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 173
173:   def list_output_formats
174:     a = get_formatter_repositories.collect { |mod| mod.constants }
175:     a.flatten!
176:     a.collect! { |x| x.to_s.downcase.intern }
177:     a
178:   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 151
151:   def output(format = :fasta, options = {})
152:     formatter_const = format.to_s.capitalize.intern
153: 
154:     formatter_class = nil
155:     get_formatter_repositories.each do |mod|
156:       begin
157:         formatter_class = mod.const_get(formatter_const)
158:       rescue NameError
159:       end
160:       break if formatter_class
161:     end
162:     unless formatter_class then
163:       raise "unknown format name #{format.inspect}"
164:     end
165: 
166:     formatter_class.output(self, options)
167:   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:

  • (optional) definition: (String) definition line
  • (optional) width: (Integer) width (default 70)
Returns:String object

[Source]

     # File lib/bio/sequence/format.rb, line 190
190:   def output_fasta(definition = nil, width = 70)
191:     output(:fasta, :header=> definition, :width => width)
192:   end

[Validate]