class MgNu::Sequence::Fastq
Attributes
header[RW]
header_description[RW]
header_name[RW]
offset[RW]
qualary[RW]
qualhdr[RW]
quality[RW]
Public Class Methods
new(options)
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create a new MgNu::Sequence::Fastq
object
Calls superclass method
MgNu::Sequence::new
# File lib/mgnu/sequence/fastq.rb, line 10 def initialize(options) super(options) options = {:offset => 64, :header => nil, :quality => nil}.merge! options @quality = options[:quality] @offset = options[:offset] @header = options[:header] temp = @header.split @header_name = temp.shift @header_description = temp.length > 0 ? temp.join(' ') : nil @qualhdr = options[:qualhdr] if options[:qualhdr] end
Public Instance Methods
to_fasta()
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# File lib/mgnu/sequence/fastq.rb, line 22 def to_fasta MgNu::Sequence::Fasta.new(:header => @header, :sequence => sequence) end
to_s()
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override to_s
representation
# File lib/mgnu/sequence/fastq.rb, line 27 def to_s "@#{@header}\n#{sequence}\n+\n#{@quality}\n" end
unpack_quality()
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Unpack the quality string and return an array of
offset-corrected integers
@params [Integer] offset platform dependent offset value to
substract from the quality score, defaults to most recent platform (i.e. illumina) (64)
@return [Array] the array of integers
# File lib/mgnu/sequence/fastq.rb, line 38 def unpack_quality # only compute this one time @quality.unpack('C*').map! { |x| x - @offset } end