pets 0.2.3 → 0.2.5

data/lib/pets/cohort.rb

@@ -0,0 +1,309 @@
+require 'json'
+require 'semtools'
+
+class Cohort
+	@@ont = {}
+	class << self # https://www.ruby-forum.com/t/attr-accessor-for-class-variable/136693
+		attr_accessor :act_ont # Which ontology use for ont related operations
+	end
+
+	attr_accessor :profiles
+
+	def self.get_ontology(ont_id)
+		return @@ont[ont_id]
+	end
+
+	def self.load_ontology(ont_name, ont_file, excluded_terms_file = nil)
+		ont = nil
+		if !ont_file.include?('.json')
+			if !excluded_terms_file.nil?
+				ont = Ontology.new(file: ont_file, load_file: true, removable_terms: read_excluded_ont_file(excluded_terms_file))
+			else
+				ont = Ontology.new(file: ont_file, load_file: true)
+			end
+		else
+			ont = Ontology.new
+			ont.read(ont_file)
+		end
+		@@ont[ont_name] = ont
+	end
+
+	def self.read_excluded_ont_file(file)
+		excluded_hpo = []
+		File.open(file).each do |line|
+			excluded_hpo << line.chomp
+		end
+		return excluded_hpo
+	end
+
+	def initialize()
+		@profiles = {}
+		@vars = {}
+		@extra_attr = {}
+		@var_idx = Genomic_Feature.new([])
+	end
+
+	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)
+		@vars.delete(id)
+	end
+
+	def select_by_profile!
+		@profiles.select!{|id, profile| yield(id, profile)}
+		current_ids = @profiles.keys
+		@vars.select!{|id, var| current_ids.include?(id)}
+	end
+
+	def select_by_var!
+		@vars.select!{|id, profile| yield(id, profile)}
+		current_ids = @vars.keys
+		@profiles.select!{|id, var| current_ids.include?(id)}
+	end
+
+	def filter_by_term_number(n_terms)
+		select_by_profile!{|id, profile| profile.length >= n_terms}
+	end
+	
+	def remove_incomplete_records # remove resc that lacks of vars or phenotypes
+		ids_with_terms = @profiles.keys
+		ids_with_vars = []
+		@vars.each{|id, regs| ids_with_vars << id if regs.length > 0}
+		full_ids = ids_with_vars & ids_with_terms
+		@profiles.select!{|id, prof| full_ids.include?(id)}
+		@vars.select!{|id, var| full_ids.include?(id)}
+	end
+
+	def add_gen_feat(id, feat_array) # [[chr1, start1, stop1],[chr1, start1, stop1]]
+		@vars[id] = Genomic_Feature.new(feat_array)
+	end
+
+	def get_profile(id)
+		return @profiles[id]
+	end
+
+	def get_vars(id)
+		return @vars[id]
+	end
+
+	def each_profile()
+		@profiles.each do |id, profile|
+			yield(id, profile)
+		end
+	end
+
+	def each_var()
+		@vars.each do |id, var_info|
+			yield(id, var_info)
+		end
+	end
+
+	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|
+				term_count[term] += 1
+			end
+		end
+		records = @profiles.length
+		general_profile = []
+		term_count.each do |term, count|
+			general_profile << term if count.fdiv(records) >= thr
+		end
+		ont = @@ont[Cohort.act_ont]
+		return ont.clean_profile_hard(general_profile)
+	end
+
+	def check(hard=false) # OLD format_patient_data
+		ont = @@ont[Cohort.act_ont]
+		rejected_terms = []
+		rejected_recs = []
+		@profiles.each do |id, terms|
+			if hard
+				terms = ont.clean_profile_hard(terms)
+				rejec_terms = []
+			else
+				terms, rejec_terms = ont.check_ids(terms)
+			end
+			if !rejec_terms.empty?
+				STDERR.puts "WARNING: record #{id} has the unknown CODES '#{rejec_terms.join(',')}'. Codes removed."
+				rejected_terms.concat(rejec_terms)
+			end
+			if terms.empty?
+				rejected_recs << id
+			else
+				@profiles[id] = terms
+			end
+		end
+		@profiles.select!{|id, record| !rejected_recs.include?(id)}
+		@vars.select!{|id, record| !rejected_recs.include?(id)}
+		return rejected_terms.uniq, rejected_recs
+	end
+
+	def link2ont(ont_id)
+		@@ont[ont_id].load_profiles(@profiles)
+	end
+
+	def get_profile_redundancy
+		ont = @@ont[Cohort.act_ont]
+		profile_sizes, parental_terms_per_profile = ont.get_profile_redundancy
+		return profile_sizes, parental_terms_per_profile
+	end
+
+	def get_profiles_terms_frequency(options={})
+		ont = @@ont[Cohort.act_ont]
+		term_stats = ont.get_profiles_terms_frequency(**options) #https://www.ruby-lang.org/en/news/2019/12/12/separation-of-positional-and-keyword-arguments-in-ruby-3-0/
+		return term_stats
+	end
+
+	def compute_term_list_and_childs()
+		ont = @@ont[Cohort.act_ont]
