Module Bio::Sequence::Format
In: lib/bio/sequence/format.rb

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)

Methods

list_output_formats   output  

Classes and Modules

Module Bio::Sequence::Format::AminoFormatter
Module Bio::Sequence::Format::Formatter
Module Bio::Sequence::Format::INSDFeatureHelper
Module Bio::Sequence::Format::NucFormatter
Class Bio::Sequence::Format::FormatterBase

Public Instance methods

list_output_formats()

Returns a list of available output formats for the sequence

Arguments:

Returns:Array of Symbols

[Source]

     # 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
output(format = :fasta, options = {})

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

[Source]

     # 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

[Validate]