pets 0.2.3 → 0.2.4

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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
8
+ 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
11
+ 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
15
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16
+ 18 - - - HP:0100543|HP:0010864|HP:0001250|HP:0001252|HP:0007319
17
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18
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+ 22 - - - HP:0100543|HP:0002342|HP:0001252|HP:0007319
22
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23
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24
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25
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26
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27
+ 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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32
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33
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34
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37
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