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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HP:0008002 3.852418992937001
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HP:0008436 4.153448988600982
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HP:0008438 4.153448988600982
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HP:0008440 4.153448988600982
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HP:0008467 4.153448988600982
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HP:0008472 4.153448988600982
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HP:0008475 4.153448988600982
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HP:0008497 3.852418992937001
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HP:0008499 3.4544789842649637
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HP:0008501 3.6763277338813203
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HP:0008504 3.852418992937001
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HP:0008513 3.250359001609039
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HP:0008517 3.852418992937001
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HP:0008518 4.153448988600982
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HP:0008523 3.3083509485867255
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HP:0008527 3.250359001609039
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HP:0008544 3.375297738217339
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HP:0008551 2.175725383312135
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HP:0008554 4.153448988600982
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HP:0008559 3.852418992937001
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HP:0008569 4.153448988600982
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HP:0008572 3.3083509485867255
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HP:0008573 4.153448988600982
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HP:0008577 3.5513889972730204
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HP:0008583 4.153448988600982
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HP:0008586 4.153448988600982
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HP:0008587 3.5513889972730204
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HP:0008589 3.852418992937001
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HP:0008591 3.6763277338813203
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1929
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HP:0008598 3.375297738217339
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1930
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HP:0008610 3.852418992937001
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1931
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HP:0008615 4.153448988600982
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1932
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HP:0008619 2.9773577295453015
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1933
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HP:0008625 3.852418992937001
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1934
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HP:0008639 4.153448988600982
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1935
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HP:0008661 4.153448988600982
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1936
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HP:0008665 3.852418992937001
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1937
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HP:0008676 4.153448988600982
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1938
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HP:0008678 4.153448988600982
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1939
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HP:0008684 4.153448988600982
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1940
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HP:0008689 2.8312296938670634
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1941
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HP:0008717 3.852418992937001
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1942
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HP:0008723 4.153448988600982
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1943
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HP:0008726 3.852418992937001
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1944
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HP:0008734 2.852418992937001
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1945
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HP:0008736 3.852418992937001
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|
1946
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HP:0008740 4.153448988600982
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1947
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HP:0008743 3.852418992937001
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|
1948
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HP:0008751 3.852418992937001
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1949
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HP:0008755 3.6763277338813203
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1950
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HP:0008760 3.6763277338813203
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1951
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HP:0008762 3.250359001609039
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1952
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HP:0008763 4.153448988600982
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1953
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HP:0008768 3.5513889972730204
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1954
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HP:0008770 4.153448988600982
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1955
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HP:0008771 3.5513889972730204
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1956
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HP:0008772 3.6763277338813203
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1957
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HP:0008780 3.852418992937001
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1958
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HP:0008807 4.153448988600982
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1959
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HP:0008846 3.3083509485867255
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HP:0008848 3.039505636294146
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1961
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HP:0008850 3.1120563034427575
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1962
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HP:0008855 3.1120563034427575
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HP:0008872 1.6592943945825398
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HP:0008873 2.949329005945058
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HP:0008883 3.039505636294146
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HP:0008897 2.2669582634285006
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HP:0008905 3.6763277338813203
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HP:0008915 2.9773577295453015
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1969
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HP:0008921 4.153448988600982
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1970
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HP:0008929 3.6763277338813203
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1971
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HP:0008935 2.609380944250707
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HP:0008936 3.3083509485867255
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HP:0008944 3.852418992937001
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1974
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HP:0008947 2.852418992937001
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1975
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HP:0008959 4.153448988600982
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1976
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HP:0008962 4.153448988600982
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1977
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HP:0008967 4.153448988600982
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1978
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HP:0008970 3.852418992937001
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1979
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HP:0008981 4.153448988600982
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1980
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HP:0008994 4.153448988600982
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1981
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HP:0008997 4.153448988600982
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1982
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HP:0009003 4.153448988600982
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1983
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HP:0009020 4.153448988600982
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1984
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HP:0009025 4.153448988600982
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1985
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HP:0009027 4.153448988600982
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1986
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HP:0009028 4.153448988600982
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1987
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HP:0009062 2.5199805330213962
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HP:0009085 3.3083509485867255
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1989
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HP:0009088 3.0742677425533578
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HP:0009099 3.1992064791616577
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HP:0009110 3.4544789842649637
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1992
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HP:0009113 4.153448988600982
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1993
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HP:0009115 4.153448988600982
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1994
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HP:0009121 4.153448988600982
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1995
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HP:0009125 3.1534489886009824
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1996
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HP:0009127 3.6763277338813203
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1997
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HP:0009129 4.153448988600982
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1998
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HP:0009173 4.153448988600982
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1999
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HP:0009184 4.153448988600982
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2000
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HP:0009185 3.5513889972730204
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2001
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HP:0009225 4.153448988600982
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2002
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HP:0009237 3.6763277338813203
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2003
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HP:0009239 4.153448988600982
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2004
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HP:0009274 4.153448988600982
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2005
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HP:0009276 4.153448988600982
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2006
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HP:0009295 4.153448988600982
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2007
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HP:0009319 4.153448988600982
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|
2008
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HP:0009370 4.153448988600982
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2009
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HP:0009371 3.852418992937001
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2010
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HP:0009380 3.1534489886009824
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|
2011
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HP:0009381 2.9773577295453015
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2012
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HP:0009447 3.852418992937001
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2013
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HP:0009465 3.1992064791616577
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2014
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HP:0009466 3.852418992937001
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|
2015
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HP:0009484 4.153448988600982
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2016
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HP:0009486 3.6763277338813203
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2017
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HP:0009487 3.5513889972730204
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2018
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HP:0009537 3.852418992937001
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HP:0009540 4.153448988600982
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2020
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HP:0009552 3.6763277338813203
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2021
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HP:0009553 3.852418992937001
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2022
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HP:0009556 4.153448988600982
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HP:0009566 4.153448988600982
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HP:0009568 4.153448988600982
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2028
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2030
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HP:0009623 2.755508979928945
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2033
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2037
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HP:0009747 3.6763277338813203
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HP:0009894 3.1992064791616577
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HP:0009896 4.153448988600982
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HP:0009897 4.153448988600982
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2100
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HP:0009898 3.852418992937001
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2101
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HP:0009899 4.153448988600982
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2102
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HP:0009900 3.0742677425533578
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HP:0009901 3.4544789842649637
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HP:0009902 4.153448988600982
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HP:0009904 2.8746953876481536
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HP:0009905 3.4544789842649637
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HP:0009906 3.3083509485867255
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2108
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HP:0009907 3.5513889972730204
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2109
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HP:0009908 3.3083509485867255
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2110
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HP:0009909 2.7062909572587635
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2111
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HP:0009910 4.153448988600982
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2112
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HP:0009912 4.153448988600982
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|
2113
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HP:0009913 4.153448988600982
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|
2114
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HP:0009914 3.6763277338813203
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|
2115
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HP:0009916 3.6763277338813203
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|
2116
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HP:0009917 3.852418992937001
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|
2117
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HP:0009918 3.852418992937001
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|
2118
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HP:0009919 3.1534489886009824
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|
2119
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HP:0009921 3.0073209529227447
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|
2120
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HP:0009924 4.153448988600982
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|
2121
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HP:0009927 3.6763277338813203
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|
2122
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HP:0009928 3.5513889972730204
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|
2123
|
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HP:0009929 3.0742677425533578
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|
2124
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