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