Class: BELParser::Language::Version1_0::Upgrades::VariationTransformation

Inherits:
Object
  • Object
show all
Includes:
AST::Processor::Mixin, TermTransformation, Parsers::AST::Sexp
Defined in:
lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb

Constant Summary

Constants included from TermTransformation

TermTransformation::ACTIVITIES, TermTransformation::PMODTYPES

Instance Method Summary collapse

Methods included from TermTransformation

#collapse, #on_argument, #on_function, #on_nested_statement, #on_object, #on_observed_term, #on_simple_statement, #on_statement, #on_subject

Methods included from Parsers::AST::Sexp

#annotation_definition, #argument, #blank_line, build, #comment, #comment_line, #document_property, #domain, #function, #identifier, #keyword, #list, #list_item, #multi_identifier, #name, #namespace_definition, #nested_statement, #object, #observed_term, #parameter, #pattern, #prefix, #relationship, #set, #simple_statement, #statement, #string, #subject, #term, #unset, #uri, #url, #value

Methods included from AST::Processor::Mixin

#handler_missing, #process, #process_all

Instance Method Details

#dna_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt) ⇒ Object

and RNA



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# File 'lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb', line 83

def dna_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt)  # and RNA
  converted_parent_func =
    case parent_func
    when 'p', 'proteinAbundance'
      'p'
    when 'g', 'geneAbundance'
      'c'
    when 'r', 'rnaAbundance'
      'r'
    end

  term(
    function(
      identifier(parent_func)),
    argument(
      parameter(
        prefix(
          identifier(param_prefix)),
        value(
          identifier(param_value)))),
    argument(
      term(
        function(
          identifier('var')),
        argument(
          parameter(
            value(
              identifier(%("#{converted_parent_func}.#{loc}#{ref}>#{alt}"))))))))
end

#dna_trunc_conversion(parent_func, param_prefix, param_value, loc) ⇒ Object

and RNA



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# File 'lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb', line 133

def dna_trunc_conversion(parent_func, param_prefix, param_value, loc)  # and RNA
  converted_parent_func =
    case parent_func
    when 'p', 'proteinAbundance'
      'p'
    when 'g', 'geneAbundance'
      'c'
    when 'r', 'rnaAbundance'
      'r'
    end

  term(
    function(
      identifier(parent_func)),
    argument(
      parameter(
        prefix(
          identifier(param_prefix)),
        value(
          identifier(param_value)))),
    argument(
      term(
        function(
          identifier('var')),
        argument(
          parameter(
            value(
              identifier(%("#{converted_parent_func}.#{loc}*"))))))))
end

#on_term(term_node) ⇒ Object 



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# File 'lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb', line 14

def on_term(term_node)
  is_parent_func = ['p', 'proteinAbundance', 'r', 'rnaAbundance', 'g', 'geneAbundance'].include?(term_node.function.identifier.string_literal)
  parent_func    = term_node.function.identifier.string_literal

  unless is_parent_func
    return term_node.updated([process(term_node.function), term_node.arguments.map! {|arg| process(arg)}].flatten())
  end

  if term_node.arguments[0].parameter?
    param_prefix = term_node.arguments[0].child.prefix.identifier.string_literal
    param_value  = term_node.arguments[0].child.value.children[0].string_literal
  end

  if term_node.arguments[1].respond_to?('child') && term_node.arguments[1].child.respond_to?('function') && term_node.arguments[1].child.function
    is_sub_func = ['sub', 'substitution'].include?(term_node.arguments[1].child.function.identifier.string_literal)
    is_trunc_func = ['trunc', 'truncation'].include?(term_node.arguments[1].child.function.identifier.string_literal)
  end

  if is_sub_func || is_trunc_func
    if is_parent_func && is_sub_func
      variant_node = term_node.arguments[1].child
      ref = variant_node.arguments[0].child.value.children[0].string_literal
      loc = variant_node.arguments[1].child.value.children[0].string_literal
      alt = variant_node.arguments[2].child.value.children[0].string_literal

      if ['p'].include?(parent_func)
        return protein_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt)
      else
        return dna_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt)
      end
    end

    if is_parent_func && is_trunc_func

      variant_node = term_node.arguments[1].child
      loc = variant_node.arguments[0].child.value.children[0].string_literal

      if ['p'].include?(parent_func)
        return protein_trunc_conversion(parent_func, param_prefix, param_value, loc)
      else
        return dna_trunc_conversion(parent_func, param_prefix, param_value, loc)
      end

    end
  else
    term_node.updated([process(term_node.function), term_node.arguments.map! {|arg| process(arg)}].flatten())
  end
end

#protein_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt) ⇒ Object 



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# File 'lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb', line 63

def protein_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt)
  term(
    function(
      identifier(parent_func)),
    argument(
      parameter(
        prefix(
          identifier(param_prefix)),
        value(
          identifier(param_value)))),
    argument(
      term(
        function(
          identifier('var')),
        argument(
          parameter(
            value(
              identifier(%("#{parent_func}.#{ref}#{loc}#{alt}"))))))))
end

#protein_trunc_conversion(parent_func, param_prefix, param_value, loc) ⇒ Object 



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# File 'lib/bel_parser/language/version1_0/upgrades/variation_transformation.rb', line 113

def protein_trunc_conversion(parent_func, param_prefix, param_value, loc)
  term(
    function(
      identifier(parent_func)),
    argument(
      parameter(
        prefix(
          identifier(param_prefix)),
        value(
          identifier(param_value)))),
    argument(
      term(
        function(
          identifier('var')),
        argument(
          parameter(
            value(
              identifier(%("#{parent_func}.#{loc}*"))))))))
end