vienna_rna 0.4.4 → 0.5.1
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- checksums.yaml +4 -4
- data/lib/vienna_rna/modules/graphing.rb +177 -0
- data/lib/vienna_rna/modules/rna.rb +5 -1
- data/lib/vienna_rna/modules/utils.rb +0 -97
- data/lib/vienna_rna/modules/xbor.rb +2 -2
- data/lib/vienna_rna.rb +3 -0
- metadata +17 -2
checksums.yaml
CHANGED
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 11244542ad92a82ba2d504e21688cf47a58d3c2b
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data.tar.gz: aed5057e2cb136a593f73b30e6ea178f58f0815b
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0472640b877355124a29e88f61293b5fb33fb1ba59badbf1dbbbf25028e40cbd0f773904d23ad55288468b84e9a7c56a1dc3377832ac3862e10c12a2592cd4a7
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data.tar.gz: e1930c78ac509d2fde5e52fbcffdf25cfc3ebe28e52573196abcbf71d750cd6afa9c74c23b4ff1f882ec488453a31f6fa05f588c3b2cfbc14fed24a0d5e0d415
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@@ -0,0 +1,177 @@
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module ViennaRna
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module Graphing
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module R
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class << self
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def graph(&block)
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begin
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(yield r_instance = RinRuby.new).tap { ap r_instance.close }
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rescue RuntimeError => e
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raise unless e.message == "Unsupported data type on R's end"
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end
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end
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def pdf(string)
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end
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def histogram(data, title: nil, x_label: "Bins", bin_size: 1, filename: false)
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half = bin_size / 2.0
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range = Range.new((data.min - half).floor, (data.max + half).ceil)
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breaks = (range.min + half).step(range.max + half, bin_size).to_a
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graph do |r|
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r.assign("histogram.data", data)
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r.assign("histogram.breaks", breaks)
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if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
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r.eval <<-STR
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pdf("#{filename}", 6, 6)
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hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}")
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dev.off()
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STR
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else
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r.eval <<-STR
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quartz("Histogram", 6, 6)
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hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}")
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STR
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end
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end
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end
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def roc(data, title = "", options = {})
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# data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]
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if R.pull("ifelse('ROCR' %in% rownames(installed.packages()), 1, -1)") > 0
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else
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puts "Please install the ROCR package for R before using this function."
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end
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# roc_curve = ROC.curve_points({ 1 => data[0], -1 => data[1] }.inject([]) { |data, (truth, values)| data.concat(values.map { |i| [i, truth] })})
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# area = roc_curve.each_cons(2).inject(0) do |sum, (a, b)|
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# delta_x, delta_y = b[0] - a[0], b[1] - a[1]
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# sum + (delta_x * delta_y / 2 + delta_x * [a[1], b[1]].min)
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# end
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# options.merge!(output: "file") if options[:filename]
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# options.merge!({ plot: { title: "%s %s %.4f" % [title, "AUC:", area] } })
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# plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
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end
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# def quick_plot(data, title = "", options = {})
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# quick_overlay([{ data: data }], title, options)
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# end
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# def quick_overlay(data, title = "", options = {})
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# # [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
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# options[:plot] = ((options[:plot] || {}).merge(title: title))
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# options.merge!(output: "file") if options[:filename]
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# plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" }.merge(hash[:options] || {}) }, options)
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# end
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end
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end
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module Gnuplot
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class << self
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def plot(data, options = {})
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Gnuplot.open do |gnuplot|
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Gnuplot::Plot.new(gnuplot) do |plot|
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plot.autoscale
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case options[:output]
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when /file/i then
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plot.output(options[:filename])
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plot.terminal("png size %s" % (options[:dimensions] || "800,600"))
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end
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(options[:plot] || {}).keys.each do |option|
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plot.send(option, options[:plot][option])
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end
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plot.data = data.map do |data_hash|
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Gnuplot::DataSet.new([data_hash[:x], data_hash[:y]]) do |dataset|
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dataset.with = data_hash[:style] || "points"
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dataset.linecolor = "rgb '#{data_hash[:color]}'" if data_hash[:color]
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data_hash[:title] ? dataset.title = data_hash[:title] : dataset.notitle
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end
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end
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end
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end
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end
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def splot(data, options = {})
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# [[x_1, y_1, z_1], [x_2, y_2, z_2], ...]
