bioroebe 0.10.80

data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb

@@ -0,0 +1,580 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::PrimerDesignWidget
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb'
+# Bioroebe::GUI::Gtk::PrimerDesignWidget.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class PrimerDesignWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::PrimerDesignWidget 
+
+  alias e puts
+
+  require 'bioroebe/toplevel_methods/nucleotides.rb'
+  require 'bioroebe/calculate/calculate_gc_content.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Primer Design'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '80% or minimum 800px'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '70% or minimum 500px'
+
+  # ========================================================================= #
+  # === PADDING_OF_THE_WHOLE_WIDGET
+  # ========================================================================= #
+  PADDING_OF_THE_WHOLE_WIDGET = 12
+
+  # ========================================================================= #
+  # === HUGE_FONT
+  # ========================================================================= #
+  HUGE_FONT = :hack_25
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :hack_18
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_17
+
+  # ========================================================================= #
+  # === COLOUR_FOR_NON_MATCHES
+  #
+  # This is the colour that will be used for non-matching nucleotides.
+  # ========================================================================= #
+  COLOUR_FOR_NON_MATCHES = :magenta
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    super(:vertical)
+    register_sigint
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    reset_the_internal_variables
+    # ======================================================================= #
+    # === @configuration
+    # ======================================================================= #
+    @configuration = [true, __dir__, NAMESPACE]
+    title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
+    use_gtk_paradise_project_css_file
+    append_project_css_file 
+    infer_the_size_automatically
+    establish_the_forward_and_reverse_sequence
+  end
+
+  # ========================================================================= #
+  # === add_the_main_label
+  # ========================================================================= #
+  def add_the_main_label
+    @main_label = gtk_left_aligned_label(TITLE)
+    @main_label.make_bold
+    @main_label.use_this_font = HUGE_FONT
+    minimal(@main_label)
+  end
+
+  # ========================================================================= #
+  # === add_the_header_bar
+  # ========================================================================= #
+  def add_the_header_bar
+    minimal(@header_bar, 4)
+  end
+
+  # ========================================================================= #
+  # === create_the_top_strand
+  # ========================================================================= #
+  def create_the_top_strand
+    @top_strand = gtk_bold_label("5'-#{@forward_sequence}-3'")
+    @top_strand.darkblue
+  end
+
+  # ========================================================================= #
+  # === create_scrolled_window                                 (scrolled tag)
+  # ========================================================================= #
+  def create_scrolled_window
+    @text_buffer = gtk_text_buffer
+    @text_view = gtk_text_view(@text_buffer)
+    # ======================================================================= #
+    # === @scrolled_window
+    # ======================================================================= #
+    @scrolled_window = gtk_scrolled_window(@text_view) { :always }
+    @scrolled_window.bblack1
+    @scrolled_window.pad8px
+    @scrolled_window.width_height(500, 400)
+  end
+
+  # ========================================================================= #
+  # === create_entries                               (entries tag, entry tag)
+  # ========================================================================= #
+  def create_entries
+    # ======================================================================= #
+    # === @amplified_area
+    # ======================================================================= #
+    @amplified_area = gtk_entry
+    @amplified_area.set_text('TACGTACG')
+    @amplified_area.clear_background
+    @amplified_area.lightblue_background
+    @amplified_area.bblack1
+    @amplified_area.pad5px
+    # ======================================================================= #
+    # === @reverse_primer
+    # ======================================================================= #
+    @reverse_primer = gtk_entry
+    @reverse_primer.yellow_background
+    @reverse_primer.bblack1
+    @reverse_primer.width_height(250, 50)
+    @reverse_primer.set_text(@reverse_sequence.reverse[0,3])
+    @reverse_primer.hint = ''
+    @reverse_primer.on_changed {
+      @reverse_primer.set_text(@reverse_primer.text?.upcase)
+      sync_the_reverse_primer
+      do_calculate_GC_content_for_the_reverse_primer
+    }
+    # ======================================================================= #
+    # === @forward_primer
+    # ======================================================================= #
+    @forward_primer = gtk_entry
+    @forward_primer.yellow_background
+    @forward_primer.bblack1
+    @forward_primer.width_height(250, 50)
+    @forward_primer.set_text('ATG')
+    @forward_primer.on_changed {
+      @forward_primer.set_text(@forward_primer.text?.upcase)
+      sync_the_forward_primer
+      do_calculate_GC_content_for_the_forward_primer
+    }
+    @forward_primer.hint = "The forward primer is the sequence "\
+      "corresponding to the sense strand (5'→3'). It appears "\
+      "on the bottom side of the above text."
