, load_fasta, load_newick
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- from phylogenie.msa import MSA
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+ from phylogenie.io import dump_fasta, load_fasta
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+ from phylogenie.msa import MSA, Sequence
15
23
  from phylogenie.skyline import (
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  SkylineMatrix,
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  SkylineMatrixCoercible,
@@ -24,29 +32,51 @@ from phylogenie.skyline import (
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  skyline_parameter,
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  skyline_vector,
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  )
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- from phylogenie.tree import Tree
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  from phylogenie.treesimulator import (
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  Birth,
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  BirthWithContactTracing,
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  Death,
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  Event,
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+ EventType,
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+ Feature,
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  Migration,
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  Mutation,
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- MutationTargetType,
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  Sampling,
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  SamplingWithContactTracing,
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+ Tree,
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+ compute_mean_leaf_pairwise_distance,
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+ compute_sackin_index,
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+ dump_newick,
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  generate_trees,
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  get_BD_events,
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  get_BDEI_events,
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  get_BDSS_events,
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  get_canonical_events,
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  get_contact_tracing_events,
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+ get_distance,
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  get_epidemiological_events,
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  get_FBD_events,
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+ get_mrca,
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+ get_mutation_id,
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+ get_node_depth_levels,
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+ get_node_depths,
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+ get_node_height_levels,
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+ get_node_heights,
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+ get_node_leaf_counts,
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+ get_node_state,
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+ load_newick,
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+ load_nexus,
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+ set_features,
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  simulate_tree,
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  )
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  __all__ = [
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+ "draw_colored_dated_tree_categorical",
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+ "draw_colored_dated_tree_continuous",
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+ "draw_colored_tree_categorical",
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+ "draw_colored_tree_continuous",
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+ "draw_dated_tree",
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+ "draw_tree",
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  "AliSimDatasetGenerator",
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  "BDEITreeDatasetGenerator",
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  "BDSSTreeDatasetGenerator",
@@ -56,38 +86,54 @@ __all__ = [
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  "DatasetGeneratorConfig",
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  "EpidemiologicalTreeDatasetGenerator",
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  "FBDTreeDatasetGenerator",
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+ "TreeDatasetGeneratorConfig",
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+ "dump_fasta",
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+ "load_fasta",
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+ "MSA",
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+ "Sequence",
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  "SkylineMatrix",
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  "SkylineMatrixCoercible",
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- "skyline_matrix",
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  "SkylineParameter",
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  "SkylineParameterLike",
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- "skyline_parameter",
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  "SkylineVector",
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  "SkylineVectorCoercible",
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  "SkylineVectorLike",
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+ "skyline_matrix",
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+ "skyline_parameter",
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  "skyline_vector",
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- "Tree",
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- "TreeDatasetGeneratorConfig",
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  "Birth",
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  "BirthWithContactTracing",
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  "Death",
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  "Event",
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+ "EventType",
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+ "Feature",
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  "Migration",
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  "Mutation",
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- "MutationTargetType",
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  "Sampling",
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  "SamplingWithContactTracing",
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+ "Tree",
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+ "compute_mean_leaf_pairwise_distance",
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+ "compute_sackin_index",
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+ "dump_newick",
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+ "generate_trees",
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119
  "get_BD_events",
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120
  "get_BDEI_events",
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  "get_BDSS_events",
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  "get_canonical_events",
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  "get_contact_tracing_events",
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+ "get_distance",
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  "get_epidemiological_events",
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  "get_FBD_events",
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- "generate_trees",
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- "simulate_tree",
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- "dump_newick",
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- "load_fasta",
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+ "get_mrca",
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+ "get_mutation_id",
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+ "get_node_depth_levels",
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+ "get_node_depths",
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+ "get_node_height_levels",
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+ "get_node_heights",
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+ "get_node_leaf_counts",
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+ "get_node_state",
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135
  "load_newick",
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- "MSA",
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+ "load_nexus",
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+ "set_features",
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+ "simulate_tree",
93
139
  ]