pheval 0.1.0__tar.gz → 0.2.0__tar.gz

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Files changed (46) hide show
  1. {pheval-0.1.0 → pheval-0.2.0}/PKG-INFO +12 -4
  2. pheval-0.2.0/pyproject.toml +66 -0
  3. pheval-0.2.0/src/pheval/analyse/__init__.py +0 -0
  4. pheval-0.2.0/src/pheval/analyse/analysis.py +703 -0
  5. pheval-0.2.0/src/pheval/analyse/generate_plots.py +312 -0
  6. pheval-0.2.0/src/pheval/analyse/generate_summary_outputs.py +186 -0
  7. pheval-0.2.0/src/pheval/analyse/rank_stats.py +61 -0
  8. {pheval-0.1.0 → pheval-0.2.0}/src/pheval/cli.py +22 -7
  9. {pheval-0.1.0 → pheval-0.2.0}/src/pheval/cli_pheval.py +37 -12
  10. pheval-0.2.0/src/pheval/cli_pheval_utils.py +246 -0
  11. pheval-0.2.0/src/pheval/config_parser.py +36 -0
  12. pheval-0.2.0/src/pheval/constants.py +1 -0
  13. {pheval-0.1.0 → pheval-0.2.0}/src/pheval/implementations/__init__.py +1 -3
  14. pheval-0.2.0/src/pheval/post_processing/__init__.py +0 -0
  15. pheval-0.2.0/src/pheval/post_processing/post_processing.py +210 -0
  16. pheval-0.2.0/src/pheval/prepare/__init__.py +0 -0
  17. pheval-0.2.0/src/pheval/prepare/create_noisy_phenopackets.py +173 -0
  18. pheval-0.2.0/src/pheval/prepare/create_spiked_vcf.py +366 -0
  19. pheval-0.2.0/src/pheval/prepare/custom_exceptions.py +47 -0
  20. pheval-0.2.0/src/pheval/prepare/update_phenopacket.py +53 -0
  21. pheval-0.2.0/src/pheval/resources/alternate_ouputs/CADA_results.txt +11 -0
  22. pheval-0.2.0/src/pheval/resources/alternate_ouputs/DeepPVP_results.txt +22 -0
  23. pheval-0.2.0/src/pheval/resources/alternate_ouputs/OVA_results.txt +11 -0
  24. pheval-0.2.0/src/pheval/resources/alternate_ouputs/Phen2Gene_results.json +814 -0
  25. pheval-0.2.0/src/pheval/resources/alternate_ouputs/Phenolyzer_results.txt +12 -0
  26. pheval-0.2.0/src/pheval/resources/alternate_ouputs/lirical_results.tsv +152 -0
  27. pheval-0.2.0/src/pheval/resources/alternate_ouputs/svanna_results.tsv +9 -0
  28. pheval-0.2.0/src/pheval/resources/hgnc_complete_set_2022-10-01.txt +43222 -0
  29. pheval-0.2.0/src/pheval/run_metadata.py +27 -0
  30. pheval-0.2.0/src/pheval/runners/__init__.py +0 -0
  31. pheval-0.2.0/src/pheval/runners/runner.py +132 -0
  32. pheval-0.2.0/src/pheval/utils/__init__.py +0 -0
  33. pheval-0.2.0/src/pheval/utils/docs_gen.py +105 -0
  34. pheval-0.2.0/src/pheval/utils/docs_gen.sh +18 -0
  35. pheval-0.2.0/src/pheval/utils/file_utils.py +88 -0
  36. pheval-0.2.0/src/pheval/utils/phenopacket_utils.py +356 -0
  37. pheval-0.2.0/src/pheval/utils/semsim_utils.py +156 -0
  38. pheval-0.1.0/pyproject.toml +0 -33
  39. pheval-0.1.0/setup.py +0 -44
  40. pheval-0.1.0/src/pheval/__init__.py +0 -5
  41. pheval-0.1.0/src/pheval/cli_pheval_utils.py +0 -29
  42. pheval-0.1.0/src/pheval/runners/runner.py +0 -51
  43. pheval-0.1.0/src/pheval/utils.py +0 -7
  44. {pheval-0.1.0 → pheval-0.2.0}/LICENSE +0 -0
  45. {pheval-0.1.0 → pheval-0.2.0}/README.md +0 -0
  46. {pheval-0.1.0/src/pheval/runners → pheval-0.2.0/src/pheval}/__init__.py +0 -0
{pheval-0.1.0 → pheval-0.2.0}/PKG-INFO RENAMED
@@ -1,10 +1,10 @@
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  Metadata-Version: 2.1
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  Name: pheval
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- Version: 0.1.0
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+ Version: 0.2.0
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  Summary:
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- Author: Nico Matentzoglu
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- Author-email: nicolas.matentzoglu@gmail.com
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- Requires-Python: >=3.9
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+ Author: Yasemin Bridges
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+ Author-email: y.bridges@qmul.ac.uk
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+ Requires-Python: >=3.9,<4.0.0
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  Classifier: Programming Language :: Python :: 3
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  Classifier: Programming Language :: Python :: 3.9
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  Classifier: Programming Language :: Python :: 3.10
@@ -12,8 +12,16 @@ Classifier: Programming Language :: Python :: 3.11
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  Requires-Dist: class-resolver (>=0.3.10,<0.4.0)
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  Requires-Dist: click (>=8.1.3)
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  Requires-Dist: deprecation (>=2.1.0)
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+ Requires-Dist: google (>=3.0.0,<4.0.0)
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  Requires-Dist: jaydebeapi (>=1.2.3)
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+ Requires-Dist: matplotlib (>=3.7.0,<4.0.0)
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+ Requires-Dist: oaklib (>=0.1.55,<0.2.0)
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  Requires-Dist: pandas (>=1.5.1)
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+ Requires-Dist: phenopackets (>=2.0.2,<3.0.0)
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+ Requires-Dist: plotly (>=5.13.0,<6.0.0)
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+ Requires-Dist: pyaml (>=21.10.1,<22.0.0)
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+ Requires-Dist: pyserde (>=0.9.8,<0.10.0)