+		suggested_childs, term_with_childs_ratio = ont.compute_term_list_and_childs()
+	end
+
+	def get_profile_ontology_distribution_tables()
+		ont = @@ont[Cohort.act_ont]
+		ontology_levels, distribution_percentage = ont.get_profile_ontology_distribution_tables
+		ontology_levels.unshift(["level", "ontology", "cohort"])
+		distribution_percentage.unshift(["level", "ontology", "weighted cohort", "uniq terms cohort"])
+		return ontology_levels, distribution_percentage
+	end
+
+	def get_ic_analysis()
+		ont = @@ont[Cohort.act_ont]
+		onto_ic, freq_ic = ont.get_observed_ics_by_onto_and_freq # IC for TERMS
+		onto_ic_profile, freq_ic_profile = ont.get_profiles_resnik_dual_ICs # IC for PROFILES
+		return onto_ic, freq_ic, onto_ic_profile, freq_ic_profile
+	end
+
+	def get_profiles_mean_size
+		ont = @@ont[Cohort.act_ont]
+		profile_mean_size = ont.get_profiles_mean_size
+		return profile_mean_size
+	end
+
+	def get_profile_length_at_percentile(perc=50, increasing_sort: false)
+		ont = @@ont[Cohort.act_ont]
+		length_percent = ont.get_profile_length_at_percentile(perc=perc, increasing_sort: increasing_sort)
+		return length_percent
+	end
+
+	def get_dataset_specifity_index(type)
+		ont = @@ont[Cohort.act_ont]
+		dsi = ont.get_dataset_specifity_index(type)
+		return dsi
+	end
+
+	def compare_profiles(options={})
+		ont = @@ont[Cohort.act_ont]
+		similarities = ont.compare_profiles(**options)
+		return similarities
+	end
+
+	def index_vars # equivalent to process_patient_data
+		each_var do |id, var|
+			@var_idx.merge(var, id)
+		end
+	end
+
+	def get_vars_sizes(summary=false)
+		if summary
+			return @var_idx.get_summary_sizes
+		else
+			return @var_idx.get_sizes
+		end
+	end
+
+	def generate_cluster_regions(meth, tag, lim)
+		@var_idx.generate_cluster_regions(meth, tag, lim)
+	end
+
+	def save(output_file, mode = :default, translate = false)
+		File.open(output_file, 'w') do |f|
+			f.puts "id\tchr\tstart\tstop\tterms" if mode == 'paco'
+			ont = @@ont[Cohort.act_ont]
+			@profiles.each do |id, terms|
+				terms, rejected = ont.translate_ids(terms) if translate
+				id_variants = @vars[id]
+				variants = []
+				if id_variants.nil? || id_variants.length == 0
+					variants << ['-', '-', '-']
+				else
+					id_variants.each do |chr, reg|
+						variants << [chr, reg[:start], reg[:stop]]
+					end	
+				end
+				variants.each do |var|
+					if mode == :default
+						f.puts "#{id}\t#{terms.join('|')}\t#{var.join("\t")}"
+					elsif mode == :paco
+						f.puts "#{id}\t#{var.join("\t")}\t#{terms.join('|')}"
+					else
+						abort('Wrong save mode option, please try default or paco')
+					end
+				end
+			end
+		end
+	end
+
+	def export_phenopackets(output_folder, genome_assembly, vcf_index: nil)
+		ont = @@ont[Cohort.act_ont]
+		metaData = {
+			"createdBy" => "PETS",
+			"resources" => [{
+				"id" => "hp",
+				"name" => "human phenotype ontology",
+				"namespacePrefix" => "HP",
+				"url" => "http://purl.obolibrary.org/obo/hp.owl",
+#				"version" => "2018-03-08",
+				"iriPrefix" => "http://purl.obolibrary.org/obo/HP_"
+			}]
+		}
+
+		@profiles.each do |id, terms|
+			phenopacket = {metaData: metaData}
+			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},
+					classOfOnset: {"id" => "HP:0003577", "label" => "Congenital onset"}
+				}
+			end
+			phenopacket[:phenotypicFeatures] = phenotypicFeatures
+			if !vcf_index.nil? && vcf_index.include?(id)
+				htsFiles = []
+				htsFiles << {
+					"uri" => "file:/" + vcf_index[id],
+			        "description" => id,
+			        "htsFormat" => "VCF",
+			        "genomeAssembly" => genome_assembly,
+			        "individualToSampleIdentifiers" => { "patient1" => id }
+				}
+				phenopacket[:htsFiles] = htsFiles
+			end
+			File.open(File.join(output_folder, id.to_s + ".json"), "w") { |f| f.write JSON.pretty_generate(phenopacket) }
+			id_variants = @vars[id]
+			variants = []
+			if id_variants.nil? || id_variants.length == 0
+				variants << ['-', '-', '-']
+			else
+				id_variants.each do |chr, reg|
+					variants << [chr, reg[:start], reg[:stop]]
+				end	
+			end
+		end
+	end
+end

