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.
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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+ require "pets/phen2reg_methods"
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+ require "pets/cohort"
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+ require "pets/genomic_features"
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  module Pets
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  class Error < StandardError; end
data/pets.gemspec CHANGED
@@ -45,6 +45,7 @@ Gem::Specification.new do |spec|
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  spec.add_dependency "report_html"
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  spec.add_dependency "numo-narray"
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  spec.add_dependency "npy"
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+ spec.add_dependency "expcalc"
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  spec.add_dependency "parallel", "~> 1.20.1"
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  end
@@ -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.exists?(plot) %>
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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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- end
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- %>
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- <%=
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- plot = File.join(@hash_vars[:temp_folder],'sim_boxplot.png')
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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>
@@ -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.translate_codes2names([h])
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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
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: 0.2.3
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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: 2021-06-09 00:00:00.000000000 Z
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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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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: 3.2.3
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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.