napistu 0.4.1__tar.gz → 0.4.3__tar.gz

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Files changed (153) hide show
  1. {napistu-0.4.1/src/napistu.egg-info → napistu-0.4.3}/PKG-INFO +1 -1
  2. {napistu-0.4.1 → napistu-0.4.3}/setup.cfg +1 -1
  3. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/consensus.py +3 -4
  4. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/gcs/constants.py +5 -5
  5. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/constants.py +51 -0
  6. napistu-0.4.3/src/napistu/ingestion/reactom_fi.py +208 -0
  7. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/constants.py +23 -1
  8. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/ig_utils.py +161 -1
  9. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/net_create.py +3 -3
  10. napistu-0.4.3/src/napistu/network/net_propagation.py +696 -0
  11. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/ng_utils.py +26 -6
  12. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/precompute.py +56 -0
  13. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/sbml_dfs_utils.py +8 -2
  14. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/source.py +243 -40
  15. napistu-0.4.3/src/napistu/statistics/__init__.py +10 -0
  16. napistu-0.4.3/src/napistu/statistics/hypothesis_testing.py +66 -0
  17. napistu-0.4.3/src/napistu/statistics/quantiles.py +82 -0
  18. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/utils.py +23 -1
  19. {napistu-0.4.1 → napistu-0.4.3/src/napistu.egg-info}/PKG-INFO +1 -1
  20. {napistu-0.4.1 → napistu-0.4.3}/src/napistu.egg-info/SOURCES.txt +6 -1
  21. napistu-0.4.3/src/tests/test_network_ig_utils.py +192 -0
  22. napistu-0.4.3/src/tests/test_network_net_propagation.py +380 -0
  23. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_precompute.py +30 -0
  24. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_sbml_dfs_utils.py +13 -0
  25. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_source.py +38 -6
  26. napistu-0.4.3/src/tests/test_statistics_hypothesis_testing.py +62 -0
  27. napistu-0.4.3/src/tests/test_statistics_quantiles.py +133 -0
  28. napistu-0.4.1/src/napistu/network/net_propagation.py +0 -146
  29. napistu-0.4.1/src/tests/test_network_ig_utils.py +0 -59
  30. napistu-0.4.1/src/tests/test_network_net_propagation.py +0 -89
  31. napistu-0.4.1/src/tests/test_set_coverage.py +0 -50
  32. {napistu-0.4.1 → napistu-0.4.3}/LICENSE +0 -0
  33. {napistu-0.4.1 → napistu-0.4.3}/README.md +0 -0
  34. {napistu-0.4.1 → napistu-0.4.3}/pyproject.toml +0 -0
  35. {napistu-0.4.1 → napistu-0.4.3}/setup.py +0 -0
  36. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/__init__.py +0 -0
  37. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/__main__.py +0 -0
  38. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/constants.py +0 -0
  39. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/context/__init__.py +0 -0
  40. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/context/discretize.py +0 -0
  41. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/context/filtering.py +0 -0
  42. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/gcs/__init__.py +0 -0
  43. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/gcs/downloads.py +0 -0
  44. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/gcs/utils.py +0 -0
  45. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/identifiers.py +0 -0
  46. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/indices.py +0 -0
  47. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/__init__.py +0 -0
  48. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/bigg.py +0 -0
  49. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/gtex.py +0 -0
  50. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/hpa.py +0 -0
  51. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/identifiers_etl.py +0 -0
  52. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/napistu_edgelist.py +0 -0
  53. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/obo.py +0 -0
  54. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/psi_mi.py +0 -0
  55. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/reactome.py +0 -0
  56. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/sbml.py +0 -0
  57. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/string.py +0 -0
  58. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/trrust.py +0 -0
  59. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/yeast.py +0 -0
  60. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/matching/__init__.py +0 -0
  61. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/matching/constants.py +0 -0
  62. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/matching/interactions.py +0 -0
  63. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/matching/mount.py +0 -0
  64. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/matching/species.py +0 -0
  65. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/__init__.py +0 -0
  66. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/__main__.py +0 -0
  67. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/client.py +0 -0
  68. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/codebase.py +0 -0
  69. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/codebase_utils.py +0 -0
  70. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/component_base.py +0 -0
  71. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/config.py +0 -0
  72. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/constants.py +0 -0
  73. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/documentation.py +0 -0
  74. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/documentation_utils.py +0 -0
  75. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/execution.py +0 -0
  76. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/health.py +0 -0
  77. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/profiles.py +0 -0
  78. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/server.py +0 -0
  79. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/tutorials.py +0 -0
  80. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/tutorials_utils.py +0 -0
  81. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/mcp/utils.py +0 -0
  82. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/__init__.py +0 -0
  83. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/constants.py +0 -0
  84. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/curation.py +0 -0
  85. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/gaps.py +0 -0
  86. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/pathwayannot.py +0 -0
