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
Source
# File lib/bio/db/fasta/qual.rb 94 def [](n) 95 data[n] 96 end
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 64 def data 65 unless defined?(@list) 66 @list = @data.strip.split(/\s+/).map {|x| x.to_i} 67 end 68 @list 69 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 83 def each 84 data.each do |x| 85 yield x 86 end 87 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 75 def length 76 data.length 77 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 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
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