+  end
+
+  # ========================================================================= #
+  # === create_the_top_primer
+  # ========================================================================= #
+  def create_the_top_primer
+    # ======================================================================= #
+    # === @top_primer
+    # ======================================================================= #
+    @top_primer = bold_label
+    @top_primer.make_selectable
+    @top_primer.tomato
+    @top_primer.hint =
+      'This is the reverse primer. A '\
+      'match will be shown in green colour, whereas a '\
+      'non-match will be shown in the '+
+      COLOUR_FOR_NON_MATCHES.to_s+'-colour.'
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    add_the_header_bar
+    add_the_main_label
+    outer_vbox = gtk_vbox
+    outer_vbox.minimal(@top_primer, 8)
+    outer_vbox.minimal(gtk_hspacer)
+    outer_vbox.minimal(@top_strand)
+    @bottom_strand = gtk_bold_label("3'-#{@reverse_sequence}-5'")
+    @bottom_strand.darkgreen
+    outer_vbox.minimal(@bottom_strand)
+    outer_vbox.minimal(gtk_hspacer)
+    outer_vbox.minimal(@bottom_primer, 8)
+    hbox = gtk_hbox
+    hbox.minimal(text('Amplified area:'), 1)
+    hbox.minimal(@amplified_area, 1)
+    outer_vbox.minimal(hbox, 1)
+    # ======================================================================= #
+    # === The reverse primer will be added here
+    # ======================================================================= #
+    hbox = return_widget_containing_the_reverse_primer_information
+    outer_vbox.minimal(hbox, 1)
+    # ======================================================================= #
+    # === The forward primer will be added here
+    # ======================================================================= #
+    hbox = return_widget_containing_the_forward_primer_information
+    outer_vbox.minimal(hbox, 1)
+    maximal(
+      add_an_up_and_down_dragger(
+        outer_vbox,
+        @scrolled_window
+      )
+    )
+    sync_forward_and_reverse_primer
+  end
+
+  # ========================================================================= #
+  # === sync_forward_and_reverse_primer
+  # ========================================================================= #
+  def sync_forward_and_reverse_primer
+    sync_forward_primer
+    sync_reverse_primer
+  end
+
+  # ========================================================================= #
+  # === sync_forward_primer
+  # ========================================================================= #
+  def sync_forward_primer
+    _ = @forward_primer.text?
+    longer_nucleotide_sequence = remove_ends(@bottom_strand.text?)
+    array = ["      5'-", :tomato]
+    _.chars.each_with_index {|char, index|
+      if char == Bioroebe.should_match_to?(longer_nucleotide_sequence[index])
+        # This is a match.
+        array << [char, :darkgreen]
+      else
+        # This is NOT a match.
+        array << [char, COLOUR_FOR_NON_MATCHES]
+      end
+      array.flatten!
+    }
+    array << ["-3'→".ljust(@forward_sequence.size+(9-_.size)), :tomato]
+    array.flatten!
+    @bottom_primer.simple_markup(array)
+  end; alias sync_the_forward_primer sync_forward_primer # === sync_the_forward_primer
+
+  # ========================================================================= #
+  # === sync_reverse_primer
+  # ========================================================================= #
+  def sync_reverse_primer
+    _ = @reverse_primer.text?
+    longer_nucleotide_sequence = remove_ends(@top_strand.text?.reverse)
+    @top_primer.set_text(
+      _.rjust(@forward_sequence.size+6)
+    )
+    array = ["←3'-".rjust(33), :tomato]
+    _.chars.reverse.each_with_index {|char, index|
+      if char == Bioroebe.should_match_to?(longer_nucleotide_sequence[index])
+        # This is a match.
+        array << [char, :darkgreen]
+      else
+        # This is NOT a match.
+        array << [char, COLOUR_FOR_NON_MATCHES]
+      end
+      array.flatten!
+    }
+    array << ["-5'".ljust(@forward_sequence.size+6), :tomato]
+    array.flatten!