  87. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/modify/uncompartmentalize.py +0 -0
  88. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/__init__.py +0 -0
  89. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/data_handling.py +0 -0
  90. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/neighborhoods.py +0 -0
  91. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/net_create_utils.py +0 -0
  92. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/ng_core.py +0 -0
  93. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/paths.py +0 -0
  94. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/__init__.py +0 -0
  95. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/constants.py +0 -0
  96. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/dogma.py +0 -0
  97. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/genodexito.py +0 -0
  98. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/id_tables.py +0 -0
  99. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/mygene.py +0 -0
  100. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/ontologies/renaming.py +0 -0
  101. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/rpy2/__init__.py +0 -0
  102. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/rpy2/callr.py +0 -0
  103. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/rpy2/constants.py +0 -0
  104. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/rpy2/rids.py +0 -0
  105. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/sbml_dfs_core.py +0 -0
  106. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/scverse/__init__.py +0 -0
  107. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/scverse/constants.py +0 -0
  108. {napistu-0.4.1 → napistu-0.4.3}/src/napistu/scverse/loading.py +0 -0
  109. {napistu-0.4.1 → napistu-0.4.3}/src/napistu.egg-info/dependency_links.txt +0 -0
  110. {napistu-0.4.1 → napistu-0.4.3}/src/napistu.egg-info/entry_points.txt +0 -0
  111. {napistu-0.4.1 → napistu-0.4.3}/src/napistu.egg-info/requires.txt +0 -0
  112. {napistu-0.4.1 → napistu-0.4.3}/src/napistu.egg-info/top_level.txt +0 -0
  113. {napistu-0.4.1 → napistu-0.4.3}/src/tests/__init__.py +0 -0
  114. {napistu-0.4.1 → napistu-0.4.3}/src/tests/conftest.py +0 -0
  115. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_consensus.py +0 -0
  116. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_constants.py +0 -0
  117. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_context_discretize.py +0 -0
  118. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_context_filtering.py +0 -0
  119. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_curation.py +0 -0
  120. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_data/__init__.py +0 -0
  121. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_gaps.py +0 -0
  122. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_gcs.py +0 -0
  123. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_identifiers.py +0 -0
  124. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_indices.py +0 -0
  125. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ingestion_napistu_edgelist.py +0 -0
  126. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ingestion_obo.py +0 -0
  127. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_matching_interactions.py +0 -0
  128. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_matching_mount.py +0 -0
  129. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_matching_species.py +0 -0
  130. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_mcp_config.py +0 -0
  131. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_mcp_documentation_utils.py +0 -0
  132. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_mcp_server.py +0 -0
  133. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_data_handling.py +0 -0
  134. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_neighborhoods.py +0 -0
  135. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_net_create.py +0 -0
  136. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_net_create_utils.py +0 -0
  137. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_ng_core.py +0 -0
  138. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_ng_utils.py +0 -0
  139. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_network_paths.py +0 -0
  140. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ontologies_genodexito.py +0 -0
  141. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ontologies_id_tables.py +0 -0
  142. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ontologies_mygene.py +0 -0
  143. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_ontologies_renaming.py +0 -0
  144. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_pathwayannot.py +0 -0
  145. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_rpy2_callr.py +0 -0
  146. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_rpy2_init.py +0 -0
  147. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_sbml.py +0 -0
  148. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_sbml_dfs_core.py +0 -0
  149. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_sbo.py +0 -0
  150. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_scverse_loading.py +0 -0
  151. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_uncompartmentalize.py +0 -0
  152. {napistu-0.4.1 → napistu-0.4.3}/src/tests/test_utils.py +0 -0
  153. {napistu-0.4.1 → napistu-0.4.3}/src/tests/utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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  Name: napistu
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- Version: 0.4.1
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+ Version: 0.4.3
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  Summary: Connecting high-dimensional data to curated pathways
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  Home-page: https://github.com/napistu/napistu-py
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  Author: Sean Hackett
@@ -1,6 +1,6 @@
1
1
  [metadata]
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  name = napistu
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- version = 0.4.1
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+ version = 0.4.3
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  description = Connecting high-dimensional data to curated pathways
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  long_description = file: README.md
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  long_description_content_type = text/markdown
@@ -426,7 +426,7 @@ def post_consensus_species_ontology_check(sbml_dfs: sbml_dfs_core.SBML_dfs) -> s
426
426
 
