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.
- checksums.yaml +4 -4
- data/Gemfile +2 -0
- data/README.md +79 -5
- data/bin/coPatReporter.rb +63 -156
- data/bin/comPatMondo.rb +1 -4
- data/bin/evidence_profiler.rb +38 -151
- data/bin/get_network_nodes.rb +79 -132
- data/bin/get_sorted_profs.rb +25 -36
- data/bin/install_deps.rb +7 -0
- data/bin/paco_translator.rb +29 -72
- data/bin/phen2reg.rb +1 -4
- data/bin/profiles2phenopacket.rb +110 -0
- data/bin/reg2phen.rb +1 -3
- data/example_datasets/associations_file.txt +757 -0
- data/example_datasets/example_patient.txt +6 -0
- data/example_datasets/example_patient_hpos.txt +15 -0
- data/example_datasets/genes.txt +8 -0
- data/example_datasets/hpo2ci.txt +2798 -0
- data/example_datasets/hummu_congenital_full_dataset.txt +4183 -0
- data/example_datasets/launch.sh +20 -0
- data/external_code/generate_boxpot.R +51 -21
- data/external_code/get_clusters.R +2 -2
- data/external_code/install_R_dependencies.R +11 -0
- data/external_code/plot_heatmap.R +34 -30
- data/lib/pets/coPatReporterMethods.rb +143 -441
- data/lib/pets/cohort.rb +307 -0
- data/lib/pets/constants.rb +7 -0
- data/lib/pets/generalMethods.rb +8 -317
- data/lib/pets/genomic_features.rb +144 -0
- data/lib/pets/io.rb +457 -0
- data/lib/pets/parsers/cohort_parser.rb +106 -0
- data/lib/pets/version.rb +1 -1
- data/lib/pets.rb +8 -0
- data/pets.gemspec +1 -0
- data/templates/cohort_report.erb +5 -7
- data/templates/patient_report.erb +1 -1
- metadata +34 -3
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+
5 175167895 175225095 HP:0040019 1.139690775305958 5.254.A.5
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|
712
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9 84031239 84032536 HP:0001510 1.0807233915720655 9.138.A.4
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|
713
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17 41464521 41521548 HP:0000164 1.2633397909824624 17.257.A.3
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|
714
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15 23641501 23656936 HP:0000189 1.339192833586086 15.38.A.39
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715
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|
716
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22 19835558 19892620 HP:0001611 6.731167853668418 22.63.A.71
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|
717
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|
718
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|
719
|
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|
720
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3 113825897 113973219 HP:0002360 2.0103214914426735 3.183.A.16
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|
721
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|
722
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|
723
|
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8 11888779 11892064 HP:0001263 1.7563653000501116 8.91.A.19
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|
724
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725
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18 61380797 62395473 HP:0001850 2.0789249809892976 18.144.A.7
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|
726
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|
727
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|
728
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2 240144798 240265780 HP:0000164 1.3700043728809097 2.565.A.18
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|
729
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22 22905039 22916553 HP:0002564 3.429547376895242 22.149.A.27
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|
730
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4 128899758 129847945 HP:0000929 2.351100585224708 4.182.A.8
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|
731
|
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|
732
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|
733
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|
734
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735
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736
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|
737
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|
738
|
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22 22508432 22548710 HP:0001629 1.3886719174522903 22.144.A.32
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|
739
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|
740
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|
741
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|
742
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|
743
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744
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3 150876508 150983389 HP:0011304 1.845944473234177 3.243.A.6
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745
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4 82113957 82125731 HP:0000324 1.6049163082103857 4.125.A.7
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|
746
|
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12 84516511 85182577 HP:0010944 1.7871475801195542 12.170.A.5
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|
747
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|
748
|
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|
749
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7 163010 194258 HP:0100737 1.6017932281314624 7.12.A.14
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750
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16 81665052 81685862 HP:0011603 1.1368018391247634 16.309.A.7
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751
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17 1130776 1151598 HP:0011821 1.3493528939054036 17.21.A.19
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752
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5 22179 26142 HP:0011994 1.2432097366051795 5.2.A.3
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|
753
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15 95839903 96128092 HP:0030791 1.209866861538179 15.243.A.13
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|
754
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|
755
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|
756
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2 98367669 98649143 HP:0100022 1.1350930290900088 2.203.A.2
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|
757
|
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15 74513500 75141527 HP:0009890 1.6367124443597774 15.189.A.13
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