+    @top_primer.simple_markup(array)
+  end; alias sync_the_reverse_primer sync_reverse_primer # === sync_the_reverse_primer
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    Thread.new {
+      sleep 0.001
+      do_startup_related_actions
+    }
+  end
+
+  # ========================================================================= #
+  # === establish_the_forward_and_reverse_sequence
+  # ========================================================================= #
+  def establish_the_forward_and_reverse_sequence
+    # ======================================================================= #
+    # === @forward_sequence
+    # ======================================================================= #
+    @forward_sequence = 'ATGAGGTTTGCAGCG'
+    # ======================================================================= #
+    # === @reverse_sequence
+    # ======================================================================= #
+    @reverse_sequence = 'TACTCCAAACGTCGC'
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    PADDING_OF_THE_WHOLE_WIDGET
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::PrimerDesignWidget.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::PrimerDesignWidget.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_size_then_automatic_title
+    r.top_left_then_run
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_entries
+    create_the_header_bar
+    create_scrolled_window
+    create_the_top_primer
+    create_the_top_strand
+    create_the_bottom_primer
+  end
+
+  # ========================================================================= #
+  # === create_the_bottom_primer
+  # ========================================================================= #
+  def create_the_bottom_primer
+    # ======================================================================= #
+    # === @bottom_primer
+    # ======================================================================= #
+    @bottom_primer = gtk_bold_label
+    @bottom_primer.make_selectable
+    @bottom_primer.tomato
+    @bottom_primer.hint = 'This is the forward primer. A '\
+      'match will be shown in green colour, whereas a '\
+      'non-match will be shown in the '+
+      COLOUR_FOR_NON_MATCHES.to_s+'-colour.'
+  end
+
+  # ========================================================================= #
+  # === create_the_header_bar
+  # ========================================================================= #
+  def create_the_header_bar
+    @header_bar = default_header_bar
+    @header_bar.pad8px
+    @header_bar.bblack1
+    event_box = gtk_event_box(image_information)
+    event_box.hint = 'Click on this image to show some information '\
+                     'about <b>primer design</b> in a PCR.'
+    event_box.on_clicked {
+      do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR
+    }
+    @header_bar.add_left(event_box)
+  end
+
+  # ========================================================================= #
+  # === do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR
+  # ========================================================================= #
+  def do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR
+    vbox = gtk_vbox
+    # ======================================================================= #
+    # Style this vbox a bit:
+    # ======================================================================= #
+    outer_vbox = gtk_vbox
+    outer_vbox.set_border_width(8)
+    outer_vbox.pad8px
+    outer_vbox.bblack1
+    vbox.pad5px
+    vbox.use_this_font = :hack_18
+    vbox.add_hspacer
+    _ = left_aligned_text(
+      'Some advice on primer design'
+    )
+    _.use_this_font = :hack_20
+    vbox.minimal(_, 10)
+    vbox.add_hspacer
+    vbox.add(
+      left_aligned_text(
+        ' - use a moderate G+C content'
+      )
+    )
+    vbox.add(
+      left_aligned_text(
+        ' - binding region should be 17-27 bp'
+      )
+    )
+    vbox.add(
+      left_aligned_text(
+        " - binding region Tm’s in the range of 50 to 65°C"
+      )
+    )
+    vbox.add(
+      left_aligned_text(
+        ' - avoid repetitive poly-N regions'
+      )
+    )
+    vbox.add(
+      left_aligned_text(
+        ' - avoid secondary structure (hairpins, '\
+        'self dimerization or primer dimer)'
+      )
+    )
+    vbox.add(
+      left_aligned_text(
+        " - primer pairs should have similar Tm's (±4°C)"
+      )
+    )
+    vbox.add_hspacer
+    outer_vbox.maximal(vbox, 2)
+    pop_up_widget(
+      over_this_widget: main_label?,
+      custom_widget:    outer_vbox
+    ).popup
+  end
+
+  # ========================================================================= #
+  # === main_label?
+  # ========================================================================= #
+  def main_label?
+    @main_label
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === do_startup_related_actions
+  # ========================================================================= #
+  def do_startup_related_actions
+    print ' '
+    @top_primer.deselect
+    do_calculate_the_GC_content_for_the_reverse_primer
+    do_calculate_the_GC_content_for_the_forward_primer
+  end
+
+  # ========================================================================= #
+  # === return_widget_containing_the_reverse_primer_information
+  #
+  # This is the widget that contains the various smaller widgets necessary
+  # for the "Reverse primer:" info, close to the bottom of this widget.
+  # ========================================================================= #
+  def return_widget_containing_the_reverse_primer_information
+    hbox = gtk_hbox
+    hbox.minimal(bold_text("Reverse primer: 5'-"),1)
+    hbox.minimal(@reverse_primer,1)
+    hbox.minimal(bold_text("-3'",1))
+    button2 = gtk_button('←')
+    button2.hint = 'Remove the last nucleotide from the primer.'