427
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  # get the sources of species in the consensus model
428
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  consensus_sbmldf_tbl_var_sc = (
429
- source.unnest_sources(sbml_dfs.species, SBML_DFS.S_SOURCE, verbose=False)
429
+ source.unnest_sources(sbml_dfs.species, verbose=False)
430
430
  .reset_index()
431
431
  .sort_values([SOURCE_SPEC.NAME])
432
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  )
@@ -504,12 +504,11 @@ def post_consensus_source_check(
504
504
  ) -> pd.DataFrame:
505
505
  """Provide sources of tables in a consensus model; the output df will be used to determine whether models are merged."""
506
506
 
507
- table_source = sbml_dfs.schema[table_name][SOURCE_SPEC.SOURCE]
508
- table_pk = sbml_dfs.schema[table_name]["pk"]
507
+ table_pk = sbml_dfs.schema[table_name][SCHEMA_DEFS.PK]
509
508
 
510
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  sbml_dfs_tbl = getattr(sbml_dfs, table_name)
511
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  sbml_dfs_tbl_pathway_source = (
512
- source.unnest_sources(sbml_dfs_tbl, table_source, verbose=False)
511
+ source.unnest_sources(sbml_dfs_tbl, verbose=False)
513
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  .reset_index()
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  .sort_values(["name"])
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  )
@@ -7,7 +7,7 @@ GCS_SUBASSET_NAMES = SimpleNamespace(
7
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  SBML_DFS="sbml_dfs",
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  NAPISTU_GRAPH="napistu_graph",
9
9
  SPECIES_IDENTIFIERS="species_identifiers",
10
- REGULATORY_DISTANCES="regulatory_distances",
10
+ PRECOMPUTED_DISTANCES="precomputed_distances",
11
11
  )
12
12
 
13
13
 
@@ -15,7 +15,7 @@ GCS_FILETYPES = SimpleNamespace(
15
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  SBML_DFS="sbml_dfs.pkl",
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  NAPISTU_GRAPH="napistu_graph.pkl",
17
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  SPECIES_IDENTIFIERS="species_identifiers.tsv",
18
- REGULATORY_DISTANCES="regulatory_distances.parquet",
18
+ PRECOMPUTED_DISTANCES="precomputed_distances.parquet",
19
19
  )
20
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21
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@@ -29,7 +29,7 @@ GCS_ASSETS = SimpleNamespace(
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  GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
30
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  GCS_SUBASSET_NAMES.NAPISTU_GRAPH: GCS_FILETYPES.NAPISTU_GRAPH,
31
31
  GCS_SUBASSET_NAMES.SPECIES_IDENTIFIERS: GCS_FILETYPES.SPECIES_IDENTIFIERS,
32
- GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
32
+ GCS_SUBASSET_NAMES.PRECOMPUTED_DISTANCES: GCS_FILETYPES.PRECOMPUTED_DISTANCES,
33
33
  },
34
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  "public_url": "https://storage.googleapis.com/shackett-napistu-public/test_pathway.tar.gz",
35
35
  },
@@ -48,9 +48,9 @@ GCS_ASSETS = SimpleNamespace(
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  GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
49
49
  GCS_SUBASSET_NAMES.NAPISTU_GRAPH: GCS_FILETYPES.NAPISTU_GRAPH,
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  GCS_SUBASSET_NAMES.SPECIES_IDENTIFIERS: GCS_FILETYPES.SPECIES_IDENTIFIERS,
51
- GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
51
+ GCS_SUBASSET_NAMES.PRECOMPUTED_DISTANCES: GCS_FILETYPES.PRECOMPUTED_DISTANCES,
52
52
  },
53
- "public_url": "https://storage.googleapis.com/calico-cpr-public/human_consensus_w_distances.tar.gz",
53
+ "public_url": "https://storage.googleapis.com/shackett-napistu-public/human_consensus_w_distances.tar.gz",
54
54
  },
55
55
  "reactome_members": {
56
56
  "file": "external_pathways/external_pathways_reactome_neo4j_members.csv",
@@ -3,6 +3,7 @@ from __future__ import annotations
3
3
 
