Class: GenomerPluginValidate::Validator::Gff3Attributes

Inherits:
Genomer::Plugin
  • Object
show all
Defined in:
lib/genomer-plugin-validate/validator/gff3_attributes.rb

Instance Method Summary collapse

Instance Method Details

#run ⇒ Object 



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# File 'lib/genomer-plugin-validate/validator/gff3_attributes.rb', line 8

def run
  annotations.
    map{|attn| attn.attributes.map{|(k,v)| [k,attn] }}.
    flatten(1).
    select{|(term,_)| term =~ (/^[A-Z]/) }.
    reject{|(term,_)| valid_gff3_attributes.include? term }.
    map{|(term,attn)| "Illegal GFF3 attribute '#{term}' for '#{attn.id}'"}
end

#valid_gff3_attributes ⇒ Object 



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# File 'lib/genomer-plugin-validate/validator/gff3_attributes.rb', line 3

def valid_gff3_attributes
  %w|ID Name Alias Parent Target Gap Derives_from Note
    Dbxref Ontology_term Is_circular|
end