class Bio::Sequence::Format::Formatter::Fasta_numeric

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

Public Class Methods

new() click to toggle source

INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.

Creates a new FastaNumericFormat generater object from the sequence.

It does not care whether the content of the quality score is consistent with the sequence or not, e.g. it does not check length of the quality score.

Arguments:

  • sequence: Bio::Sequence object

  • (optional) :header => header: (String) (default nil)

  • (optional) :width => width: (Fixnum) (default 70)

   # File lib/bio/db/fasta/format_qual.rb
28 def initialize; end

Public Instance Methods

output() click to toggle source

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

   # File lib/bio/db/fasta/format_qual.rb
41 def output
42   header = @options[:header]
43   width = @options.has_key?(:width) ? @options[:width] : 70
44   seq = @sequence.seq.to_s
45   entry_id = @sequence.entry_id || 
46     "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
47   definition = @sequence.definition
48   header ||= "#{entry_id} #{definition}"
49 
50   sc = fastanumeric_quality_scores(seq)
51   if width then
52     if width <= 0 then
53       main = sc.join("\n")
54     else
55       len = 0
56       main = sc.collect do |x|
57         str = (len == 0) ? "#{x}" : " #{x}"
58         len += str.size
59         if len > width then
60           len = "#{x}".size
61           str = "\n#{x}"
62         end
63         str
64       end.join('')
65     end
66   else
67     main = sc.join(' ')
68   end
69 
70   ">#{header}\n#{main}\n"
71 end