4
4
  from types import SimpleNamespace
5
5
 
6
+ from napistu.constants import SBOTERM_NAMES
6
7
 
7
8
  SPECIES_FULL_NAME_HUMAN = "Homo sapiens"
8
9
  SPECIES_FULL_NAME_MOUSE = "Mus musculus"
@@ -90,6 +91,56 @@ REACTOME_PATHWAYS_URL = "https://reactome.org/download/current/ReactomePathways.
90
91
  REACTOME_PATHWAY_INDEX_COLUMNS = ["file", "source", "species", "pathway_id", "name"]
91
92
  REACTOME_PATHWAY_LIST_COLUMNS = ["pathway_id", "name", "species"]
92
93
 
94
+ # REACTOME FI
95
+ REACTOME_FI_URL = "http://cpws.reactome.org/caBigR3WebApp2025/FIsInGene_04142025_with_annotations.txt.zip"
96
+
97
+ REACTOME_FI = SimpleNamespace(
98
+ GENE1="Gene1",
99
+ GENE2="Gene2",
100
+ ANNOTATION="Annotation",
101
+ DIRECTION="Direction",
102
+ SCORE="Score",
103
+ )
104
+
105
+ REACTOME_FI_DIRECTIONS = SimpleNamespace(
106
+ UNDIRECTED="-",
107
+ STIMULATED_BY="<-",
108
+ STIMULATES="->",
109
+ STIMULATES_AND_STIMULATED_BY="<->",
110
+ INHIBITED_BY="|-",
111
+ INHIBITS="-|",
112
+ INHIBITS_AND_INHIBITED_BY="|-|",
113
+ STIMULATES_AND_INHIBITED_BY="|->",
114
+ INHIBITS_AND_STIMULATED_BY="<-|",
115
+ )
116
+
117
+ VALID_REACTOME_FI_DIRECTIONS = REACTOME_FI_DIRECTIONS.__dict__.values()
118
+
119
+ REACTOME_FI_RULES_REVERSE = SimpleNamespace(
120
+ NAME_RULES={"catalyzed by": SBOTERM_NAMES.CATALYST},
121
+ DIRECTION_RULES={
122
+ REACTOME_FI_DIRECTIONS.STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
123
+ REACTOME_FI_DIRECTIONS.STIMULATES_AND_STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
124
+ REACTOME_FI_DIRECTIONS.INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
125
+ REACTOME_FI_DIRECTIONS.INHIBITS_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
126
+ REACTOME_FI_DIRECTIONS.STIMULATES_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
127
+ REACTOME_FI_DIRECTIONS.UNDIRECTED: SBOTERM_NAMES.INTERACTOR,
128
+ },
129
+ )
130
+
131
+ REACTOME_FI_RULES_FORWARD = SimpleNamespace(
132
+ NAME_RULES={"catalyze(;$)": SBOTERM_NAMES.CATALYST},
133
+ DIRECTION_RULES={
134
+ REACTOME_FI_DIRECTIONS.STIMULATES: SBOTERM_NAMES.STIMULATOR,
135
+ REACTOME_FI_DIRECTIONS.STIMULATES_AND_STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
136
+ REACTOME_FI_DIRECTIONS.STIMULATES_AND_INHIBITED_BY: SBOTERM_NAMES.STIMULATOR,
137
+ REACTOME_FI_DIRECTIONS.INHIBITS: SBOTERM_NAMES.INHIBITOR,
138
+ REACTOME_FI_DIRECTIONS.INHIBITS_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
139
+ REACTOME_FI_DIRECTIONS.INHIBITS_AND_STIMULATED_BY: SBOTERM_NAMES.INHIBITOR,
140
+ REACTOME_FI_DIRECTIONS.UNDIRECTED: SBOTERM_NAMES.INTERACTOR,
141
+ },
142
+ )
143
+
93
144
  # SBML
94
145
  SBML_DEFS = SimpleNamespace(
95
146
  ERROR_NUMBER="error_number",
@@ -0,0 +1,208 @@
1
+ import logging
2
+ import pandas as pd
3
+
4
+ from napistu.identifiers import Identifiers
5
+ from napistu import utils
6
+ from napistu.ingestion.constants import (
7
+ REACTOME_FI,
8
+ REACTOME_FI_RULES_FORWARD,
9
+ REACTOME_FI_RULES_REVERSE,
10
+ REACTOME_FI_URL,
11
+ VALID_REACTOME_FI_DIRECTIONS,
12
+ )
13
+
14
+
15
+ logger = logging.getLogger(__name__)
16
+
17
+
18
+ def download_reactome_fi(target_uri: str, url: str = REACTOME_FI_URL) -> None:
19
+ """
20
+ Download the Reactome Functional Interactions (FI) dataset as a TSV file.
21
+
22
+ Parameters
23
+ ----------
24
+ target_uri : str
25
+ The URI where the Reactome FI data should be saved. Should end with .tsv
26
+ url : str, optional
27
+ URL to download the zipped Reactome functional interactions TSV from.
28
+ Defaults to REACTOME_FI_URL.
29
+
30
+ Returns
31
+ -------
32
+ None
33
+
34
+ Raises
35
+ ------
36
+ ValueError
37
+ If target_uri does not end with .tsv
38
+ """
39
+
40
+ if not target_uri.endswith(".tsv"):
41
+ raise ValueError(f"Target URI must end with .tsv, got {target_uri}")
42
+
43
+ file_ext = url.split(".")[-1]
44
+ target_filename = url.split("/")[-1].split(f".{file_ext}")[0]
45
+ logger.info("Start downloading proteinatlas %s to %s", url, target_uri)
46
+ # target_filename is the name of the file in the zip file which will be renamed to target_uri
47
+ utils.download_wget(url, target_uri, target_filename=target_filename)
48
+
49
+ return None
50
+
51
+
52
+ def format_reactome_fi_edgelist(interactions: pd.DataFrame):
53
+ """
54
+ Format the Reactome FI interactions DataFrame as an edgelist for network analysis.
55
+
56
+ Parameters
57
+ ----------
58
+ interactions : pd.DataFrame
59
+ DataFrame containing Reactome FI interactions.
60
+
61
+ Returns
62
+ -------
63
+ Dictonary of:
64
+
65
+ interaction_edgelist : pd.DataFrame
66
+ Table containing molecular interactions with columns:
67
+ - upstream_name : str, matches "s_name" from species_df
68
+ - downstream_name : str, matches "s_name" from species_df
69