data/lib/pets/common_optparse.rb

@@ -0,0 +1,30 @@
+options[:chromosome_col] = nil
+opts.on("-c", "--chromosome_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the chromosome") do |data|
+  options[:chromosome_col] = data
+end
+
+options[:id_col] = nil
+opts.on("-d", "--pat_id_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the patient id") do |data|
+  options[:id_col] = data
+end
+
+options[:end_col] = nil
+opts.on("-e", "--end_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the end mutation coordinate") do |data|
+  options[:end_col] = data
+end
+
+options[:genome_assembly] = 'hg38'
+opts.on("-G", "--genome_assembly STRING", "Genome assembly version. Please choose between hg18, hg19 and hg38. Default hg38") do |data|
+  options[:genome_assembly] = data
+end
+
+options[:header] = true
+#chr\tstart\tstop
+opts.on("-H", "--header", "Set if the file has a line header. Default true") do 
+  options[:header] = false
+end
+
+options[:sex_col] = nil
+opts.on("-x", "--sex_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the patient sex") do |data|
+  options[:sex_col] = data
+end

data/lib/pets/constants.rb

@@ -0,0 +1,8 @@
+# Needs define ROOT_PATH constant in file requiring this file
+COMMON_OPTPARSE = File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'pets', 'common_optparse.rb'))
+REPORT_FOLDER = File.expand_path(File.join(ROOT_PATH, '..', 'templates'))
+EXTERNAL_DATA = File.expand_path(File.join(ROOT_PATH, '..', 'external_data'))
+EXTERNAL_CODE = File.expand_path(File.join(ROOT_PATH, '..', 'external_code'))
+HPO_FILE = File.join(EXTERNAL_DATA, 'hp.json')
+MONDO_FILE = File.join(EXTERNAL_DATA, 'mondo.obo')
+IC_FILE = File.join(EXTERNAL_DATA, 'uniq_hpo_with_CI.txt')