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
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, line 94 def [](n) data[n] end
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, line 64 def data unless defined?(@list) @list = @data.strip.split(/\s+/).map {|x| x.to_i} end @list end
Yields on each elements of the numerical data.
Yields |
(Integer) a numerical data element |
Returns |
(undefined) |
# File lib/bio/db/fasta/qual.rb, line 83 def each data.each do |x| yield x end 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 |
# File lib/bio/db/fasta/qual.rb, line 75 def length data.length 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 |
# File lib/bio/db/fasta/qual.rb, line 114 def to_biosequence s = Bio::Sequence.adapter(self, Bio::Sequence::Adapter::FastaNumericFormat) s.seq = Bio::Sequence::Generic.new('') s end
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