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

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

Returns a list of available output formats for the sequence


Arguments:

Returns:Array of Symbols

[Source]

     # 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:

  • (required) format: :fasta, :genbank, or :embl
Returns:String object

[Source]

     # 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

[Validate]