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orthogonal_data = data.inject([[], [], []]) { |array, list| array.zip(list).map { |a, e| a << e } }
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Gnuplot.open do |gnuplot|
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Gnuplot::SPlot.new(gnuplot) do |plot|
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plot.autoscale
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case options[:output]
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when /file/i then
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plot.output(options[:filename])
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plot.terminal("png size 800,600")
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end
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(options[:plot] || {}).keys.each do |option|
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plot.send(option, options[:plot][option])
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end
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plot.data = [
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Gnuplot::DataSet.new(orthogonal_data) do |dataset|
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dataset.with = options[:style] || "lines"
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end
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]
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end
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end
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end
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def histogram(data, title = "", options = {})
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bin_size = options.delete(:bin_size) || 1
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half = bin_size / 2.0
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range = Range.new((data.min - half).floor, (data.max + half).ceil)
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groups = (range.min + half).step(range.max, bin_size).map { |x| [x, data.count { |i| i >= x - half && i < x + half }] }
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options.merge!(output: "file") if options[:filename]
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options[:plot] = (options[:plot] || {}).merge({
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title: title,
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yrange: "[0:#{groups.map(&:last).max * 1.1}]",
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xtics: "#{[bin_size, 5].max}",
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style: "fill solid 0.5 border"
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})
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plot([{ x: groups.map(&:first), y: groups.map(&:last), style: "boxes" }], options)
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end
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def roc(data, title = "", options = {})
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# data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]~
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roc_curve = ROC.curve_points({ 1 => data[0], -1 => data[1] }.inject([]) { |data, (truth, values)| data.concat(values.map { |i| [i, truth] })})
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area = roc_curve.each_cons(2).inject(0) do |sum, (a, b)|
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delta_x, delta_y = b[0] - a[0], b[1] - a[1]
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sum + (delta_x * delta_y / 2 + delta_x * [a[1], b[1]].min)
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end
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options.merge!(output: "file") if options[:filename]
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options.merge!({ plot: { title: "%s %s %.4f" % [title, "AUC:", area] } })
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plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
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end
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def quick_plot(data, title = "", options = {})
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quick_overlay([{ data: data }], title, options)
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end
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def quick_overlay(data, title = "", options = {})
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# [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
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options[:plot] = ((options[:plot] || {}).merge(title: title))
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options.merge!(output: "file") if options[:filename]
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plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" }.merge(hash[:options] || {}) }, options)
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end
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end
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end
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end
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end
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@@ -63,7 +63,11 @@ module ViennaRna
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end
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def run(module_name, options = {})
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-
ViennaRna.const_missing("#{module_name}".camelize)
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if rna_module = ViennaRna.const_missing("#{module_name}".camelize)
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rna_module.run(self, options)
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else
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raise ArgumentError.new("#{module_name} can't be resolved as an executable")
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end
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end
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private
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@@ -29,103 +29,6 @@ module ViennaRna
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((x_matrix.transpose * x_matrix).inverse * x_matrix.transpose * y_matrix).transpose.to_a[0]
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end
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-
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def plot(data, options = {})
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34
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Gnuplot.open do |gnuplot|
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35
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Gnuplot::Plot.new(gnuplot) do |plot|
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plot.autoscale
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case options[:output]
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when /file/i then
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plot.output(options[:filename])
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plot.terminal("png size %s" % (options[:dimensions] || "800,600"))
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end
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-
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(options[:plot] || {}).keys.each do |option|
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plot.send(option, options[:plot][option])
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end
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47
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-
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plot.data = data.map do |data_hash|
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49
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Gnuplot::DataSet.new([data_hash[:x], data_hash[:y]]) do |dataset|
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50
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dataset.with = data_hash[:style] || "points"
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dataset.linecolor = "rgb '#{data_hash[:color]}'" if data_hash[:color]
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-
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data_hash[:title] ? dataset.title = data_hash[:title] : dataset.notitle
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end
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end
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end
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end
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end
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-
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60
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def splot(data, options = {})
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61
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# [[x_1, y_1, z_1], [x_2, y_2, z_2], ...]