+    button2.bblack1
+    button2.on_clicked {
+      @reverse_primer.try_to_remove_the_last_character
+    }
+    hbox.minimal(button2)
+    text_showing_the_GC_content = left_aligned_text(' GC content:')
+    text_showing_the_GC_content.use_this_font = smaller_font?
+    text_showing_the_GC_content.make_bold
+    hbox.minimal(text_showing_the_GC_content, 5)
+    @text_GC_content_for_the_reverse_primer_as_percentage = left_aligned_text
+    @text_GC_content_for_the_reverse_primer_as_percentage.use_this_font = smaller_font?
+    @text_GC_content_for_the_reverse_primer_as_percentage.make_bold
+    hbox.minimal(@text_GC_content_for_the_reverse_primer_as_percentage, 5)
+    return hbox
+  end
+
+  # ========================================================================= #
+  # === return_widget_containing_the_forward_primer_information
+  # ========================================================================= #
+  def return_widget_containing_the_forward_primer_information
+    hbox = gtk_hbox
+    hbox.minimal(bold_text("Forward primer: 5'-"), 1)
+    hbox.minimal(@forward_primer, 1)
+    hbox.minimal(bold_text("-3'",1))
+    button1 = gtk_button('←')
+    button1.hint = 'Remove the last nucleotide from the primer.'
+    button1.bblack1
+    button1.on_clicked {
+      @forward_primer.try_to_remove_the_last_character
+    }
+    hbox.minimal(button1)
+    text_showing_the_GC_content = left_aligned_text(' GC content:')
+    text_showing_the_GC_content.use_this_font = smaller_font?
+    text_showing_the_GC_content.make_bold
+    hbox.minimal(text_showing_the_GC_content, 5)
+    @text_GC_content_for_the_forward_primer_as_percentage = left_aligned_text
+    @text_GC_content_for_the_forward_primer_as_percentage.use_this_font = smaller_font?
+    @text_GC_content_for_the_forward_primer_as_percentage.make_bold
+    hbox.minimal(@text_GC_content_for_the_forward_primer_as_percentage, 5)
+    return hbox
+  end
+
+  # ========================================================================= #
+  # === do_calculate_the_GC_content_for_the_reverse_primer
+  # ========================================================================= #
+  def do_calculate_the_GC_content_for_the_reverse_primer
+    _ = ::Bioroebe.gc_content_of_this_sequence(
+      @reverse_primer.text?.to_s, 1 # The second number is for how much to round.
+    )
+    _ = 0 if _ == 'NaN'
+    @text_GC_content_for_the_reverse_primer_as_percentage.set_text("#{_}%")
+  end; alias do_calculate_GC_content_for_the_reverse_primer do_calculate_the_GC_content_for_the_reverse_primer # === do_calculate_GC_content_for_the_reverse_primer
+
+  # ========================================================================= #
+  # === do_calculate_the_GC_content_for_the_forward_primer
+  # ========================================================================= #
+  def do_calculate_the_GC_content_for_the_forward_primer
+    _ = ::Bioroebe.gc_content_of_this_sequence(
+      @forward_primer.text?.to_s, 1 # The second number is for how much to round.
+    )
+    _ = 0 if _ == 'NaN'
+    @text_GC_content_for_the_forward_primer_as_percentage.set_text("#{_}%")
+  end; alias do_calculate_GC_content_for_the_forward_primer do_calculate_the_GC_content_for_the_forward_primer # === do_calculate_GC_content_for_the_forward_primer
+
+  # ========================================================================= #
+  # === remove_ends
+  # ========================================================================= #
+  def remove_ends(
+      i = "3'-TACGTACGTACGTACG-5'"
+    )
+    i = i.dup
+    i.sub!(/3'-/,'')
+    i.sub!(/-5'/,'')
+    i.sub!(/5'-/,'')
+    i.sub!(/'3-/,'')
+    i.sub!(/-'5/,'')
+    return i
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::PrimerDesignWidget.run
+end # gtkprimerdesignwidget

data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config

@@ -0,0 +1,6 @@
+width:                                      1440
+height:                                      880
+padding:                                       6
+title:                 Protein to DNA conversion
+favicon:                                 :tabble
+font_in_use:                             Sans 24