Module: Mspire::LipidMaps

Defined in:
lib/mspire/lipid_maps.rb

Constant Summary collapse

DEFAULTS = 
{
  :high_res_mass => true,
  :rubabel_molecules => false,
  :molecular_formula_objects => true,
}

Class Method Summary collapse

Class Method Details

.parse_file(lipidmaps_tsv, opts = {}) ⇒ Object

returns an array of Lipids if high_res_mass is true (default), then the formula is used to calculate a higher resolution mass than what is in lipidmaps

:high_res_mass => true (ensures that a high res mass is present or calculated)



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# File 'lib/mspire/lipid_maps.rb', line 18

def self.parse_file(lipidmaps_tsv, opts={})
  require 'rubabel' if opts[:rubabel_molecules]

  opts = DEFAULTS.merge(opts)

  io = File.open(lipidmaps_tsv)
  header = io.readline.split("\t")
  # the lipidmaps_filetype
  lm_ft = case header.size
          when 8
            :programmatic
          when 20
            :download
          when 21
            :download_sd
          end
  index_mapping = 
    case lm_ft
    when :programmatic
      (0...(Mspire::Lipid.members.size)).to_a
    when :download, :download_sd
      indices = {
        :lm_id => 0,
        :systematic_name => 1,
        :category => 3,
        :main_class => 4,
        :mass => 5,
        :formula => 6,
        :pubchem_id => 7,
        :inchi_key => 8,
        :common_name => 11,
        :kegg_id => 12,
        :chebi_id => 13,
        :sub_class => 14,
        :structure => 20,
      }
      Mspire::Lipid.members.map {|key| indices[key] }
    end
  
  formula_i = index_mapping[Mspire::Lipid.members.index(:formula)]

  lipids = io.each_line.map do |line|
    line.chomp!
    data = line.split("\t")
    if data[formula_i] =~ /[A-Z]/  # <- there is a formula!
      lipid = Mspire::Lipid.new( *index_mapping.map {|i| data[i] } )
      lipid.mass = lipid.mass.to_f
      lipid
    end
  end.compact

  if opts.values_at(:molecular_formula_objects, :rubabel_molecules).any? || (opts[:high_res_mass] && lm_ft == :programmatic)
    lipids.each do |lipid|
      if opts[:molecular_formula_objects]
        lipid.formula = Mspire::MolecularFormula.from_string(lipid.formula)
      end
      if lm_ft == :programmatic && opts[:high_res_mass]
        lipid.mass = Mspire::Mass.formula_to_exact_mass(lipid.formula)
      end
      if opts[:rubabel_molecules]
        lipid.structure = Rubabel::Molecule.from_string(lipid.structure.gsub('|', "\n"), :sdf)
      end
    end
  end
  lipids
end