pets 0.2.3 → 0.2.4

data/lib/pets.rb

@@ -1,4 +1,12 @@
 require "pets/version"
+require "pets/constants"
+require "parsers/cohort_parser"
+require "pets/coPatReporterMethods"
+require "pets/generalMethods"
+require "pets/io"
+require "pets/phen2reg_methods"
+require "pets/cohort"
+require "pets/genomic_features"
 
 module Pets
   class Error < StandardError; end

data/pets.gemspec

@@ -45,6 +45,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency "report_html" 
   spec.add_dependency "numo-narray" 
   spec.add_dependency "npy" 
+  spec.add_dependency "expcalc" 
   spec.add_dependency "parallel", "~> 1.20.1"  
 
 end

data/templates/cohort_report.erb

@@ -161,17 +161,15 @@
 	<% 
 		@hash_vars[:clustering_methods].each do |clust_method|
 			plot = File.join(@hash_vars[:temp_folder], "#{clust_method}_heatmap.png")
-			if File.exists?(plot) %>
+			if File.exist?(plot) %>
 				<%= embed_img(plot, 'width="800" height="800"') %>
 			<% else
 				puts 'File not found or method not specified.'
 			end
-		end
-	%>
-	<%= 
-		plot = File.join(@hash_vars[:temp_folder],'sim_boxplot.png')
-		if File.exists?(plot)
-			embed_img(plot, 'width="800" height="800"') 
+			plot = File.join(@hash_vars[:temp_folder], clust_method + '_sim_boxplot.png')
+			if File.exist?(plot) %>
+				<%= embed_img(plot, 'width="800" height="800"') %> 
+			<% end
 		end
 	%>	
 </div>

data/templates/patient_report.erb

@@ -141,7 +141,7 @@
 			row.each_with_index do |cell, i|
 				if i == 3
 					row[i] = cell.map{|h|
-						hpo_names, rejected = hpo.translate_codes2names([h])
+						hpo_names, rejected = hpo.translate_names([h])
 						"#{get_hpo_link(h)}: #{hpo_names.first}"
 					}.join("\n<br>")
 				elsif i == 4

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pets
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
 platform: ruby
 authors:
 - Elena Rojano, Pedro Seoane
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-06-09 00:00:00.000000000 Z
+date: 2022-05-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -136,6 +136,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: expcalc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: parallel
   requirement: !ruby/object:Gem::Requirement
@@ -173,12 +187,14 @@ executables:
 - get_PR_values.rb
 - get_network_nodes.rb
 - get_sorted_profs.rb
+- install_deps.rb
 - merge_by_cluster.rb
 - merge_pairs.rb
 - paco_translator.rb
 - phen2reg.rb
 - phen2reg_predictor_check.rb
 - profile_cleaner.rb
+- profiles2phenopacket.rb
 - reg2phen.rb
 - region_to_patients_generator.rb
 - relate_CI_to_association_value.rb
@@ -204,18 +220,28 @@ files:
 - bin/get_PR_values.rb
 - bin/get_network_nodes.rb
 - bin/get_sorted_profs.rb
+- bin/install_deps.rb
 - bin/merge_by_cluster.rb
 - bin/merge_pairs.rb
 - bin/paco_translator.rb
 - bin/phen2reg.rb
 - bin/phen2reg_predictor_check.rb
 - bin/profile_cleaner.rb
+- bin/profiles2phenopacket.rb
 - bin/reg2phen.rb
 - bin/region_to_patients_generator.rb
 - bin/relate_CI_to_association_value.rb
 - bin/setup
+- example_datasets/associations_file.txt
+- example_datasets/example_patient.txt
+- example_datasets/example_patient_hpos.txt
+- example_datasets/genes.txt
+- example_datasets/hpo2ci.txt
+- example_datasets/hummu_congenital_full_dataset.txt
+- example_datasets/launch.sh
 - external_code/generate_boxpot.R
 - external_code/get_clusters.R
+- external_code/install_R_dependencies.R
 - external_code/lines.R
 - external_code/plot_area.R
 - external_code/plot_boxplot.R
@@ -242,7 +268,12 @@ files:
 - external_data/uniq_hpo_with_CI.txt
 - lib/pets.rb
 - lib/pets/coPatReporterMethods.rb
+- lib/pets/cohort.rb
+- lib/pets/constants.rb
 - lib/pets/generalMethods.rb
+- lib/pets/genomic_features.rb
+- lib/pets/io.rb
+- lib/pets/parsers/cohort_parser.rb
 - lib/pets/phen2reg_methods.rb
 - lib/pets/reg2phen_methods.rb
 - lib/pets/version.rb
@@ -272,7 +303,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.2.15
 signing_key:
 specification_version: 4
 summary: Suite with predictive tools.