cohort.rb in pets-0.2.5

- old
+ new

@@ -22,15 +22,10 @@
 				ont = Ontology.new(file: ont_file, load_file: true)
 			end
 		else
 			ont = Ontology.new
 			ont.read(ont_file)
-			if !excluded_terms_file.nil?
-				ont.add_removable_terms(read_excluded_ont_file(excluded_terms_file))
-				ont.remove_removable()
-				ont.build_index()
-			end
 		end
 		@@ont[ont_name] = ont
 	end
 
 	def self.read_excluded_ont_file(file)
@@ -42,16 +37,18 @@
 	end
 
 	def initialize()
 		@profiles = {}
 		@vars = {}
+		@extra_attr = {}
 		@var_idx = Genomic_Feature.new([])
 	end
 
-	def add_record(rec) #[id, [profile], [[chr1, start1, stop1],[chr1, start1, stop1]]]
+	def add_record(rec, extra_attr = nil) #[id, [profile], [[chr1, start1, stop1],[chr1, start1, stop1]]]
 		id, profile, vars = rec
 		@profiles[id] = profile.map{|t| t.to_sym} if !profile.nil? 
+		@extra_attr[id] = extra_attr if !extra_attr.nil? 
 		add_gen_feat(id, vars) if !vars.nil?
 	end
 
 	def delete(id)
 		@profiles.delete(id)
@@ -109,11 +106,11 @@
 
 	def get_general_profile(thr=0) # TODO move funcionality to semtools
 		term_count = Hash.new(0)
 		each_profile do |id, prof|
 			prof.each do |term|
-				general_profile[prof] += 1
+				term_count[term] += 1
 			end
 		end
 		records = @profiles.length
 		general_profile = []
 		term_count.each do |term, count|
@@ -269,10 +266,15 @@
 			}]
 		}
 
 		@profiles.each do |id, terms|
 			phenopacket = {metaData: metaData}
-			phenopacket[:subject] = {id: id}
+			query_sex = @extra_attr.dig(id, :sex)
+			sex = query_sex.nil? ? 'UNKNOWN_SEX' : query_sex
+			phenopacket[:subject] = {
+				id: id,
+				sex: sex
+			}
 			phenotypicFeatures = []
 			terms.each do |term|
 				term_name = ont.translate_id(term)
 				phenotypicFeatures << {
 					type: { id: term, label: term_name},