Module: Bio::Sequence::Format

Included in:
Bio::Sequence
Defined in:
lib/bio/sequence/format.rb

Overview

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)

Defined Under Namespace

Modules: AminoFormatter, Formatter, INSDFeatureHelper, NucFormatter Classes: FormatterBase

Instance Method Summary collapse

Instance Method Details

#list_output_formats ⇒ Object

Returns a list of available output formats for the sequence

Arguments:

Returns

Array of Symbols



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# File 'lib/bio/sequence/format.rb', line 173

def list_output_formats
  a = get_formatter_repositories.collect { |mod| mod.constants }
  a.flatten!
  a.collect! { |x| x.to_s.downcase.intern }
  a
end

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

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



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# File 'lib/bio/sequence/format.rb', line 151

def output(format = :fasta, options = {})
  formatter_const = format.to_s.capitalize.intern

  formatter_class = nil
  get_formatter_repositories.each do |mod|
    begin
      formatter_class = mod.const_get(formatter_const)
    rescue NameError
    end
    break if formatter_class
  end
  unless formatter_class then
    raise "unknown format name #{format.inspect}"
  end

  formatter_class.output(self, options)
end

#output_fasta(definition = nil, width = 70) ⇒ Object

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



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# File 'lib/bio/sequence/format.rb', line 190

def output_fasta(definition = nil, width = 70)
  output(:fasta, :header=> definition, :width => width)
end