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.
Returns the n-th element. If out of range, returns nil.
Arguments:
Returns: | (Integer or nil) the value |
# 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 |
# 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
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 114 114: 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