pheval 0.6.3__py3-none-any.whl → 0.6.5__py3-none-any.whl

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Files changed (32) hide show
  1. pheval/analyse/benchmark.py +10 -25
  2. pheval/analyse/benchmark_output_type.py +12 -5
  3. pheval/analyse/binary_classification_curves.py +3 -9
  4. pheval/analyse/binary_classification_stats.py +1 -4
  5. pheval/analyse/generate_plots.py +8 -18
  6. pheval/analyse/generate_rank_comparisons.py +1 -2
  7. pheval/analyse/rank_stats.py +8 -25
  8. pheval/analyse/run_data_parser.py +9 -12
  9. pheval/cli.py +1 -1
  10. pheval/cli_pheval_utils.py +10 -23
  11. pheval/config_parser.py +1 -1
  12. pheval/implementations/__init__.py +3 -5
  13. pheval/infra/exomiserdb.py +7 -15
  14. pheval/post_processing/phenopacket_truth_set.py +10 -31
  15. pheval/post_processing/post_processing.py +12 -33
  16. pheval/post_processing/validate_result_format.py +2 -4
  17. pheval/prepare/create_noisy_phenopackets.py +18 -29
  18. pheval/prepare/create_spiked_vcf.py +25 -56
  19. pheval/prepare/custom_exceptions.py +6 -7
  20. pheval/prepare/prepare_corpus.py +6 -17
  21. pheval/prepare/update_phenopacket.py +6 -17
  22. pheval/utils/docs_gen.py +3 -3
  23. pheval/utils/file_utils.py +1 -2
  24. pheval/utils/phenopacket_utils.py +41 -73
  25. pheval/utils/semsim_utils.py +6 -10
  26. pheval/utils/utils.py +3 -4
  27. {pheval-0.6.3.dist-info → pheval-0.6.5.dist-info}/METADATA +1 -1
  28. pheval-0.6.5.dist-info/RECORD +57 -0
  29. pheval-0.6.3.dist-info/RECORD +0 -57
  30. {pheval-0.6.3.dist-info → pheval-0.6.5.dist-info}/LICENSE +0 -0
  31. {pheval-0.6.3.dist-info → pheval-0.6.5.dist-info}/WHEEL +0 -0
  32. {pheval-0.6.3.dist-info → pheval-0.6.5.dist-info}/entry_points.txt +0 -0
pheval-0.6.3.dist-info/RECORD DELETED
@@ -1,57 +0,0 @@
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- pheval/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- pheval/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- pheval/analyse/benchmark.py,sha256=s4ZHsvnZY9XNsbbBp_0JEny1bUpxLbcg0ls3J-wUtC8,7085
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- pheval/analyse/benchmark_db_manager.py,sha256=zS1TI76YuV2_YXLipHLSyh-XDR5kTxyOwhRhHRFHfjQ,764
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- pheval/analyse/benchmark_output_type.py,sha256=CBZmRhfz_g7cegYlZtcK2j18YY0iwjjAgNdb70sQiSM,1513
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- pheval/analyse/binary_classification_curves.py,sha256=Crb45rJWc5rxDdx82sgoHRvYHE2D5pus91fgl39FyRw,5007
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- pheval/analyse/binary_classification_stats.py,sha256=sOuEp6IxZ6SVp-KC6MJkZNTkZucZTNK25xApP5tU6Mk,6944
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- pheval/analyse/generate_plots.py,sha256=g98DxhTw1dPRfRRYoKBmt51XfIa2KzlL_Z7weFSoBUg,14550
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- pheval/analyse/generate_rank_comparisons.py,sha256=KcQJ9rm1nvvTcqLNuxAkXRXuV18vEsiP0giQ-ryHyYc,1684
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- pheval/analyse/rank_stats.py,sha256=JLgbaumayUzVzpRh0IXlY7454HWShVJQVImifC0U4GA,8489
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- pheval/analyse/run_data_parser.py,sha256=UjuC9R2Ag3v6BDU-xjVn1iFfYDQLlmE2ajl5gXwF9uQ,3688
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- pheval/cli.py,sha256=Yow7JLwYvtFc8W1U0V1g5bzxMICsv05NWm2PAsFwqvM,1591
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- pheval/cli_pheval.py,sha256=N8xp3r8avYqLswPhakxtTQyemVdgHAvnpAIj_FmoN5k,3510
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- pheval/cli_pheval_utils.py,sha256=sh6kx36jYfuSIWBMlrdW3g-LPftxBy-xw4b7hg8bdj4,16545
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- pheval/config_parser.py,sha256=eUa1wMRuCy2iq-oRSxTZGltLxaw5NjsISN2GRBpuQWM,1358
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- pheval/implementations/__init__.py,sha256=L0y_qPxKGcm4zCi-YmPa_YgtYoD9QsL7IHqoB7bfO4Y,1346
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- pheval/implementations/pheval_class_resolver.py,sha256=YNNk3PoQbSvbKmbihlt_bsHNxRM95O-VrtUIbQnfBcw,1567
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- pheval/infra/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- pheval/infra/exomiserdb.py,sha256=pM9-TfjrgurtH4OtM1Enk5oVhIxGQN3rKRlrxHuObTM,5080
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- pheval/post_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
21
- pheval/post_processing/mondo_mapping.py,sha256=Vetk0acOtR__FXnx9wy2pcDDWFz1mQkc88alKUn0muI,937
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- pheval/post_processing/phenopacket_truth_set.py,sha256=xSP9uu6Qxuog4HFXJiRJdBdQXn6GLSKBgSDpH4TtgD4,10301
