bioroebe 0.10.80

data/lib/bioroebe/dotplots/advanced_dotplot.rb

@@ -0,0 +1,256 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::AdvancedDotplot
+#
+# This class does an advanced dotplot.
+#
+# You must input the two strings that have to be compared. We will
+# then output the corresponding matches.
+#
+# Usage example:
+#
+#   Bioroebe::AdvancedDotplot.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/dotplots/advanced_dotplot.rb'
+# Bioroebe::AdvancedDotplot.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class AdvancedDotplot < ::Bioroebe::CommandlineApplication # === Bioroebe::AdvancedDotplot
+
+  # ========================================================================= #
+  # === DEFAULT_VALUE_FOR_A_MATCH
+  #
+  # This is the default value to use for a dotplot. We could also use
+  # a '*' token of course.
+  # ========================================================================= #
+  DEFAULT_VALUE_FOR_A_MATCH = '*' # 2
+    MATCH = DEFAULT_VALUE_FOR_A_MATCH # === MATCH
+
+  # ========================================================================= #
+  # === NON_MATCH
+  # ========================================================================= #
+  NON_MATCH = 0
+
+  # ========================================================================= #
+  # === USE_COLOURS_IN_THIS_CLASS
+  #
+  # Whether to have this class handle colours on the commandline or
+  # not.
+  # ========================================================================= #
+  USE_COLOURS_IN_THIS_CLASS = true
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      string1     = ARGV[0],
+      string2     = nil,
+      run_already = true
+    )
+    reset
+    # ======================================================================= #
+    # If the first argument is an Array, and if it has at the least two
+    # elements, then we need to assign the last element to string2.
+    # ======================================================================= #
+    if string1.is_a?(Array) and (string1.size > 1) and string2.nil?
+      string2 = string1.pop
+    end
+    set_string1(string1)
+    set_string2(string2)
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === :use_asterisk
+      # ===================================================================== #
+      when :use_asterisk
+        set_match_token('*')
+      end
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    set_match # Use the default in this case.
+    # ======================================================================= #
+    # === @non_match
+    # ======================================================================= #
+    @non_match = NON_MATCH
+    if USE_COLOURS_IN_THIS_CLASS
+      @non_match = lightgreen(@non_match)
+    end
+  end
+
+  # ========================================================================= #
+  # === set_match
+  #
+  # This method will determine which character is to be used when a
+  # match was found. Typically this is the '*' character, but the
+  # constant defined on top of this .rb file can be changed to use
+  # another character.
+  # ========================================================================= #
+  def set_match(i = MATCH)
+    @match = i
+    if USE_COLOURS_IN_THIS_CLASS # And use colours.
+      @match = orange(@match)
+    end
+  end; alias set_match_token set_match # === set_match_token
+
+  # ========================================================================= #
+  # === set_string1
+  #
+  # string1 is on the left side of the 2d diagramm.
+  # ========================================================================= #
+  def set_string1(i)
+    i = i.join  if i.is_a? Array
+    i = i.chars if i.is_a? String
+    @string1 = i
+  end
+
+  # ========================================================================= #
+  # === set_string2
+  #
+  # string2 is on the top side of the 2d diagramm.
+  # ========================================================================= #
+  def set_string2(i)
+    i = i.join  if i.is_a? Array
+    i = i.chars if i.is_a? String
+    @string2 = i
+  end
+
+  # ========================================================================= #
+  # === string2?
+  # ========================================================================= #
+  def string2?
+    @string2
+  end; alias string2 string2? # === string2
+
+  # ========================================================================= #
+  # === string1?
+  # ========================================================================= #
+  def string1?
+    @string1
+  end; alias string1 string1? # === string1
+
+  # ========================================================================= #
+  # === match?
+  # ========================================================================= #
+  def match?
+    @match
+  end; alias match match? # === match
+
+  # ========================================================================= #
+  # === top_row
+  # ========================================================================= #
+  def top_row
+    "  #{string2.join(' ')}"
+  end
+
+  # ========================================================================= #
+  # === explain_to_the_user_what_the_asterisk_mean
+  #
+  # We have to explain to the user what the meaning of this is.