+ - upstream_compartment : str, matches "c_name" from compartments_df
70
+ - downstream_compartment : str, matches "c_name" from compartments_df
71
+ - r_name : str, name for the interaction
72
+ - sbo_term : str, SBO term defining interaction type
73
+ - r_Identifiers : identifiers.Identifiers, supporting identifiers
74
+ - r_isreversible : bool, whether reaction is reversible
75
+ species_df : pd.DataFrame
76
+ Table defining molecular species with columns:
77
+ - s_name : str, name of molecular species
78
+ - s_Identifiers : identifiers.Identifiers, species identifiers
79
+ compartments_df : pd.DataFrame
80
+ Table defining compartments with columns:
81
+ - c_name : str, name of compartment
82
+ - c_Identifiers : identifiers.Identifiers, compartment identifiers
83
+
84
+ Notes
85
+ -----
86
+ This function is not yet implemented and will raise NotImplementedError.
87
+ """
88
+
89
+ raise NotImplementedError("TO DO - This function is incomplete")
90
+
91
+ formatted_annotations = _parse_reactome_fi_annotations(interactions)
92
+
93
+ # this join will expand some rows to 2 since the bidirectional relationships are captured as separate edges in Napistu
94
+ annotated_interactions = interactions.merge(
95
+ formatted_annotations,
96
+ on=[REACTOME_FI.ANNOTATION, REACTOME_FI.DIRECTION],
97
+ how="left",
98
+ )
99
+
100
+ # flip reverse entries so all relationships are forward or undirected
101
+ formatted_interactions = (
102
+ pd.concat(
103
+ [
104
+ annotated_interactions.query("polarity == 'forward'"),
105
+ (
106
+ annotated_interactions.query("polarity == 'reverse'").rename(
107
+ columns={
108
+ REACTOME_FI.GENE1: REACTOME_FI.GENE2,
109
+ REACTOME_FI.GENE2: REACTOME_FI.GENE1,
110
+ }
111
+ )
112
+ ),
113
+ ]
114
+ )[[REACTOME_FI.GENE1, REACTOME_FI.GENE2, "sbo_term_name", "Score"]]
115
+ # looks like they were already unique edges
116
+ .sort_values("Score", ascending=False)
117
+ .groupby([REACTOME_FI.GENE1, REACTOME_FI.GENE2])
118
+ .first()
119
+ )
120
+
121
+ fi_edgelist = (
122
+ formatted_interactions.reset_index()
123
+ .rename(
124
+ columns={
125
+ REACTOME_FI.GENE1: "upstream_name",
126
+ REACTOME_FI.GENE2: "downstream_name",
127
+ }
128
+ )
129
+ .assign(r_Identifiers=Identifiers([]))
130
+ )
131
+
132
+ return fi_edgelist
133
+
134
+
135
+ def _parse_reactome_fi_annotations(interactions: pd.DataFrame) -> pd.DataFrame:
136
+ """
137
+ Parse and annotate Reactome FI interaction types and directions using regex-based rules.
138
+
139
+ Parameters
140
+ ----------
141
+ interactions : pd.DataFrame
142
+ DataFrame containing Reactome FI interactions, with annotation and direction columns.
143
+
144
+ Returns
145
+ -------
146
+ pd.DataFrame
147
+ DataFrame with annotation, direction, SBO term name, and polarity for each unique annotation/direction pair.
148
+
149
+ Raises
150
+ ------
151
+ ValueError
152
+ If an annotation/direction pair cannot be matched to a rule or if invalid directions are found.
153
+ """
154
+
155
+ distinct_annotations = (
156
+ interactions[[REACTOME_FI.ANNOTATION, REACTOME_FI.DIRECTION]]
157
+ .drop_duplicates()
158
+ .reset_index(drop=True)
159
+ )
160
+ invalid_directions = distinct_annotations.loc[
161
+ ~distinct_annotations[REACTOME_FI.DIRECTION].isin(VALID_REACTOME_FI_DIRECTIONS),
162
+ "Direction",
163
+ ]
164
+ if len(invalid_directions) > 0:
165
+ raise ValueError(f"Invalid directions: {invalid_directions}")
166
+
167
+ annotations = list()
168
+ for _, vals in distinct_annotations.iterrows():
169
+ annot, direction = vals
170
+
171
+ forward_match = utils.match_regex_dict(
172
+ annot, REACTOME_FI_RULES_FORWARD.NAME_RULES
173
+ )
174
+ if not forward_match:
175
+ if direction in REACTOME_FI_RULES_FORWARD.DIRECTION_RULES:
176
+ forward_match = REACTOME_FI_RULES_FORWARD.DIRECTION_RULES[direction]
177
+
178
+ reverse_match = utils.match_regex_dict(
179
+ annot, REACTOME_FI_RULES_REVERSE.NAME_RULES
180
+ )
181
+ if not reverse_match:
182
+ if direction in REACTOME_FI_RULES_REVERSE.DIRECTION_RULES:
183
+ reverse_match = REACTOME_FI_RULES_REVERSE.DIRECTION_RULES[direction]
184
+
185
+ if not (forward_match or reverse_match):
186
+ raise ValueError(f"No match found for {annot} with direction {direction}")
187
+
188
+ if forward_match:
189
+ annotations.append(
190
+ {
191
+ REACTOME_FI.ANNOTATION: annot,
192
+ REACTOME_FI.DIRECTION: direction,
193
+ "sbo_term_name": forward_match,
194
+ "polarity": "forward",
195
+ }
196
+ )
197
+
198
+ if reverse_match:
199
+ annotations.append(
200
+ {
201
+ REACTOME_FI.ANNOTATION: annot,
202
+ REACTOME_FI.DIRECTION: direction,
203
+ "sbo_term_name": reverse_match,
204
+ "polarity": "reverse",
205
+ }
206
+ )
207
+
208
+ return pd.DataFrame(annotations)
@@ -4,6 +4,7 @@ from __future__ import annotations
4
4
 