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62
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-
orthogonal_data = data.inject([[], [], []]) { |array, list| array.zip(list).map { |a, e| a << e } }
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63
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-
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64
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Gnuplot.open do |gnuplot|
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Gnuplot::SPlot.new(gnuplot) do |plot|
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plot.autoscale
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-
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68
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case options[:output]
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when /file/i then
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plot.output(options[:filename])
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plot.terminal("png size 800,600")
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end
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-
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(options[:plot] || {}).keys.each do |option|
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plot.send(option, options[:plot][option])
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end
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77
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-
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78
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plot.data = [
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79
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Gnuplot::DataSet.new(orthogonal_data) do |dataset|
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80
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dataset.with = options[:style] || "lines"
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end
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]
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end
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84
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end
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85
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end
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86
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-
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87
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-
def histogram(data, title = "", options = {})
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88
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-
bin_size = options.delete(:bin_size) || 1
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89
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-
half = bin_size / 2.0
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90
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-
range = Range.new((data.min - half).floor, (data.max + half).ceil)
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91
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-
groups = (range.min + half).step(range.max, bin_size).map { |x| [x, data.count { |i| i >= x - half && i < x + half }] }
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92
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-
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93
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options.merge!(output: "file") if options[:filename]
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options[:plot] = (options[:plot] || {}).merge({
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-
title: title,
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96
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-
yrange: "[0:#{groups.map(&:last).max * 1.1}]",
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97
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xtics: "#{[bin_size, 5].max}",
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style: "fill solid 0.5 border"
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})
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-
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plot([{ x: groups.map(&:first), y: groups.map(&:last), style: "boxes" }], options)
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-
end
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103
|
-
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104
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-
def roc(data, title = "", options = {})
|
|
105
|
-
# data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]~
|
|
106
|
-
roc_curve = ROC.curve_points({ 1 => data[0], -1 => data[1] }.inject([]) { |data, (truth, values)| data.concat(values.map { |i| [i, truth] })})
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107
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-
area = roc_curve.each_cons(2).inject(0) do |sum, (a, b)|
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108
|
-
delta_x, delta_y = b[0] - a[0], b[1] - a[1]
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109
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sum + (delta_x * delta_y / 2 + delta_x * [a[1], b[1]].min)
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110
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-
end
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111
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-
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112
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-
options.merge!(output: "file") if options[:filename]
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113
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-
options.merge!({ plot: { title: "%s %s %.4f" % [title, "AUC:", area] } })
|
|
114
|
-
|
|
115
|
-
plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
|
|
116
|
-
end
|
|
117
|
-
|
|
118
|
-
def quick_plot(data, title = "", options = {})
|
|
119
|
-
quick_overlay([{ data: data }], title, options)
|
|
120
|
-
end
|
|
121
|
-
|
|
122
|
-
def quick_overlay(data, title = "", options = {})
|
|
123
|
-
# [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
|
|
124
|
-
options[:plot] = ((options[:plot] || {}).merge(title: title))
|
|
125
|
-
options.merge!(output: "file") if options[:filename]
|
|
126
|
-
|
|
127
|
-
plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" }.merge(hash[:options] || {}) }, options)
|
|
128
|
-
end
|
|
129
32
|
end
|
|
130
33
|
end
|
|
131
34
|
end
|
|
@@ -50,7 +50,7 @@ module ViennaRna
|
|
|
50
50
|
end
|
|
51
51
|
|
|
52
52
|
def quick_plot(options = {})
|
|
53
|
-
ViennaRna::
|
|
53
|
+
ViennaRna::Graphing::Gnuplot.quick_plot(
|
|
54
54
|
k_p_points,
|
|
55
55
|
options[:title] || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure],
|
|
56
56
|
options
|
|
@@ -58,7 +58,7 @@ module ViennaRna
|
|
|
58
58
|
end
|
|
59
59
|
|
|
60
60
|
def inspect
|
|
61
|
-
"
|
|
61
|
+
"#<#{self.class.name} #{data.inspect}>"
|
|
62
62
|
end
|
|
63
63
|
end
|
|
64
64
|
end
|
data/lib/vienna_rna.rb
CHANGED
|
@@ -3,11 +3,14 @@ require "bio"
|
|
|
3
3
|
require "shuffle"
|
|
4
4
|
require "matrix"
|
|
5
5
|
require "gnuplot"
|
|
6
|
+
require "rinruby"
|
|
6
7
|
require "rroc"
|
|
7
8
|
require "active_support/inflector"
|
|
8
9
|
require "active_support/core_ext/class"
|
|
9
10
|
require "active_support/core_ext/module/aliasing"
|
|
10
11
|
|
|
12
|
+
begin; R.quit; rescue IOError; end
|
|
13
|
+
|
|
11
14
|
module ViennaRna
|
|
12
15
|
@debug = true
|
|
13
16
|
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: vienna_rna
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.5.1
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Evan Senter
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2013-06-
|
|
11
|
+
date: 2013-06-20 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bio
|
|
@@ -66,6 +66,20 @@ dependencies:
|
|
|
66
66
|
- - '>='
|
|
67
67
|
- !ruby/object:Gem::Version
|
|
68
68
|
version: 2.5.0
|
|
69
|
+
- !ruby/object:Gem::Dependency
|
|
70
|
+
name: rinruby
|
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
|
72
|
+
requirements:
|
|
73
|
+
- - '>='
|
|
74
|
+
- !ruby/object:Gem::Version
|
|
75
|
+
version: 2.0.3
|
|
76
|
+
type: :runtime
|
|
77
|
+
prerelease: false
|
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
79
|
+
requirements:
|
|
80
|
+
- - '>='
|
|
81
|
+
- !ruby/object:Gem::Version
|
|
82
|
+
version: 2.0.3
|
|
69
83
|
- !ruby/object:Gem::Dependency
|
|
70
84
|
name: rroc
|
|
71
85
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -94,6 +108,7 @@ files:
|
|
|
94
108
|
- lib/vienna_rna/modules/ffthairpin.rb
|
|
95
109
|
- lib/vienna_rna/modules/fftmultiloop.rb
|
|
96
110
|
- lib/vienna_rna/modules/fold.rb
|
|
111
|
+
- lib/vienna_rna/modules/graphing.rb
|
|
97
112
|
- lib/vienna_rna/modules/heat.rb
|
|
98
113
|
- lib/vienna_rna/modules/parser.rb
|
|
99
114
|
- lib/vienna_rna/modules/rna.rb
|