+  # ========================================================================= #
+  def explain_to_the_user_what_the_asterisk_mean
+    e
+    erev "Note that the #{@match}#{rev} denotes a dot (== match) here."
+    e
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    e
+    e rev+top_row
+    left_side = string1?
+    left_side.each_with_index {|token, index|
+      # ===================================================================== #
+      # Also show that token
+      # ===================================================================== #
+      print rev, token, ' '
+      # ===================================================================== #
+      # Inner loop
+      # ===================================================================== #
+      string2.each_with_index {|inner_token, inner_index|
+        if inner_token == token
+          print @match
+        else
+          print @non_match
+        end
+        print ' '
+      }
+      e
+    }
+    explain_to_the_user_what_the_asterisk_mean
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::AdvancedDotplot.[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end
+
+  # ========================================================================= #
+  # === Bioroebe.dotplot_array
+  #
+  # This method can be used to return a 2D dotplot-array of two input
+  # sequences. Be careful with large data as input - the RAM usage
+  # may go up, so this method has NOT been optimized for such
+  # situations. It is deliberately kept simple.
+  # ========================================================================= #
+  def self.dotplot_array(dna_x, dna_y)
+    dotplot_matrix = Array.new(
+      dna_y.size, Array.new(dna_x.size, 0)
+    )
+    dotplot_matrix = Array.new(dna_y.size) {
+      Array.new(dna_x.size) { 0 }
+    }
+    dna_x.chars.each_with_index {|x_value, x_index|
+      # ===================================================================== #
+      # Next, we work from top-to-bottom.
+      # ===================================================================== #
+      dna_y.chars.each_with_index {|y_value, y_index|
+        if x_value == y_value
+          dotplot_matrix[y_index][x_index] = 1
+        end
+      }
+    }
+    return dotplot_matrix
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  alias e puts
+  # ========================================================================= #
+  # The following code is just for testing purposes really. The main code
+  # in use is available via bioroebe/bin/advanced_dotplot instead.
+  # ========================================================================= #
+  Bioroebe::AdvancedDotplot.new(ARGV[0], ARGV[1]) { :use_asterisk }
+
+  e
+  e 'Next, additional functionality will be used, via: Bioroebe.dotplot_array()'
+  e
+              #123456789012
+  dna_string1 = 'TAATGCCTGAAT'
+  dna_string2 = 'CTCTATGCC'
+
+  matrix = Bioroebe.dotplot_array(dna_string1, dna_string2)
+  matrix.each {|inner_array|
+    e inner_array.join(' ')
+  }
+end # advanceddotplot CDDCDDCCCCC DDCCDDCDCCCC

data/lib/bioroebe/dotplots/dotplot.rb

@@ -0,0 +1,184 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Dotplot
+#
+# This script will generate a dotplot. However had, it has not been checked
+# for quite some time, so it may no longer work appropriately.
+#
+# Usage examples:
+#
+#   Bioroebe::Dotplot.new
+#
+# =========================================================================== #
+# require 'bioroebe/dotplots/dotplot.rb'
+# =========================================================================== #
+require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
+class Dotplot < Base # === Bioroebe::Dotplot
+
+  # ========================================================================= #
+  # === DEFAULT_X_AXIS
+  # ========================================================================= #
+  DEFAULT_X_AXIS = 14
+
+  # ========================================================================= #
+  # === DEFAULT_Y_AXIS
+  # ========================================================================= #
+  DEFAULT_Y_AXIS =  9
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # First argument is x-axis
+  # ========================================================================= #
+  def initialize(
+      x_axis      = nil,
+      y_axis      = nil,
+      run_already = true
+    )
+    reset
+    set_x_axis(x_axis)
+    set_y_axis(y_axis)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @indent_level
+    # ======================================================================= #
+    @indent_level = 0
+  end
+
+  # ========================================================================= #
+  # === set_x_axis
+  # ========================================================================= #
+  def set_x_axis(i = nil)
+    i = DEFAULT_X_AXIS if i.nil?