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- pheval/post_processing/post_processing.py,sha256=g99MBjGzl5qPi8CK6CLKH0XAFdkt1uSye25VbzqV1Kg,10166
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- pheval/post_processing/validate_result_format.py,sha256=w7zbpbS-fxwQuUwkqJPsD2nQV4SZxxVk3e7-MZEBV8I,2891
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- pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
26
- pheval/prepare/create_noisy_phenopackets.py,sha256=kYFwQjBJN6gla2I51X3zfucVmnRB7kwH2uqi1ElWzkg,12291
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- pheval/prepare/create_spiked_vcf.py,sha256=dxl2LlAzekc8-Awd5RRVdya5UTqmlFqtQ7jpok5bJa4,24666
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- pheval/prepare/custom_exceptions.py,sha256=_G3_95dPtHIs1SviYBV1j7cYc-hxlhuw8hhnYdzByYY,1719
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- pheval/prepare/prepare_corpus.py,sha256=iOV3g3s01uwoFbE-bVdv3ORiSc7B01MmvswUteLA5VA,5458
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- pheval/prepare/update_phenopacket.py,sha256=uPwc5kJR5j_IGigUlszWj0pW5XjzvkuhsEBGsrJs7gk,5651
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- pheval/resources/alternate_ouputs/CADA_results.txt,sha256=Rinn2TtfwFNsx0aEWegKJOkjKnBm-Mf54gdaT3bWP0k,547
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- pheval/resources/alternate_ouputs/DeepPVP_results.txt,sha256=MF9MZJYa4r4PEvFzALpi-lNGLxjENOnq_YgrgFMn-oQ,1508
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- pheval/resources/alternate_ouputs/OVA_results.txt,sha256=_5XFCR4W04D-W7DObpALLsa0-693g2kiIUB_uo79aHk,9845
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- pheval/resources/alternate_ouputs/Phen2Gene_results.json,sha256=xxKsuiHKW9qQOz2baFlLW9RYphA4kxjoTsg1weZkTY8,14148
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- pheval/resources/alternate_ouputs/Phenolyzer_results.txt,sha256=TltiEzYm2PY79u6EdZR3f4ZqadNDCUN_d4f0TFF-t5A,594
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- pheval/resources/alternate_ouputs/lirical_results.tsv,sha256=0juf5HY6ttg-w7aWgYJUmSP5zmoaooEQDY8xhOcerLk,431068
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- pheval/resources/alternate_ouputs/svanna_results.tsv,sha256=OpTamPhJwh12wkdAxoIGb0wWs_T7TcqNWgqkQzgOek4,714
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- pheval/resources/hgnc_complete_set.txt,sha256=9-aNcyGZzarD1DnO_780NK0r-ppwbyu9e4-cQDmtUC8,16593567
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- pheval/resources/metadata.json,sha256=aabSMPCwE-KR6cAxBCMRZmDD1fGD7qCeSvPLduvO3gA,112
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- pheval/resources/mondo.sssom.tsv,sha256=Egu8UqHPL6TbSRQKlRgQ7kNq5S4e1VElR5JWHWgc7F0,12700455
41
- pheval/run_metadata.py,sha256=isEs63c-O6LZ6TBmk9wmAOmzjNE3Nf_k9V9uiYu0x8s,1122
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- pheval/runners/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
43
- pheval/runners/runner.py,sha256=zkS6yvbnC6UBCtV2VR3FEfr5naWRDdNcQFN1CoH1ha8,4902
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- pheval/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
45
- pheval/utils/docs_gen.py,sha256=6FGtHicBC0rZKi0tdL3Epsg8d4osE44I9f1Ga0j4JLA,3193
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- pheval/utils/docs_gen.sh,sha256=LyKLKjaZuf4UJ962CWfM-XqkxtvM8O2N9wHZS5mcb9A,477
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- pheval/utils/exomiser.py,sha256=m2u0PH2z9lFPaB3LVkZCmPmH5e55q1NoTzNl46zRRP8,683
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- pheval/utils/file_utils.py,sha256=m21cz-qjDYqnI8ClUv3J9fKizex98a-9bSEerQ75i_c,3576
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- pheval/utils/logger.py,sha256=5DZl5uMltUDQorhkvg_B7_ZhFwApAmEkWneFIOKfRGQ,1566
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- pheval/utils/phenopacket_utils.py,sha256=XGnFLarvXezFR0W5frzyGTwEbhcA3zuGJPg1r5YBscg,27326
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- pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
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- pheval/utils/utils.py,sha256=23bQPL-HmzHnMRJSe4doJdj6rtmFyfO77FOH3wyFZZI,4518
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- pheval-0.6.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- pheval-0.6.3.dist-info/METADATA,sha256=Q0AX7IoMMvNPMpEYNLY2Ijdp5vSZgmpvDB6r2Q9zZgA,6494
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- pheval-0.6.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- pheval-0.6.3.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
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- pheval-0.6.3.dist-info/RECORD,,
{pheval-0.6.3.dist-info → pheval-0.6.5.dist-info}/WHEEL RENAMED
File without changes