BioDSL 1.0.0

data/lib/BioDSL/html_report.rb

@@ -0,0 +1,200 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program 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 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program 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 this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Class for creating HTML reports from an executed BioDSL pipeline.
+  class HtmlReport
+    require 'tilt/haml'
+    require 'base64'
+    require 'BioDSL/helpers/options_helper'
+
+    include OptionsHelper
+
+    # Constructor for HtmlReport.
+    #
+    # @param pipeline [BioPeices::Pipeline] Pipeline object
+    def initialize(pipeline)
+      @pipeline = pipeline
+      @commands = pipeline.commands
+    end
+
+    # Render HTML output.
+    def to_html
+      render('layout.html.haml', self, pipeline: @pipeline.to_s,
+                                       commands: @commands)
+    end
+
+    private
+
+    # Render HTML templates.
+    #
+    # @param template [Path]   Path to template file.
+    # @param scope    [Object] Scope.
+    # @param args     [Hash]   Argument hash.
+    def render(template, scope, args = {})
+      Tilt.new(File.join(root_dir, template)).render(scope, args)
+    end
+
+    # Render HTML CSS section.
+    def render_css
+      render('css.html.haml', self)
+    end
+
+    # Render HTML pipeline section
+    #
+    # @param pipeline [String] String from BioDSL::Pipeline#to_s
+    def render_pipeline(pipeline)
+      pipeline = pipeline.scan(/[^.]+\(.*?\)|[^.(]+/).join(".\n").sub(/\n/, '')
+
+      render('pipeline.html.haml', self, pipeline: pipeline)
+    end
+
+    # Render HTML overview section.
+    #
+    # @param commands [Array] List of commands from a pipeline.
+    def render_overview(commands)
+      render('overview.html.haml', self, commands: commands)
+    end
+
+    # Render HTML command section.
+    #
+    # @param command [BioDSL::Command] Command object.
+    def render_command(command, index)
+      render('command.html.haml', self, command: command, index: index)
+    end
+
+    # Render HTML status section.
+    #
+    # @param command [BioDSL::Command] Command object.
+    def render_status(command)
+      stats = command.status.reject { |k, _| k.to_s[0..3] == 'time' }
+      render('status.html.haml', self, exit_status: command.run_status,
+                                       statsus: stats)
+    end
+
+    # Render HTML time section.
+    #
+    # @param status [BioDSL::Status] Status object.
+    def render_time(status)
+      render('time.html.haml', self, status: status)
+    end
+
+    # Render HTML input files section.
+    #
+    # @param options [Hash] Command options hash.
+    def render_input_files(options)
+      render('input_files.html.haml', self,
+             files: options_glob(options[:input]))
+    end
+
+    # Render HTML output file section.
+    #
+    # @param options [Hash] Command options hash.
+    def render_output_files(options)
+      render('output_files.html.haml', self, options: options)
+    end
+
+    # Render PNG data.
+    #
+    # @param options [Hash] Command options hash.
+    def render_png(options)
+      path = options[:output]
+      png_data = 'data:image/png;base64,'
+
+      File.open(path, 'r') do |ios|
+        png_data << Base64.encode64(ios.read)
+      end
+
+      render('png.html.haml', self, path: path, png_data: png_data)
+    end
+
+    # Detect if any input options are set.
+    #
+    # @param options [Hash] Options hash.
+    # @option options [String] :input File glob expression.
+    #
+    # @return [Boolean]
+    def input?(options)
+      if options[:input]
+        true
+      else
+        false
+      end
+    end
+
+    # Detect if any output options are set.
+    #
+    # @param options [Hash] Options hash.
+    # @option options [String] :output Path to output file.
+    #
+    # @return [Boolean]
+    def output?(options)
+      if options[:output]
+        true
+      else
+        false
+      end
+    end
+
+    # Detect if any PNG file is available.
+    #
+    # @param options [Hash] Options hash.
+    # @option options [String] :output Path to output file.
+    # @option options [Symbol] :terminal Plot type.
+    #
+    # @return [Boolean]
+    def png?(options)
+      if options[:output]   &&
+         options[:terminal] &&
+         options[:terminal] == :png &&
+         File.exist?(options[:output])
+        true
+      else
+        false
+      end
+    end
+
+    # Return the path of the HTML root dir.
+    #
+    # @return [String] Root dir.
+    def root_dir
+      File.join(File.dirname(__FILE__), '..', '..', 'www')
+    end
+
+    # Return the help URL for a given command.
+    #
+    # @param command [Symbol] Command name.
+    #
+    # @return [String] HTML link.
+    def help_url(command)
+      camel = command.to_s.split('_').map(&:capitalize).join
+
+      'http://www.rubydoc.info/gems/BioDSL/' \
+      "#{BioDSL::VERSION}/BioDSL/#{camel}"
+    end
+  end
+end

