Class: BELParser::Language::Version1_0::Upgrades::VariationTransformation
- Inherits:
-
Object
- Object
- BELParser::Language::Version1_0::Upgrades::VariationTransformation
- 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
-
#dna_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt) ⇒ Object
and RNA.
-
#dna_trunc_conversion(parent_func, param_prefix, param_value, loc) ⇒ Object
and RNA.
- #on_term(term_node) ⇒ Object
- #protein_sub_conversion(parent_func, param_prefix, param_value, ref, loc, alt) ⇒ Object
- #protein_trunc_conversion(parent_func, param_prefix, param_value, loc) ⇒ Object
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 |