5
5
  from types import SimpleNamespace
6
6
 
7
+
7
8
  from napistu.constants import SBML_DFS
8
9
  from napistu.constants import SBOTERM_NAMES
9
10
 
@@ -13,7 +14,7 @@ NAPISTU_GRAPH_DIRECTEDNESS = SimpleNamespace(
13
14
  DIRECTED="directed", UNDIRECTED="undirected"
14
15
  )
15
16
 
16
- NAPISTU_GRAPH_NODES = SimpleNamespace(NAME="name")
17
+ NAPISTU_GRAPH_VERTICES = SimpleNamespace(NAME="name")
17
18
 
18
19
  NAPISTU_GRAPH_EDGES = SimpleNamespace(
19
20
  DIRECTED="directed",
@@ -198,3 +199,24 @@ SCORE_CALIBRATION_POINTS_DICT = {
198
199
  }
199
200
 
200
201
  SOURCE_VARS_DICT = {"string_wt": 10}
202
+
203
+ # network propagation
204
+ NET_PROPAGATION_DEFS = SimpleNamespace(PERSONALIZED_PAGERANK="personalized_pagerank")
205
+
206
+ # null distributions
207
+ NULL_STRATEGIES = SimpleNamespace(
208
+ UNIFORM="uniform",
209
+ PARAMETRIC="parametric",
210
+ NODE_PERMUTATION="node_permutation",
211
+ EDGE_PERMUTATION="edge_permutation",
212
+ )
213
+
214
+ VALID_NULL_STRATEGIES = NULL_STRATEGIES.__dict__.values()
215
+
216
+ PARAMETRIC_NULL_DEFAULT_DISTRIBUTION = "norm"
217
+
218
+ # masks
219
+
220
+ MASK_KEYWORDS = SimpleNamespace(
221
+ ATTR="attr",
222
+ )
@@ -9,7 +9,7 @@ from __future__ import annotations
9
9
 
10
10
  import logging
11
11
  import random
12
- from typing import Any, Optional, Sequence
12
+ from typing import Any, Optional, Sequence, List, Dict, Union
13
13
 
14
14
  import igraph as ig
15
15
  import numpy as np
@@ -384,3 +384,163 @@ def _get_top_n_nodes(
384
384
  top_node_attrs = [graph.vs[idx].attributes() for idx in top_idxs]
385
385
  top_vals = [vals[idx] for idx in top_idxs]
386
386
  return [{val_name: val, **node} for val, node in zip(top_vals, top_node_attrs)]
387
+
388
+
389
+ def _parse_mask_input(
390
+ mask_input: Optional[Union[str, np.ndarray, List, Dict]], attributes: List[str]
391
+ ) -> Dict[str, Union[str, np.ndarray, List, None]]:
392
+ """
393
+ Parse mask input and convert to attribute-specific mask specifications.
394
+
395
+ Parameters
396
+ ----------
397
+ mask_input : str, np.ndarray, List, Dict, or None
398
+ Mask specification that can be:
399
+ - None: use all nodes for all attributes
400
+ - "attr": use each attribute as its own mask
401
+ - np.ndarray/List: use same mask for all attributes
402
+ - Dict: attribute-specific mask specifications
403
+ attributes : List[str]
404
+ List of attribute names.
405
+
406
+ Returns
407
+ -------
408
+ Dict[str, Union[str, np.ndarray, List, None]]
409
+ Dictionary mapping each attribute to its mask specification.
410
+ """
411
+ if mask_input is None:
412
+ return {attr: None for attr in attributes}
413
+ elif isinstance(mask_input, str):
414
+ if mask_input == "attr":
415
+ return {attr: attr for attr in attributes}
416
+ else:
417
+ # Single attribute name used for all
418
+ return {attr: mask_input for attr in attributes}
419
+ elif isinstance(mask_input, (np.ndarray, list)):
420
+ # Same mask for all attributes
421
+ return {attr: mask_input for attr in attributes}
422
+ elif isinstance(mask_input, dict):
423
+ # Validate all attributes are present
424
+ for attr in attributes:
425
+ if attr not in mask_input:
426
+ raise ValueError(f"Attribute '{attr}' not found in mask dictionary")
427
+ return mask_input
428
+ else:
429
+ raise ValueError(f"Invalid mask input type: {type(mask_input)}")
430
+
431
+
432
+ def _get_attribute_masks(
433
+ graph: ig.Graph,
434
+ mask_specs: Dict[str, Union[str, np.ndarray, List, None]],
435
+ ) -> Dict[str, np.ndarray]:
436
+ """
437
+ Generate boolean masks for each attribute based on specifications.
438
+
439
+ Parameters
440
+ ----------
441
