Class Bio::FastaNumericFormat
In: lib/bio/db/fasta/qual.rb
Parent: FastaFormat

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.

Methods

[]   data   each   length   to_biosequence   to_seq  

Public Instance methods

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


Arguments:

  • (required) n: (Integer) position
Returns:(Integer or nil) the value

[Source]

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

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


Returns:(Array containing Integer) numbers

[Source]

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

Yields on each elements of the numerical data.


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

[Source]

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

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

[Source]

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

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

[Source]

     # File lib/bio/db/fasta/qual.rb, line 114
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
to_seq()

Alias for to_biosequence

[Validate]