data/lib/BioDSL/math.rb

@@ -0,0 +1,55 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program 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 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program 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 this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Adding methods to Math module.
+  module Math
+    # Class method to calculate the distance from at point to a line.
+    # The point and line are given as pairs of coordinates.
+    def self.dist_point2line(
+      px,  # point  x coordinate
+      py,  # point  y coordinate
+      x1,  # line 1 x coordinate
+      y1,  # line 1 y coordinate
+      x2,  # line 2 x coordinate
+      y2   # line 2 y coordinate
+    )
+
+      a = (y2 - y1).to_f / (x2 - x1).to_f
+      b = y1 - a * x1
+
+      (a * px + b - py).abs / ::Math.sqrt(a**2 + 1)
+    end
+
+    # Class method to calculate the distance between two points given
+    # as pairs of coordinates.
+    def self.dist_point2point(x1, y1, x2, y2)
+      ::Math.sqrt((x2.to_f - x1.to_f)**2 + (y2.to_f - y1.to_f)**2)
+    end
+  end
+end

data/lib/BioDSL/mummer.rb

@@ -0,0 +1,216 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program 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 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program 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 this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BipPieces.
+module BioDSL
+  # Error class for Mummer errors.
+  MummerError = Class.new(StandardError)
+
+  # rubocop: disable ClassLength
+
+  # Class for executing MUMmer and parsing MUMmer results.
+  class Mummer
+    # @param seq1    [BioDSL::Seq] Sequence 1.
+    # @param seq2    [BioPeices::Seq] Sequence 2.
+    # @param options [Hash]           Options hash.
+    #
+    # @yield [Mummer::Match] A match object
+    # @return [Enumerable] An Enumerable
+    def self.each_mem(seq1, seq2, options = {})
+      mummer = new(seq1, seq2, options)
+
+      if block_given?
+        mummer.each_mem { |mem| yield mem }
+      else
+        mummer.each_mem
+      end
+    end
+
+    # Constructor for Mummer class.
+    #
+    # @param seq1    [BioDSL::Seq] Sequence 1.
+    # @param seq2    [BioPeices::Seq] Sequence 2.
+    # @param options [Hash]           Options hash.
+    #
+    # @return [Mummer] Class instance.
+    def initialize(seq1, seq2, options = {})
+      @seq1    = seq1
+      @seq2    = seq2
+      @options = options
+      @command = []
+      @q_id    = nil
+      @dir     = nil
+
+      default_options
+      check_options
+    end
+
+    # @yield [Mummer::Match] A match object
+    # @return [Enumerable] An Enumerable
+    def each_mem
+      return to_enum :each_mem unless block_given?
+
+      TmpDir.create('in1', 'in2', 'out') do |file_in1, file_in2, file_out|
+        BioDSL::Fasta.open(file_in1, 'w') { |io| io.puts @seq1.to_fasta }
+        BioDSL::Fasta.open(file_in2, 'w') { |io| io.puts @seq2.to_fasta }
+
+        execute(file_in1, file_in2, file_out)
+
+        File.open(file_out) do |io|
+          while (match = get_match(io))
+            yield match
+          end
+        end
+      end
+    end
+
+    private
+
+    # Get a match if possible.
+    #
+    # @param io [IO] IO stream.
+    #
+    # @return [Match, nil] match or nil whether a match was found.
+    def get_match(io)
+      io.each do |line|
+        line.chomp!
+
+        case line
+        when /^> (\S+)\s+Reverse\s+Len = \d+$/
