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 179 179: def list_output_formats 180: a = get_formatter_repositories.collect { |mod| mod.constants } 181: a.flatten! 182: a.collect! { |x| x.to_s.downcase.intern } 183: a 184: 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 157 157: def output(format = :fasta, options = {}) 158: formatter_const = format.to_s.capitalize.intern 159: 160: formatter_class = nil 161: get_formatter_repositories.each do |mod| 162: begin 163: formatter_class = mod.const_get(formatter_const) 164: rescue NameError 165: end 166: break if formatter_class 167: end 168: unless formatter_class then 169: raise "unknown format name #{format.inspect}" 170: end 171: 172: formatter_class.output(self, options) 173: end
The same as output(:fasta, :header=>definition, :width=>width) This method is intended to replace Bio::Sequence#to_fasta.
s = Bio::Sequence.new('atgc') puts s.output_fasta #=> "> \natgc\n"
Arguments:
Returns: | String object |
# File lib/bio/sequence/format.rb, line 196 196: def output_fasta(definition = nil, width = 70) 197: output(:fasta, :header=> definition, :width => width) 198: end