+ graph : ig.Graph
442
+ Input graph.
443
+ attributes : List[str]
444
+ List of attribute names.
445
+ mask_specs : Dict[str, Union[str, np.ndarray, List, None]]
446
+ Dictionary mapping each attribute to its mask specification.
447
+
448
+ Returns
449
+ -------
450
+ Dict[str, np.ndarray]
451
+ Dictionary mapping each attribute to its boolean mask array.
452
+ """
453
+ n_nodes = graph.vcount()
454
+ masks = {}
455
+
456
+ invalid_attrs = set(mask_specs.keys()).difference(graph.vs.attributes())
457
+ if invalid_attrs:
458
+ raise ValueError(f"Attributes {invalid_attrs} not found in graph")
459
+
460
+ for attr in mask_specs.keys():
461
+
462
+ mask_spec = mask_specs[attr]
463
+
464
+ if mask_spec is None:
465
+ masks[attr] = np.ones(n_nodes, dtype=bool)
466
+ elif isinstance(mask_spec, str):
467
+ attr_values = np.array(graph.vs[mask_spec])
468
+ masks[attr] = attr_values > 0
469
+ elif isinstance(mask_spec, np.ndarray):
470
+ masks[attr] = mask_spec.astype(bool)
471
+ elif isinstance(mask_spec, list):
472
+ mask_array = np.zeros(n_nodes, dtype=bool)
473
+ if isinstance(mask_spec[0], str):
474
+ # Node names
475
+ node_names = (
476
+ graph.vs["name"] if "name" in graph.vs.attributes() else None
477
+ )
478
+ if node_names is None:
479
+ raise ValueError("Graph has no 'name' attribute for string mask")
480
+ for name in mask_spec:
481
+ idx = node_names.index(name)
482
+ mask_array[idx] = True
483
+ else:
484
+ # Node indices
485
+ mask_array[mask_spec] = True
486
+ masks[attr] = mask_array
487
+ else:
488
+ raise ValueError(
489
+ f"Invalid mask specification for attribute '{attr}': {type(mask_spec)}"
490
+ )
491
+
492
+ return masks
493
+
494
+
495
+ def _ensure_valid_attribute(graph: ig.Graph, attribute: str, non_negative: bool = True):
496
+ """
497
+ Ensure a vertex attribute is present, numeric, and optionally non-negative for all vertices.
498
+
499
+ This utility checks that the specified vertex attribute exists, is numeric, and (optionally) non-negative
500
+ for all vertices in the graph. Missing or None values are treated as 0. Raises ValueError
501
+ if the attribute is missing for all vertices, if all values are zero, or if any value is negative (if non_negative=True).
502
+
503
+ Parameters
504
+ ----------
505
+ graph : NapistuGraph or ig.Graph
506
+ The input graph (NapistuGraph or igraph.Graph).
507
+ attribute : str
508
+ The name of the vertex attribute to check.
509
+ non_negative : bool, default True
510
+ Whether to require all values to be non-negative.
511
+
512
+ Returns
513
+ -------
514
+ np.ndarray
515
+ Array of attribute values (with missing/None replaced by 0).
516
+
517
+ Raises
518
+ ------
519
+ ValueError
520
+ If the attribute is missing for all vertices, all values are zero, or any value is negative (if non_negative=True).
521
+ """
522
+ all_missing = all(
523
+ (attribute not in v.attributes() or v[attribute] is None) for v in graph.vs
524
+ )
525
+ if all_missing:
526
+ raise ValueError(f"Vertex attribute '{attribute}' is missing for all vertices.")
527
+
528
+ values = [
529
+ (
530
+ v[attribute]
531
+ if (attribute in v.attributes() and v[attribute] is not None)
532
+ else 0.0
533
+ )
534
+ for v in graph.vs
535
+ ]
536
+
537
+ arr = np.array(values, dtype=float)
538
+
539
+ if np.all(arr == 0):
540
+ raise ValueError(
541
+ f"Vertex attribute '{attribute}' is zero for all vertices; cannot use as reset vector."
542
+ )
543
+ if non_negative and np.any(arr < 0):
544
+ raise ValueError(f"Attribute '{attribute}' contains negative values.")
545
+
546
+ return arr
@@ -26,7 +26,7 @@ from napistu.constants import (
26
26
  )
27
27
 
