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Contents
# Copyright 2014, 2015 Ryan Moore
# Contact: moorer@udel.edu
#
# This file is part of parse_fasta.
#
# parse_fasta is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# parse_fasta is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
require 'spec_helper'
require 'bio'
describe Quality do
let(:qual_string) { qual_string = Quality.new('ab%63:K') }
let(:bioruby_qual_scores) do
Bio::Fastq.new("@seq1\nACTGACT\n+\n#{qual_string}").quality_scores
end
describe "#qual_scores" do
context "with illumina style quality scores" do
it "returns an array of quality scores" do
expect(qual_string.qual_scores).to eq bioruby_qual_scores
end
end
end
describe "#mean_qual" do
it "returns the mean quality for the quality string" do
len = qual_string.length.to_f
mean_quality = qual_string.qual_scores.reduce(:+) / len
expect(qual_string.mean_qual).to eq mean_quality
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems