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Versions: 8
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Stored size: 1.15 KB
Contents
require 'validator'
class Validator::TruePos < Validator
include Precision::Calculator
attr_reader :fasta
attr_accessor :correct_wins
# correct_wins means that only a single protein from a pep.aaseq must match
# the fasta object for the pep hit to be considered valid. Otherwise, all
# must be a match
def initialize(fasta_obj, correct_wins = true)
@fasta = fasta_obj
@fasta_headers = @fasta.prots.map {|prot| prot.header }
@correct_wins = correct_wins
end
def partition(peps)
if @correct_wins
peps.partition do |pep|
@fasta_headers.any? do |header|
pep.prots.any? do |pepprot|
header.include? pepprot.reference
end
end
end
else
peps.partition do |pep|
pep.prots.all? do |pepprot|
@fasta_headers.any? do |header|
header.include? pepprot.reference
end
end
end
end
end
def pephit_precision(peps)
(tp, fp) = partition(peps)
calc_precision(tp.size, fp.size)
end
def to_param_string
"true_positives(tps)=" + ["{fasta=#{@fasta.filename}", "correct_wins=#{@correct_wins}}"].join(", ")
end
end
Version data entries
8 entries across 8 versions & 1 rubygems