Class: Cohort_Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/pets/parsers/cohort_parser.rb

Class Method Summary collapse

Class Method Details

.check_variants(vars) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 100

def self.check_variants(vars)
	checked_vars = []
	vars.each do |var| #[chr, start, stop]
		if var.first == '-' # the chr must be defined
			STDERR.puts "WARNING: variant #{var.join(',')} has been removed"
		else
			checked_vars << var
		end
	end
	return vars
end

.create_cohort(records, options) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 66

def self.create_cohort(records, options)
	ont = Cohort.get_ontology(Cohort.act_ont)
	rejected_terms = []
	rejected_recs = []
	cohort = Cohort.new()
	records.each do |id, record|
		rec = record.first
		terms = rec.first
		if options[:names] # Translate hpo names 2 codes
			init_term_number = terms.length
			terms, rec_rejected_terms = ont.translate_names(terms)
			if !rec_rejected_terms.empty?
				STDERR.puts "WARNING: record #{id} has the unknown term NAMES '#{rec_rejected_terms.join(',')}'. Terms removed."
				rejected_terms.concat(rec_rejected_terms)
			end
			if terms.empty? && init_term_number > 0
				rejected_recs << id
				next
			end
		end
		if rec.length > 1 # there is genomic region attributes
			variants = record.map{|v| v[1..3] }
		else
			variants = [] # Not exists genomic region attributes so we create a empty array
		end
		other_attr = {}
		if options[:extracted_fields].include?(:sex_col) # Check for additional attributes. -1 is applied to ignore :id in extracted fields
			other_attr[:sex] = record.first[options[:extracted_fields].index(:sex_col) -1]
		end
		cohort.add_record([id, terms, check_variants(variants)], other_attr)
	end
	return cohort, rejected_terms.uniq, rejected_recs
end

.get_field_numbers2extract(field_names, fields2extract) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 60

def self.get_field_numbers2extract(field_names, fields2extract)
	fields2extract.each do |field, name|
		fields2extract[field] = field_names.index(name)
	end
end

.get_fields2extract(options) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 48

def self.get_fields2extract(options)
	fields2extract = {}
	[:id_col, :ont_col, :chromosome_col, :start_col, :end_col, :sex_col].each do |field|
		col = options[field]
		if !col.nil?
			col = col.to_i if !options[:header]
			fields2extract[field] = col
		end
	end
	return fields2extract
end

.load(options) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 2

def self.load(options)
	fields2extract = get_fields2extract(options)
	field_numbers = fields2extract.values
	records = read_records(options, fields2extract, field_numbers)
	options[:extracted_fields] = fields2extract.keys
	cohort, rejected_terms, rejected_recs = create_cohort(records, options)
	return cohort, rejected_terms, rejected_recs
end

.read_records(options, fields2extract, field_numbers) ⇒ Object 



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# File 'lib/pets/parsers/cohort_parser.rb', line 11

def self.read_records(options, fields2extract, field_numbers)
	records = {}
	count = 0
	File.open(options[:input_file]).each do |line|
		line.chomp!
		if options[:header] && count == 0
			line.gsub!(/#\s*/,'') # correct comment like	headers
			field_names = line.split("\t")
			get_field_numbers2extract(field_names, fields2extract)
			field_numbers = fields2extract.values
		else
			fields = line.split("\t")
			record = field_numbers.map{|n| fields[n]}
			if fields2extract[:id_col].nil?
				id = "rec_#{count}" #generate ids
			else
				id = record.shift
			end
			if !record[0].nil?
				record[0] = record[0].split(options[:separator])
			else
				record[0] = []
			end
			record[2] = record[2].to_i if !options[:start_col].nil?
			record[3] = record[3].to_i if !options[:end_col].nil?
			query = records[id]
			if query.nil?
				records[id] = [record]
			else
				query << record
			end
		end
		count +=1
	end
	return records
end