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+ Requires-Dist: seaborn (>=0.12.2,<0.13.0)
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  Requires-Dist: tqdm (>=4.64.1)
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  Description-Content-Type: text/markdown
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pheval-0.2.0/pyproject.toml ADDED
@@ -0,0 +1,66 @@
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+ [tool.poetry]
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+ name = "pheval"
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+ version = "0.2.0"
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+ description = ""
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+ authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
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+ "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
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+ "Nico Matentzoglu <nicolas.matentzoglu@gmail.com>",
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+ "Vinícius de Souza <souzadevinicius@gmail.com>"]
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+ readme = "README.md"
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+ packages = [{include = "pheval", from = "src"}]
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+
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+ [tool.poetry.dependencies]
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+ python = ">=3.9,<4.0.0"
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+ jaydebeapi = ">=1.2.3"
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+ tqdm = ">=4.64.1"
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+ pandas = ">=1.5.1"
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+ deprecation = ">=2.1.0"
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+ click = ">=8.1.3"
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+ class-resolver = "^0.3.10"
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+ phenopackets = "^2.0.2"
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+ oaklib = "^0.1.55"
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+ google = "^3.0.0"
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+ pyaml = "^21.10.1"
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+ plotly = "^5.13.0"
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+ seaborn = "^0.12.2"
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+ matplotlib = "^3.7.0"
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+ pyserde = "^0.9.8"
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+
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+ [tool.poetry.dev-dependencies]
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+ pytest = "^7.2.0"
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+ coverage = "^6.5.0"
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+
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+ [tool.poetry.scripts]
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+ pheval = "pheval.cli:pheval"
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+ pheval-utils = "pheval.cli:pheval_utils"
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+
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+ [tool.poetry.group.docs.dependencies]
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+ mkdocs = "^1.4.2"
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+ pymdown-extensions = "^9.9"
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+ mkdocs-material = "^8.5.11"
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+ mkdocstrings = "^0.19.1"
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+ mkdocstrings-python = "^0.8.2"
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+ mkdocs-include-dir-to-nav = "^1.2.0"
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+ mkdocs-click = "^0.8.0"
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+ [tool.poetry.group.dev.dependencies]
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+ black = "^22.12.0"
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+
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+ [tool.pytest.ini_options]
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+ pythonpath = [
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+ "src"
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+ ]
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+
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+ [tool.black]
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+ line-length = 100
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+ target-version = ["py39", "py310"]
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+
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+ [tool.isort]
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+ profile = "black"
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+ multi_line_output = 3
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+ line_length = 100
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+ include_trailing_comma = true
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+ reverse_relative = true
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+
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+ [build-system]
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+ requires = ["poetry-core"]
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+ build-backend = "poetry.core.masonry.api"
pheval-0.2.0/src/pheval/analyse/__init__.py ADDED
File without changes