class Bio::FastaNumericFormat

Treats a FASTA formatted numerical entry, such as:

>id and/or some comments                    <== comment line
24 15 23 29 20 13 20 21 21 23 22 25 13      <== numerical data
22 17 15 25 27 32 26 32 29 29 25

The precedent ‘>’ can be omitted and the trailing ‘>’ will be removed automatically.

— Bio::FastaNumericFormat.new(entry)

Stores the comment and the list of the numerical data.

— Bio::FastaNumericFormat#definition

The comment line of the FASTA formatted data.

FASTA format (Wikipedia) en.wikipedia.org/wiki/FASTA_format
Phred quality score (WikiPedia) en.wikipedia.org/wiki/Phred_quality_score

Public Instance Methods

[](n) click to toggle source

Returns the n-th element. If out of range, returns nil.

Arguments:

(required) n: (Integer) position

Returns: (Integer or nil) the value

   # File lib/bio/db/fasta/qual.rb
94 def [](n)
95   data[n]
96 end

data() click to toggle source

Returns the list of the numerical data (typically the quality score of its corresponding sequence) as an Array.

Returns: (Array containing Integer) numbers

   # File lib/bio/db/fasta/qual.rb
64 def data
65   unless defined?(@list)
66     @list = @data.strip.split(/\s+/).map {|x| x.to_i}
67   end
68   @list
69 end

each() { |x| ... } click to toggle source

Yields on each elements of the numerical data.

Yields: (Integer) a numerical data element
Returns: (undefined)

   # File lib/bio/db/fasta/qual.rb
83 def each
84   data.each do |x|
85     yield x
86   end
87 end

length() click to toggle source

Returns the number of elements in the numerical data, which will be the same of its corresponding sequence length.

Returns: (Integer) the number of elements

   # File lib/bio/db/fasta/qual.rb
75 def length
76   data.length
77 end

to_biosequence() click to toggle source

Returns the data as a Bio::Sequence object. In the returned sequence object, the length of the sequence is zero, and the numeric data is stored to the Bio::Sequence#quality_scores attirbute.

Because the meaning of the numeric data is unclear, Bio::Sequence#quality_score_type is not set by default.

Note: If you modify the returned Bio::Sequence object, the sequence or definition in this FastaNumericFormat object might also be changed (but not always be changed) because of efficiency.

Arguments:

Returns: (Bio::Sequence) sequence object

    # File lib/bio/db/fasta/qual.rb
114 def to_biosequence
115   s = Bio::Sequence.adapter(self,
116                             Bio::Sequence::Adapter::FastaNumericFormat)
117   s.seq = Bio::Sequence::Generic.new('')
118   s
119 end

Also aliased as: to_seq

to_seq()

Alias for: to_biosequence