+    i = i.join.strip if i.is_a? Array
+    @string1 = i
+    i = i.size if i.is_a? String
+    i = i.to_i
+    @x_axis = i
+  end
+
+  # ========================================================================= #
+  # === set_y_axis
+  # ========================================================================= #
+  def set_y_axis(i = nil)
+    i = DEFAULT_Y_AXIS if i.nil?
+    i = i.join.strip if i.is_a? Array
+    @string2 = i
+    i = i.size if i.is_a? String
+    i = i.to_i
+    @y_axis = i
+  end
+
+  # ========================================================================= #
+  # === string2?
+  # ========================================================================= #
+  def string2?
+    @string2.chars
+  end
+
+  # ========================================================================= #
+  # === string1?
+  # ========================================================================= #
+  def string1?
+    @string1.chars
+  end
+
+  # ========================================================================= #
+  # === display_y_axis
+  # ========================================================================= #
+  def display_y_axis
+    @y_axis.times {|entry|
+      entry += 1
+      e "#{entry}#{N}#{N}"
+    }
+  end
+
+  # ========================================================================= #
+  # === display_x_axis
+  # ========================================================================= #
+  def display_x_axis
+    print '    '
+    @x_axis.times {|entry|
+      entry += 1
+      ee "#{entry}  "
+    }; e
+  end
+
+  # ========================================================================= #
+  # === display_grid
+  # ========================================================================= #
+  def display_grid
+    display_x_axis
+    display_y_axis # Show the y coordinate.
+    display_x_axis
+    print ' ' * (3.0 * @x_axis)+'-> (x axis)'; e
+    zipped = string1?.zip(string2?)
+    zipped.each {|first, second|
+      if first == second
+        output_match
+      else # else don't make a dot.
+        increase_indent_level
+      end
+    }
+    run2
+  end
+
+  # ========================================================================= #
+  # === run2
+  #
+  # Try it again.
+  # ========================================================================= #
+  def run2
+    # First, we can show the x-axis:
+    show_x_axis
+  end
+
+  # ========================================================================= #
+  # === show_x_axis
+  # ========================================================================= #
+  def show_x_axis
+    string1?.each {|char|
+      ee "#{char} "
+    }
+  end
+
+  # ========================================================================= #
+  # === increase_indent_level
+  # ========================================================================= #
+  def increase_indent_level
+    @indent_level += 2
+  end
+
+  # ========================================================================= #
+  # === output_match
+  # ========================================================================= #
+  def output_match
+    ee (' '*@indent_level)+'*'+N # Make a dot in this case.
+    increase_indent_level
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    display_grid
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::Dotplot.new(ARGV[0], ARGV[1])
+end # dotplot 14 9
+    # dotplot ABCDEFGHICCCCC ABCCCCCCCCC

data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb

@@ -0,0 +1,191 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# ============================================================================= #
+# === Bioroebe::ElectronMicroscopy::CoordinateAnalyzer
+#
+# Usage example:
+#
+#   Bioroebe::ElectronMicroscopy::CoordinateAnalyzer.new(ARGV)
+#
+# ============================================================================= #
+# require 'bioroebe/electron_microscopy/coordinate_analyzer.rb'
+# ============================================================================= #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::CoordinateAnalyzer
+
+  # =========================================================================== #
+  # === NAMESPACE
+  # =========================================================================== #
+  NAMESPACE = inspect
+
+  # =========================================================================== #
+  # === STORE_HERE
+  # =========================================================================== #
+  STORE_HERE = "#{::Bioroebe.log_dir?}total_amount_of_particles"
+
+  # =========================================================================== #
+  # === initialize
+  # =========================================================================== #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # =========================================================================== #
+  # === reset                                                       (reset tag)
+  # =========================================================================== #
+  def reset
+    super()
+    # ========================================================================= #
+    # === @namespace
+    # ========================================================================= #
+    @namespace = NAMESPACE
+    # ========================================================================= #
+    # === @dataset
+    # ========================================================================= #
+    @dataset = []
+    # ========================================================================= #
+    # === @n_total_particles
+    # ========================================================================= #
+    @n_total_particles = 0
+  end
+
+  # =========================================================================== #
+  # === get_all_image_directories
+  # =========================================================================== #
+  def get_all_image_directories
+    @directories = Dir[base?]
