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
data/lib/pets.rb
CHANGED
@@ -1,4 +1,12 @@
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require "pets/version"
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+
require "pets/constants"
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+
require "parsers/cohort_parser"
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+
require "pets/coPatReporterMethods"
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+
require "pets/generalMethods"
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require "pets/io"
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7
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+
require "pets/phen2reg_methods"
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8
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+
require "pets/cohort"
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9
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+
require "pets/genomic_features"
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module Pets
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class Error < StandardError; end
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data/pets.gemspec
CHANGED
data/templates/cohort_report.erb
CHANGED
@@ -161,17 +161,15 @@
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<%
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@hash_vars[:clustering_methods].each do |clust_method|
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plot = File.join(@hash_vars[:temp_folder], "#{clust_method}_heatmap.png")
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-
if File.
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+
if File.exist?(plot) %>
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<%= embed_img(plot, 'width="800" height="800"') %>
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<% else
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puts 'File not found or method not specified.'
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end
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-
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-
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-
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-
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-
if File.exists?(plot)
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-
embed_img(plot, 'width="800" height="800"')
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+
plot = File.join(@hash_vars[:temp_folder], clust_method + '_sim_boxplot.png')
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if File.exist?(plot) %>
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<%= embed_img(plot, 'width="800" height="800"') %>
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<% end
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end
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%>
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</div>
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@@ -141,7 +141,7 @@
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row.each_with_index do |cell, i|
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if i == 3
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row[i] = cell.map{|h|
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-
hpo_names, rejected = hpo.
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+
hpo_names, rejected = hpo.translate_names([h])
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"#{get_hpo_link(h)}: #{hpo_names.first}"
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}.join("\n<br>")
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elsif i == 4
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: pets
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version: !ruby/object:Gem::Version
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-
version: 0.2.
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version: 0.2.4
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platform: ruby
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authors:
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- Elena Rojano, Pedro Seoane
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autorequire:
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bindir: bin
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cert_chain: []
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-
date:
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+
date: 2022-05-19 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -136,6 +136,20 @@ dependencies:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: expcalc
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: parallel
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requirement: !ruby/object:Gem::Requirement
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@@ -173,12 +187,14 @@ executables:
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- get_PR_values.rb
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- get_network_nodes.rb
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- get_sorted_profs.rb
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+
- install_deps.rb
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- merge_by_cluster.rb
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- merge_pairs.rb
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- paco_translator.rb
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- phen2reg.rb
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- phen2reg_predictor_check.rb
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- profile_cleaner.rb
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+
- profiles2phenopacket.rb
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- reg2phen.rb
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- region_to_patients_generator.rb
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- relate_CI_to_association_value.rb
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@@ -204,18 +220,28 @@ files:
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- bin/get_PR_values.rb
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- bin/get_network_nodes.rb
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- bin/get_sorted_profs.rb
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+
- bin/install_deps.rb
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- bin/merge_by_cluster.rb
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- bin/merge_pairs.rb
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- bin/paco_translator.rb
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- bin/phen2reg.rb
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- bin/phen2reg_predictor_check.rb
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- bin/profile_cleaner.rb
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+
- bin/profiles2phenopacket.rb
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- bin/reg2phen.rb
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- bin/region_to_patients_generator.rb
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- bin/relate_CI_to_association_value.rb
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- bin/setup
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+
- example_datasets/associations_file.txt
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- example_datasets/example_patient.txt
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- example_datasets/example_patient_hpos.txt
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- example_datasets/genes.txt
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- example_datasets/hpo2ci.txt
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- example_datasets/hummu_congenital_full_dataset.txt
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- example_datasets/launch.sh
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- external_code/generate_boxpot.R
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- external_code/get_clusters.R
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+
- external_code/install_R_dependencies.R
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- external_code/lines.R
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- external_code/plot_area.R
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- external_code/plot_boxplot.R
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@@ -242,7 +268,12 @@ files:
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- external_data/uniq_hpo_with_CI.txt
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- lib/pets.rb
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- lib/pets/coPatReporterMethods.rb
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+
- lib/pets/cohort.rb
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+
- lib/pets/constants.rb
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- lib/pets/generalMethods.rb
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+
- lib/pets/genomic_features.rb
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- lib/pets/io.rb
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- lib/pets/parsers/cohort_parser.rb
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- lib/pets/phen2reg_methods.rb
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- lib/pets/reg2phen_methods.rb
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- lib/pets/version.rb
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@@ -272,7 +303,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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-
rubygems_version: 3.2.
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rubygems_version: 3.2.15
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signing_key:
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specification_version: 4
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summary: Suite with predictive tools.
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