pets 0.2.3 → 0.2.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (37) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +2 -0
  3. data/README.md +79 -5
  4. data/bin/coPatReporter.rb +63 -156
  5. data/bin/comPatMondo.rb +1 -4
  6. data/bin/evidence_profiler.rb +38 -151
  7. data/bin/get_network_nodes.rb +79 -132
  8. data/bin/get_sorted_profs.rb +25 -36
  9. data/bin/install_deps.rb +7 -0
  10. data/bin/paco_translator.rb +29 -72
  11. data/bin/phen2reg.rb +1 -4
  12. data/bin/profiles2phenopacket.rb +110 -0
  13. data/bin/reg2phen.rb +1 -3
  14. data/example_datasets/associations_file.txt +757 -0
  15. data/example_datasets/example_patient.txt +6 -0
  16. data/example_datasets/example_patient_hpos.txt +15 -0
  17. data/example_datasets/genes.txt +8 -0
  18. data/example_datasets/hpo2ci.txt +2798 -0
  19. data/example_datasets/hummu_congenital_full_dataset.txt +4183 -0
  20. data/example_datasets/launch.sh +20 -0
  21. data/external_code/generate_boxpot.R +51 -21
  22. data/external_code/get_clusters.R +2 -2
  23. data/external_code/install_R_dependencies.R +11 -0
  24. data/external_code/plot_heatmap.R +34 -30
  25. data/lib/pets/coPatReporterMethods.rb +143 -441
  26. data/lib/pets/cohort.rb +307 -0
  27. data/lib/pets/constants.rb +7 -0
  28. data/lib/pets/generalMethods.rb +8 -317
  29. data/lib/pets/genomic_features.rb +144 -0
  30. data/lib/pets/io.rb +457 -0
  31. data/lib/pets/parsers/cohort_parser.rb +106 -0
  32. data/lib/pets/version.rb +1 -1
  33. data/lib/pets.rb +8 -0
  34. data/pets.gemspec +1 -0
  35. data/templates/cohort_report.erb +5 -7
  36. data/templates/patient_report.erb +1 -1
  37. metadata +34 -3
data/example_datasets/hummu_congenital_full_dataset.txt ADDED
@@ -0,0 +1,4183 @@
1
+ patient_id chr start stop phenotypes
2
+ 2 - - - HP:0100543|HP:0002342|HP:0000708|HP:0001252|HP:0000252|HP:0004322|HP:0000119|HP:0010935
3
+ 3 22 31738718 32422971 HP:0001252
4
+ 5 - - - HP:0100543|HP:0002342|HP:0000708|HP:0001252|HP:0004322
5
+ 6 - - - HP:0100543|HP:0002342|HP:0000708|HP:0001252|HP:0007319
6
+ 7 - - - HP:0001250|HP:0001252|HP:0007319
7
+ 8 - - - HP:0100543|HP:0010864|HP:0004322
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+ 10 - - - HP:0100543|HP:0002342|HP:0000708|HP:0002564|HP:0000119|HP:0000811
9
+ 11 - - - HP:0100543|HP:0001256|HP:0004322
10
+ 12 - - - HP:0100543|HP:0010864|HP:0001250|HP:0001252|HP:0007319|HP:0004322
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+ 13 - - - HP:0100543|HP:0002342|HP:0001252|HP:0000252|HP:0001511|HP:0004322|HP:0002564|HP:0001671|HP:0001710
12
+ 14 13 100391121 101075206 HP:0100543|HP:0001256|HP:0001511
13
+ 15 - - - HP:0001252|HP:0007319|HP:0000119|HP:0000811
14
+ 16 - - - HP:0100543|HP:0000708|HP:0000729
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23
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+ 30 4 93769725 99612792 HP:0001252|HP:0007319|HP:0000252|HP:0004322|HP:0000119|HP:0000811
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29
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30
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