+  end
+
+  # =========================================================================== #
+  # === base?
+  # 
+  # Which internal base directory to use.
+  # =========================================================================== #
+  def base?
+    "#{ROEBE_HOME_DIR}Image*"
+  end
+
+  # =========================================================================== #
+  # === add
+  # =========================================================================== #
+  def add(i)
+    if i.is_a? Array
+      i.each {|entry| add(entry) }
+    else
+      if File.exist? i
+        @dataset << i
+      end
+    end
+  end
+
+  # =========================================================================== #
+  # === analyze_dataset
+  #
+  # Use this method to analyze the dataset finally.
+  # =========================================================================== #
+  def analyze_dataset
+    if @dataset.empty?
+      opnn; e 'Can not analyze anything as the dataset (from '+
+               simp(base?)+') is empty.'
+    else
+      opnn; e 'Analyzing the dataset.'
+      @dataset.sort.each_with_index {|entry, index|
+        index += 1
+        index = '%02d' % index
+        data = File.readlines(entry)
+        data = data.select {|inner_entry| inner_entry.include? '    ' }
+        n_lines = data.size
+        entry = '%-41s' % entry
+        opnn; e '  '+sfile(entry)+' has '+simp(n_lines.to_s)+' particles.'
+        # Next, we store this directly into the file.
+        append_what_into('Image '+index+': '+n_lines.to_s+N, store_where?)
+        @n_total_particles += n_lines
+      }
+    end
+  end
+  
+  # =========================================================================== #
+  # === report_how_many_particles_we_have_found
+  # =========================================================================== #
+  def report_how_many_particles_we_have_found
+    n_images = @dataset.size
+    unless @dataset.empty?
+      opnn; e 'We have found '+simp(@n_total_particles)+' particles in '+
+              'a total of '+bold_blue(n_images.to_s)+' images.'
+    end
+  end
+
+  # =========================================================================== #
+  # === generate_a_report
+  #
+  # This method will generate a report status.
+  #
+  # It will generate the file total_amount_of_particles. 
+  # =========================================================================== #
+  def generate_a_report
+    opnn; e "Now generating a report into `#{sfile(store_where?)}`."
+    append_what_into(N+N+'Total: '+@n_total_particles.to_s+N,
+      store_where?)
+  end
+
+  # =========================================================================== #
+  # === startup_message
+  # =========================================================================== #
+  def startup_message
+    opnn; e 'We attempt to analyze the coordinates next.'
+  end
+
+  # =========================================================================== #
+  # === remove_old_file
+  # =========================================================================== #
+  def remove_old_log_file(this_file = store_where?)
+    if File.exist? this_file
+      remove_file(this_file)
+    end
+  end
+
+  # =========================================================================== #
+  # === store_where?
+  # =========================================================================== #
+  def store_where?
+    STORE_HERE
+  end
+
+  # =========================================================================== #
+  # === obtain_all_pos_files
+  # =========================================================================== #
+  def obtain_all_pos_files
+    @directories.each {|directory|
+      location = Dir[directory+'/*.pos'].reject {|entry| entry.include? 'fixed_coordinates' }.
+                                         reject {|entry| entry.include? 'from' }
+      add(location)
+    }
+  end
+
+  # =========================================================================== #
+  # === run                                                           (run tag)
+  # =========================================================================== #
+  def run
+    startup_message
+    remove_old_log_file
+    get_all_image_directories
+    obtain_all_pos_files # After this step we have all .pos files.
+    analyze_dataset
+    report_how_many_particles_we_have_found
+    generate_a_report
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ElectronMicroscopy::CoordinateAnalyzer.new(ARGV)
+end # coordinateanalyzer