Module | Bio::Sequence::Format |
In: |
lib/bio/sequence/format.rb
|
Returns a list of available output formats for the sequence
Arguments:
Returns: | Array of Symbols |
# File lib/bio/sequence/format.rb, line 163 163: def list_output_formats 164: a = get_formatter_repositories.collect { |mod| mod.constants } 165: a.flatten! 166: a.collect! { |x| x.to_s.downcase.intern } 167: a 168: end
Using Bio::Sequence::Format, return a String with the Bio::Sequence object formatted in the given style.
Formats currently implemented are: ‘fasta’, ‘genbank’, and ‘embl‘
s = Bio::Sequence.new('atgc') puts s.output(:fasta) #=> "> \natgc\n"
The style argument is given as a Ruby Symbol(www.ruby-doc.org/core/classes/Symbol.html)
Arguments:
Returns: | String object |
# File lib/bio/sequence/format.rb, line 141 141: def output(format = :fasta, options = {}) 142: formatter_const = format.to_s.capitalize.intern 143: 144: formatter_class = nil 145: get_formatter_repositories.each do |mod| 146: begin 147: formatter_class = mod.const_get(formatter_const) 148: rescue NameError 149: end 150: break if formatter_class 151: end 152: unless formatter_class then 153: raise "unknown format name #{format.inspect}" 154: end 155: 156: formatter_class.output(self, options) 157: end