pets 0.2.3 → 0.2.5

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Files changed (42) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +2 -0
  3. data/README.md +79 -5
  4. data/bin/coPatReporter.rb +68 -156
  5. data/bin/comPatMondo.rb +1 -4
  6. data/bin/evidence_profiler.rb +102 -150
  7. data/bin/get_gen_features.rb +146 -0
  8. data/bin/get_network_nodes.rb +79 -132
  9. data/bin/get_sorted_profs.rb +25 -36
  10. data/bin/install_deps.rb +8 -0
  11. data/bin/paco_translator.rb +29 -72
  12. data/bin/phen2reg.rb +1 -4
  13. data/bin/profiles2phenopacket.rb +86 -0
  14. data/bin/reg2phen.rb +1 -3
  15. data/example_datasets/associations_file.txt +757 -0
  16. data/example_datasets/example_patient.txt +6 -0
  17. data/example_datasets/example_patient_hpos.txt +15 -0
  18. data/example_datasets/genes.txt +8 -0
  19. data/example_datasets/hpo2ci.txt +2798 -0
  20. data/example_datasets/hummu_congenital_full_dataset.txt +4183 -0
  21. data/example_datasets/launch.sh +20 -0
  22. data/external_code/generate_boxpot.R +51 -21
  23. data/external_code/get_clusters.R +2 -2
  24. data/external_code/install_R_dependencies.R +16 -0
  25. data/external_code/plot_heatmap.R +34 -30
  26. data/lib/pets/coPatReporterMethods.rb +172 -424
  27. data/lib/pets/cohort.rb +309 -0
  28. data/lib/pets/common_optparse.rb +30 -0
  29. data/lib/pets/constants.rb +8 -0
  30. data/lib/pets/generalMethods.rb +29 -319
  31. data/lib/pets/genomic_features.rb +240 -0
  32. data/lib/pets/io.rb +481 -0
  33. data/lib/pets/parsers/cohort_parser.rb +111 -0
  34. data/lib/pets/parsers/reference_parser.rb +39 -0
  35. data/lib/pets/version.rb +1 -1
  36. data/lib/pets.rb +9 -0
  37. data/pets.gemspec +7 -3
  38. data/templates/cluster_report.erb +25 -5
  39. data/templates/cohort_report.erb +5 -7
  40. data/templates/evidence_profile.erb +20 -4
  41. data/templates/patient_report.erb +1 -1
  42. metadata +96 -5
data/example_datasets/hpo2ci.txt ADDED
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