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#
# = bio/sequence/quality_score.rb - Sequence quality score manipulation modules
#
# Copyright:: Copyright (C) 2009
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# == Description
#
# Sequence quality score manipulation modules, mainly used by Bio::Fastq
# and related classes.
#
# == References
#
# * FASTQ format specification
# http://maq.sourceforge.net/fastq.shtml
#
module Bio
require 'bio/sequence' unless const_defined?(:Sequence)
class Sequence
# Bio::Sequence::QualityScore is a name space for quality score modules.
# BioRuby internal use only (mainly from Bio::Fastq).
module QualityScore
# Converter methods between PHRED and Solexa quality scores.
module Converter
# Converts PHRED scores to Solexa scores.
#
# The values may be truncated or incorrect if overflows/underflows
# occurred during the calculation.
# ---
# *Arguments*:
# * (required) _scores_: (Array containing Integer) quality scores
# *Returns*:: (Array containing Integer) quality scores
def convert_scores_from_phred_to_solexa(scores)
sc = scores.collect do |q|
t = 10 ** (q / 10.0) - 1
t = Float::MIN if t < Float::MIN
r = 10 * Math.log10(t)
r.finite? ? r.round : r
end
sc
end
# Converts Solexa scores to PHRED scores.
#
# The values may be truncated if overflows/underflows occurred
# during the calculation.
# ---
# *Arguments*:
# * (required) _scores_: (Array containing Integer) quality scores
# *Returns*:: (Array containing Integer) quality scores
def convert_scores_from_solexa_to_phred(scores)
sc = scores.collect do |q|
r = 10 * Math.log10(10 ** (q / 10.0) + 1)
r.finite? ? r.round : r
end
sc
end
# Does nothing and simply returns the given argument.
#
# ---
# *Arguments*:
# * (required) _scores_: (Array containing Integer) quality scores
# *Returns*:: (Array containing Integer) quality scores
def convert_nothing(scores)
scores
end
end #module Converter
# Bio::Sequence::QualityScore::Phred is a module having quality calculation
# methods for the PHRED quality score.
#
# BioRuby internal use only (mainly from Bio::Fastq).
module Phred
include Converter
# Type of quality scores.
# ---
# *Returns*:: (Symbol) the type of quality score.
def quality_score_type
:phred
end
# PHRED score to probability conversion.
# ---
# *Arguments*:
# * (required) _scores_: (Array containing Integer) scores
# *Returns*:: (Array containing Float) probabilities (0<=p<=1)
def phred_q2p(scores)
scores.collect do |q|
r = 10 ** (- q / 10.0)
if r > 1.0 then
r = 1.0
#elsif r < 0.0 then
# r = 0.0
end
r
end
end
alias q2p phred_q2p
module_function :q2p
public :q2p
# Probability to PHRED score conversion.
#
# The values may be truncated or incorrect if overflows/underflows
# occurred during the calculation.
# ---
# *Arguments*:
# * (required) _probabilities_: (Array containing Float) probabilities
# *Returns*:: (Array containing Float) scores
def phred_p2q(probabilities)
probabilities.collect do |p|
p = Float::MIN if p < Float::MIN
q = -10 * Math.log10(p)
q.finite? ? q.round : q
end
end
alias p2q phred_p2q
module_function :p2q
public :p2q
alias convert_scores_from_phred convert_nothing
alias convert_scores_to_phred convert_nothing
alias convert_scores_from_solexa convert_scores_from_solexa_to_phred
alias convert_scores_to_solexa convert_scores_from_phred_to_solexa
module_function :convert_scores_to_solexa
public :convert_scores_to_solexa
end #module Phred
# Bio::Sequence::QualityScore::Solexa is a module having quality
# calculation methods for the Solexa quality score.
#
# BioRuby internal use only (mainly from Bio::Fastq).
module Solexa
include Converter
# Type of quality scores.
# ---
# *Returns*:: (Symbol) the type of quality score.
def quality_score_type
:solexa
end
# Solexa score to probability conversion.
# ---
# *Arguments*:
# * (required) _scores_: (Array containing Integer) scores
# *Returns*:: (Array containing Float) probabilities
def solexa_q2p(scores)
scores.collect do |q|
t = 10 ** (- q / 10.0)
t /= (1.0 + t)
if t > 1.0 then
t = 1.0
#elsif t < 0.0 then
# t = 0.0
end
t
end
end
alias q2p solexa_q2p
module_function :q2p
public :q2p
# Probability to Solexa score conversion.
# ---
# *Arguments*:
# * (required) _probabilities_: (Array containing Float) probabilities
# *Returns*:: (Array containing Float) scores
def solexa_p2q(probabilities)
probabilities.collect do |p|
t = p / (1.0 - p)
t = Float::MIN if t < Float::MIN
q = -10 * Math.log10(t)
q.finite? ? q.round : q
end
end
alias p2q solexa_p2q
module_function :p2q
public :p2q
alias convert_scores_from_solexa convert_nothing
alias convert_scores_to_solexa convert_nothing
alias convert_scores_from_phred convert_scores_from_phred_to_solexa
alias convert_scores_to_phred convert_scores_from_solexa_to_phred
module_function :convert_scores_to_phred
public :convert_scores_to_phred
end #module Solexa
end #module QualityScore
end #class Sequence
end #module Bio
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