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#
# = bio/db/fasta/qual.rb - Qual format, FASTA formatted numeric entry
#
# Copyright:: Copyright (C) 2001, 2002, 2009
# Naohisa Goto <ng@bioruby.org>,
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
# QUAL format, FASTA formatted numeric entry.
#
# == Examples
#
# See documents of Bio::FastaNumericFormat class.
#
# == References
#
# * FASTA format (WikiPedia)
# http://en.wikipedia.org/wiki/FASTA_format
#
# * Phred quality score (WikiPedia)
# http://en.wikipedia.org/wiki/Phred_quality_score
#
# * Fasta format description (NCBI)
# http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
#
require 'bio/db/fasta'
module Bio
# 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)
# http://en.wikipedia.org/wiki/FASTA_format
#
# * Phred quality score (WikiPedia)
# http://en.wikipedia.org/wiki/Phred_quality_score
#
class FastaNumericFormat < FastaFormat
# Returns the list of the numerical data (typically the quality score
# of its corresponding sequence) as an Array.
# ---
# *Returns*:: (Array containing Integer) numbers
def data
unless defined?(@list)
@list = @data.strip.split(/\s+/).map {|x| x.to_i}
end
@list
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
def length
data.length
end
# Yields on each elements of the numerical data.
# ---
# *Yields*:: (Integer) a numerical data element
# *Returns*:: (undefined)
def each
data.each do |x|
yield x
end
end
# Returns the n-th element. If out of range, returns nil.
# ---
# *Arguments*:
# * (required) _n_: (Integer) position
# *Returns*:: (Integer or nil) the value
def [](n)
data[n]
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
def to_biosequence
s = Bio::Sequence.adapter(self,
Bio::Sequence::Adapter::FastaNumericFormat)
s.seq = Bio::Sequence::Generic.new('')
s
end
alias to_seq to_biosequence
undef query, blast, fasta, seq, naseq, nalen, aaseq, aalen
end #class FastaNumericFormat
end #module Bio
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