module Bio::Sequence::Format

DESCRIPTION ↑

A Mixin of methods used by Bio::Sequence#output to output sequences in common bioinformatic formats. These are not called in isolation.

USAGE ↑

# Given a Bio::Sequence object,
puts s.output(:fasta)
puts s.output(:genbank)
puts s.output(:embl)

Public Instance Methods

list_output_formats() click to toggle source

Returns a list of available output formats for the sequence

Arguments:

Returns

Array of Symbols

    # File lib/bio/sequence/format.rb
174 def list_output_formats
175   a = get_formatter_repositories.collect { |mod| mod.constants }
176   a.flatten!
177   a.collect! { |x| x.to_s.downcase.intern }
178   a
179 end
output(format = :fasta, options = {}) click to toggle source

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:

  • (required) format: :fasta, :genbank, or :embl

Returns

String object

    # File lib/bio/sequence/format.rb
152 def output(format = :fasta, options = {})
153   formatter_const = format.to_s.capitalize.intern
154 
155   formatter_class = nil
156   get_formatter_repositories.each do |mod|
157     begin
158       formatter_class = mod.const_get(formatter_const)
159     rescue NameError
160     end
161     break if formatter_class
162   end
163   unless formatter_class then
164     raise "unknown format name #{format.inspect}"
165   end
166 
167   formatter_class.output(self, options)
168 end
output_fasta(definition = nil, width = 70) click to toggle source

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:

  • (optional) definition: (String) definition line

  • (optional) width: (Integer) width (default 70)

Returns

String object

    # File lib/bio/sequence/format.rb
191 def output_fasta(definition = nil, width = 70)
192   output(:fasta, :header=> definition, :width => width)
193 end