pets 0.2.3 → 0.2.5

data/templates/cluster_report.erb

@@ -25,14 +25,34 @@
 <div style="width: 90%; background-color:#ecf0f1; margin: 0 auto;"> 
 	<h1 style="text-align: center; background-color:#d6eaf8">Patient HPO profiles by cluster.</h1>
 		<%= table(id: :clusters, header: true, border: 2, row_names: false, text: true, 
-			cell_align: %w( center )) do |data|
-				data.each do |element|
+			cell_align: %w( center ), styled: 'dt', attrib: {'class' => 'table'}) do |data|
+				patient_list = []
+				data.each do |element| # Cluster
+					clID, patient_number, patient_ids, hpo_codes, hpo_names = element
+					# TODO: mostrar registro por paciente
 					#STDERR.puts element.inspect
-					element[2] = element[2].map{|patID| "<p>#{patID}</p>" }.join("\n")
-					element[3] = element[3].map{|profile| "<p>#{profile.map{|hpo_code| get_hpo_link(hpo_code)}.join(', ')}</p>" }.join("\n")
-					element[4] = element[4].map{|transl_profile| "<p>#{transl_profile.join(', ')}</p>"}.join("\n")
+					patient_ids.each_with_index do |patID, i|
+						patient_record = [clID, patient_number]
+						patient_record << patID
+						patient_record << hpo_codes[i].map{|hpo_code| get_hpo_link(hpo_code)}.join(', ')
+						patient_record << hpo_names[i].join(', ')
+						patient_list << patient_record
+					end
 				end
+				data.clear
+				data.concat(patient_list) 
 				data.unshift(["Cluster ID","Patients in Cluster","Patient IDs", "HPO codes", "Phenotypes"])				
 			end
 		%>
 </div>
+
+<div style="width: 90%; background-color:#ecf0f1; margin: 0 auto;"> 
+	<h1 style="text-align: center; background-color:#d6eaf8"> Cluster detailed view.</h1>
+	<%
+		@hash_vars[:sim_mat4cluster].each do |clID, sim_matrix|
+			@hash_vars[:sim_matrix] = sim_matrix %>
+			<%= heatmap(id: :sim_matrix, header: true, row_names: true, title: "Cluster #{clID}" )%>
+		<% end
+	%>
+
+</div>

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/evidence_profile.erb

@@ -4,7 +4,7 @@
 	<% @hash_vars[:similarity_matrixs].each do |pair, similarity_matrix| %>
 		<% 
 			matrix_name = pair + '_sim_matrix'
-			if pair == 'gene_HP'
+			if pair.include?('gene_HP')
 				dict = @hash_vars[:evidences][pair][:id2lab]
 				header = similarity_matrix.first
 				header.map! do |item|
@@ -27,8 +27,24 @@
 	<% end %>
 	<%=circular_genome(id: :candidates, header: false, row_names: true, transpose: false, 
 		 genomic_coordinates: @hash_vars[:genomic_coordinates] )%>
-	<% if !@hash_vars[:var_ids].nil? %>
-		<%=circular_genome(id: :var_ids, header: false, row_names: true, transpose: false, 
-		 genomic_coordinates: @hash_vars[:var_coordinates] )%>
+	<% if !@hash_vars[:var_ids].nil? 
+		if @hash_vars[:var_ids].length > 200 %>
+			<p> Too much variant records</p>
+		<% else %>
+			<%=circular_genome(id: :var_ids, header: false, 
+				row_names: true, transpose: false, 
+		 		genomic_coordinates: @hash_vars[:var_coordinates] )%>
+		<% end %>
 	<% end %>
+
+	<h1 style="text-align: center; background-color:#d6eaf8">Candidate regions</h1>
+
+	<%=  table(id: :hotspot_table) do |data|
+			data.each do |row|
+				row[1] = row[1].join(" ")
+				row[2] = row[2].join(",")
+				row[3] = row[3].join(",")
+			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: 0.2.5
 platform: ruby
 authors:
 - Elena Rojano, Pedro Seoane
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-06-09 00:00:00.000000000 Z
+date: 2023-08-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.10.0
+        version: 3.11.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.10.0
+        version: 3.11.0
 - !ruby/object:Gem::Dependency
   name: statistics2
   requirement: !ruby/object:Gem::Requirement
@@ -94,6 +94,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: NetAnalyzer
+  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: report_html
   requirement: !ruby/object:Gem::Requirement
@@ -136,6 +150,34 @@ 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: bio-vcf
+  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
@@ -150,6 +192,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.20.1
+- !ruby/object:Gem::Dependency
+  name: net-ftp
+  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: net-http
+  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'
 description: PETS suite includes three different tools. CohortAnalyzer performs the
   calculation of several statistics that gives an overview of a cohort of patients
   to analyse. Reg2Phen uses associations between pathological phenotypes and regions
@@ -171,14 +241,17 @@ executables:
 - fmeasure_index.rb
 - generate_HPO_IC_table.rb
 - get_PR_values.rb
+- get_gen_features.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
@@ -202,20 +275,31 @@ files:
 - bin/fmeasure_index.rb
 - bin/generate_HPO_IC_table.rb
 - bin/get_PR_values.rb
+- bin/get_gen_features.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 +326,14 @@ files:
 - external_data/uniq_hpo_with_CI.txt
 - lib/pets.rb
 - lib/pets/coPatReporterMethods.rb
+- lib/pets/cohort.rb
+- lib/pets/common_optparse.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/parsers/reference_parser.rb
 - lib/pets/phen2reg_methods.rb
 - lib/pets/reg2phen_methods.rb
 - lib/pets/version.rb
@@ -272,7 +363,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.3.7
 signing_key:
 specification_version: 4
 summary: Suite with predictive tools.