28
28
  from napistu.network.constants import (
29
- NAPISTU_GRAPH_NODES,
29
+ NAPISTU_GRAPH_VERTICES,
30
30
  NAPISTU_GRAPH_EDGES,
31
31
  NAPISTU_GRAPH_EDGE_DIRECTIONS,
32
32
  NAPISTU_GRAPH_NODE_TYPES,
@@ -152,7 +152,7 @@ def create_napistu_graph(
152
152
 
153
153
  # rename nodes to name since it is treated specially
154
154
  network_nodes_df = pd.concat(network_nodes).rename(
155
- columns={"node_id": NAPISTU_GRAPH_NODES.NAME}
155
+ columns={"node_id": NAPISTU_GRAPH_VERTICES.NAME}
156
156
  )
157
157
 
158
158
  logger.info(f"Formatting edges as a {wiring_approach} graph")
@@ -234,7 +234,7 @@ def create_napistu_graph(
234
234
  vertices=network_nodes_df.to_dict("records"),
235
235
  edges=unique_edges.to_dict("records"),
236
236
  directed=directed,
237
- vertex_name_attr=NAPISTU_GRAPH_NODES.NAME,
237
+ vertex_name_attr=NAPISTU_GRAPH_VERTICES.NAME,
238
238
  edge_foreign_keys=(NAPISTU_GRAPH_EDGES.FROM, NAPISTU_GRAPH_EDGES.TO),
239
239
  )
240
240