pheval 0.1.0__py3-none-any.whl → 0.2.0__py3-none-any.whl

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Files changed (42) hide show
  1. pheval/__init__.py +0 -5
  2. pheval/analyse/__init__.py +0 -0
  3. pheval/analyse/analysis.py +703 -0
  4. pheval/analyse/generate_plots.py +312 -0
  5. pheval/analyse/generate_summary_outputs.py +186 -0
  6. pheval/analyse/rank_stats.py +61 -0
  7. pheval/cli.py +22 -7
  8. pheval/cli_pheval.py +37 -12
  9. pheval/cli_pheval_utils.py +225 -8
  10. pheval/config_parser.py +36 -0
  11. pheval/constants.py +1 -0
  12. pheval/implementations/__init__.py +1 -3
  13. pheval/post_processing/__init__.py +0 -0
  14. pheval/post_processing/post_processing.py +210 -0
  15. pheval/prepare/__init__.py +0 -0
  16. pheval/prepare/create_noisy_phenopackets.py +173 -0
  17. pheval/prepare/create_spiked_vcf.py +366 -0
  18. pheval/prepare/custom_exceptions.py +47 -0
  19. pheval/prepare/update_phenopacket.py +53 -0
  20. pheval/resources/alternate_ouputs/CADA_results.txt +11 -0
  21. pheval/resources/alternate_ouputs/DeepPVP_results.txt +22 -0
  22. pheval/resources/alternate_ouputs/OVA_results.txt +11 -0
  23. pheval/resources/alternate_ouputs/Phen2Gene_results.json +814 -0
  24. pheval/resources/alternate_ouputs/Phenolyzer_results.txt +12 -0
  25. pheval/resources/alternate_ouputs/lirical_results.tsv +152 -0
  26. pheval/resources/alternate_ouputs/svanna_results.tsv +9 -0
  27. pheval/resources/hgnc_complete_set_2022-10-01.txt +43222 -0
  28. pheval/run_metadata.py +27 -0
  29. pheval/runners/runner.py +92 -11
  30. pheval/utils/__init__.py +0 -0
  31. pheval/utils/docs_gen.py +105 -0
  32. pheval/utils/docs_gen.sh +18 -0
  33. pheval/utils/file_utils.py +88 -0
  34. pheval/utils/phenopacket_utils.py +356 -0
  35. pheval/utils/semsim_utils.py +156 -0
  36. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/METADATA +12 -4
  37. pheval-0.2.0.dist-info/RECORD +41 -0
  38. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/WHEEL +1 -1
  39. pheval/utils.py +0 -7
  40. pheval-0.1.0.dist-info/RECORD +0 -13
  41. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/LICENSE +0 -0
  42. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/entry_points.txt +0 -0
pheval/resources/alternate_ouputs/svanna_results.tsv ADDED
@@ -0,0 +1,9 @@
1
+ contig start end id vtype failed_filters psv
2
+ 17 31150798 31157725 Hsiao-2015-26189818-NF1-UAB_1-FigS1 DEL 124.97852180540217
3
+ 17 43100079 43110335 Musani-2017-29310340-BRCA1-proband-FigS2 DEL 5.731265530741487
4
+ 2 109923337 110405062 Koyama-2017-28347285-NPHP1-II_2-FigS3 DEL 4.426802033585173
5
+ X 64205190 64206761 Mi-2020-33265914-AMER1-Proband_B-FigS6 DEL 3.6926304444154807
6
+ 3 9725702 9737931 Mizuguchi-2020-33157260-BRPF1-II_1-FigS5 INV 2.600504464629789
7
+ 3 11007012 11007013 Pesz-2018-29621621-SLC6A1-proband-FigS8 BND 2.155736527404235
8
+ 13 72835296 72835332 Hebbar-2018-29695797-PIBF1-proband-FigS4 DUP 1.3833777539105
9
+ 12 6124705 6124718 Othman-2010-20696945-VWF-index-FigS7 DEL 0.7608952519440781