Class: Bio::Sequence::Format::Formatter::Fasta_numeric

Inherits:
Bio::Sequence::Format::FormatterBase show all
Defined in:
lib/bio/db/fasta/format_qual.rb

Overview

INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS. Simple FastaNumeric format output class for Bio::Sequence.

Direct Known Subclasses

Qual

Instance Method Summary collapse

Methods inherited from Bio::Sequence::Format::FormatterBase

output

Constructor Details

#initializeFasta_numeric

Returns a new instance of Fasta_numeric



33
# File 'lib/bio/db/fasta/format_qual.rb', line 33

def initialize; end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Bio::Sequence::Format::FormatterBase

Instance Method Details

#outputObject

INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.

Output the FASTA format string of the sequence.

Currently, this method is used in Bio::Sequence#output like so,

s = Bio::Sequence.new('atgc')
s.quality_scores = [ 70, 80, 90, 100 ]
puts s.output(:fasta_numeric)

Returns

String object



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# File 'lib/bio/db/fasta/format_qual.rb', line 46

def output
  header = @options[:header]
  width = @options.has_key?(:width) ? @options[:width] : 70
  seq = @sequence.seq.to_s
  entry_id = @sequence.entry_id || 
    "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
  definition = @sequence.definition
  header ||= "#{entry_id} #{definition}"

  sc = fastanumeric_quality_scores(seq)
  if width then
    if width <= 0 then
      main = sc.join("\n")
    else
      len = 0
      main = sc.collect do |x|
        str = (len == 0) ? "#{x}" : " #{x}"
        len += str.size
        if len > width then
          len = "#{x}".size
          str = "\n#{x}"
        end
        str
      end.join('')
    end
  else
    main = sc.join(' ')
  end

  ">#{header}\n#{main}\n"
end