+          @q_id  = Regexp.last_match(1)
+          @dir   = 'reverse'
+        when /^> (\S+)\s+Len = \d+$/
+          @q_id  = Regexp.last_match(1)
+          @dir   = 'forward'
+        when /^\s*(.\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/
+          s_id    = Regexp.last_match(1)
+          s_beg   = Regexp.last_match(2).to_i - 1
+          q_beg   = Regexp.last_match(3).to_i - 1
+          hit_len = Regexp.last_match(4).to_i
+
+          return Match.new(@q_id, s_id, @dir, s_beg, q_beg, hit_len)
+        end
+      end
+
+      nil
+    end
+
+    # Check that the options are OK
+    def check_options
+      check_length_min_value
+      check_length_min_type
+      check_direction
+    end
+
+    # Check the that the value of :length_min is OK.
+    #
+    # @raise [BioDSL::MummerError] on bad length_min value.
+    def check_length_min_value
+      return if @options[:length_min] > 0
+
+      fail MummerError, "Bad length_min: #{@options[:length_min]}"
+    end
+
+    # Check that the type of :length_min is OK.
+    #
+    # @raise [BioDSL::MummerError] on bad length_min type.
+    def check_length_min_type
+      return if @options[:length_min].class == Fixnum
+
+      fail MummerError, "Bad length_min type: #{@options[:length_min].class}"
+    end
+
+    # Check that the value of :direction is OK.
+    #
+    # @raise [BioDSL::MummerError] on bad direction.
+    def check_direction
+      return if @options[:direction] == :forward ||
+                @options[:direction] == :reverse ||
+                @options[:direction] == :both
+
+      fail MummerError, "Bad direction: #{@options[:direction]}"
+    end
+
+    # Set some sensible default options.
+    def default_options
+      @options[:length_min] ||= 20
+      @options[:direction]  ||= :both
+    end
+
+    # Execute MUMmer.
+    #
+    # @param file_in1 [String] Path to sequence filen.
+    # @param file_in1 [String] Path to sequence filen.
+    # @param file_out [String] Path to output file.
+    def execute(file_in1, file_in2, file_out)
+      cmd = compile_command(file_in1, file_in2, file_out)
+
+      $stderr.puts "Running command: #{cmd}" if BioDSL.verbose
+
+      system(cmd)
+
+      fail "Error running command: #{cmd}" unless $CHILD_STATUS.success?
+    end
+
+    # Compile a command for execution of mummer.
+    #
+    # @param file_in1 [String] Path to sequence filen.
+    # @param file_in1 [String] Path to sequence filen.
+    # @param file_out [String] Path to output file.
+    #
+    # @return [String] Command string.
+    def compile_command(file_in1, file_in2, file_out)
+      @command << 'mummer'
+      @command << '-c' # report position of revcomp match relative to query seq.
+      @command << '-L' # show length of query seq in header.
+      @command << '-F' # force 4-column output.
+      @command << "-l #{@options[:length_min]}"
+      @command << '-n' # nucleotides only [atcg].
+
+      case @options[:direction]
+      when :reverse then @command << '-r' # only compute reverse matches.
+      when :both    then @command << '-b' # compute forward and reverse matches.
+      end
+
+      @command << file_in1
+      @command << file_in2
+      @command << "> #{file_out}"
+      @command << '2>&1' unless BioDSL.verbose
+
+      @command.join(' ')
+    end
+
+    Match = Struct.new(:q_id, :s_id, :dir, :s_beg, :q_beg, :hit_len) do
+      def q_end
+        q_beg + hit_len - 1
+      end
+
+      def s_end
+        s_beg + hit_len - 1
+      end
+    end
+  end
+end