bioroebe 0.10.80 → 0.11.25

data/lib/bioroebe/parsers/genbank_parser.rb

@@ -4,10 +4,29 @@
 # =========================================================================== #
 # === Bioroebe::GenbankParser
 #
-# This class can be used to parse genbank-files. Their file extension is
-# typically ".gbk".
+# This class can be used to parse genbank-files (typically stored as .genbank
+# or .gbk, so their file extension is usually ".gbk").
+#
+# Since as of the rewrite in July 2022 the class can also handle multiple
+# fasta entries now.
+#
+# The class is similar to class FastaParser, but instead it will only
+# select the content between "ORIGIN" and "VERSION" entries.
+#
+# The user can pass the content of a genbank-file to this class, and it
+# can then report the nucleotide sequence, e. g. the part starting after
+# the ORIGIN string.
+#
+# The reason why this class has been created was because it is sometimes
+# necessary to parse a genebank file.
+#
+# Usage example:
+#
+#   Bioroebe::GenbankParser.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/parsers/genbank_parser.rb'
+# require 'bioroebe/genbank/genbank_parser.rb'
+# genbank_parser = Bioroebe::GenbankParser.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
 
@@ -20,59 +39,369 @@ class GenbankParser < ::Bioroebe::CommandlineApplication # === Bioroebe::Genbank
   # ========================================================================= #
   NAMESPACE = inspect
 
+  # ========================================================================= #
+  # === UPCASE_THE_SEQUENCE
+  #
+  # Setting this constant to true will cause this class to store the
+  # FASTA sequence in an upcased variant, e. g. "AGCAGCTA" rather
+  # than "acgatcag".
+  # ========================================================================= #
+  UPCASE_THE_SEQUENCE = true
+
+  # ========================================================================= #
+  # === TEST_STRING
+  #
+  # Our example test-string, to see how such a genbank file usually looks
+  # like.
+  #
+  # This will contain two different FASTA sequences.
+  # ========================================================================= #
+  TEST_STRING = '                   /note="internal transcribed spacer 2"
+ORIGIN      
+        1 cgtaacaagg tttccgtagg tgaaccttcg gaaggatcat tgttgagacc cccaaaaaaa
+       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt ggctactgtg
+      121 gtggccgtga atttccgtcg aacctccttg ggagaattct tgatggcaat tgaacccttg
+      181 gcccggcgca gtttcgcccc aagtcaaatg agatggaacc ggcggagggc atcgtcctcc
+      241 atggaaccgg ggagggccgg cgttcttccg ttccccccat gaattttttt ttgacaactc
+      301 tcggcaacgg atatctcggc tctttgcatc cgatgaaaga acccagcgaa atgtgataag
+      361 tggtgtgaat tgcagaatcc cgtgaaccat cgagtctttg aacgcaagtt gcgcccgagg
+      421 ccatcaggct aagggcacgc ctgcctgggc gttgcgtgct gcatctctct cccattgcta
+      481 aggctgaaca ggcatactgt tcggccggcg cggatgagtg tttggcccct tgttcttcgg
+      541 tgcgatgggt ccaagacctg ggcttttgac ggccggaaat ccggcaagag gtggacggac
+      601 ggtggctgcg acgaagctgt cgtgcgaatg ccctacgctg tcgtatttga tgggccggaa
+      661 taaatccctt ttgagcccca ttggaggcac gtcaacccgt gggcggtcga cggccatttg
+      721 gatgcaaccc caggtcaggt gagga
+//
+LOCUS       Z78510                   750 bp    DNA     linear   PLN 30-NOV-2006
+DEFINITION  P.caricinum 5.8S rRNA gene and ITS1 and ITS2 DNA.
+ACCESSION   Z78510
+VERSION     Z78510.1  GI:2765635
+KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
+            ITS1; ITS2.
+SOURCE      Phragmipedium caricinum
+  ORGANISM  Phragmipedium caricinum
+            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
+            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
+            Cypripedioideae; Phragmipedium.
+REFERENCE   1
+  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
+  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
+            Orchidaceae): nuclear rDNA ITS sequences
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 750)
+  AUTHORS   Cox,A.V.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
+            Richmond, Surrey TW9 3AB, UK
+FEATURES             Location/Qualifiers
+     source          1..750
+                     /organism="Phragmipedium caricinum"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:53127"
+     misc_feature    1..380
+                     /note="internal transcribed spacer 1"
+     gene            381..550
+                     /gene="5.8S rRNA"
+     rRNA            381..550
+                     /gene="5.8S rRNA"
+                     /product="5.8S ribosomal RNA"
+     misc_feature    551..750
+                     /note="internal transcribed spacer 2"
+ORIGIN      
+        1 ctaaccaggg ttccgaggtg accttcggga ggattccttt ttaagccccc gaaaaaacga
+       61 tcgaattaaa ccggaggacc ggtttaattt ggtctcccca ggggctttcc ccccttggtg
+      121 gccgtgaatt tccatcgaac ccccctggga gaattcttgg tggccaatgg acccttggcc
+      181 cggcgcaatt tcccccccaa tcaaatgaga taggaccggc agggggcgtc cccccccatg
+      241 gaaccgggga gggccggcat tcttccgttc ccccctcgga ttttttgaca actctcgcaa
+      301 cggatatctc gcctctttgc atcggatgga agaacgcagc gaaatgtgat aagtggtgtg
+      361 aattgcagaa tcccgtgaac catcgagtct ttgaacgcaa gttgcgcccg aggccatcag
+      421 gctaagggca cgcctgcctg ggcgttgcgt gctgcatctc tcccattgct aaggttgaac
+      481 gggcatactg ttcggccggc gcggatgaga gattggcccc ttgttcttcg gtgcgatggg
+      541 tccaagacct gggcttttga cggtccaaaa tccggcaaga ggtggacgga cggtggctgc
+      601 gacaaagctg tcgtgcgaat gccctgcgtt gtcgtttttg atgggccgga ataaatccct
+      661 tttgaacccc attggaggca cgtcaaccca tgggcggttg acggccattt ggatgcaacc
+      721 ccaggtcagg tgagccaccc gctgagttta
+//
+LOCUS       Z78509                   731 bp    DNA     linear   PLN 30-NOV-2006
+DEFINITION  P.pearcei 5.8S rRNA gene and ITS1 and ITS2 DNA.
+ACCESSION   Z78509
+VERSION     Z78509.1  GI:2765634
+KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
+            ITS1; ITS2.
+SOURCE      Phragmipedium pearcei
+  ORGANISM  Phragmipedium pearcei
+            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
+            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
+            Cypripedioideae; Phragmipedium.
+REFERENCE   1
+  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
+  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
+            Orchidaceae): nuclear rDNA ITS sequences
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 731)
+  AUTHORS   Cox,A.V.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
+            Richmond, Surrey TW9 3AB, UK
+FEATURES             Location/Qualifiers
+     source          1..731
+                     /organism="Phragmipedium pearcei"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:53135"
+     misc_feature    1..380
+                     /note="internal transcribed spacer 1"
+     gene            381..550
+                     /gene="5.8S rRNA"
+     rRNA            381..550
+                     /gene="5.8S rRNA"
+                     /product="5.8S ribosomal RNA"
+     misc_feature    551..731
+                     /note="internal transcribed spacer 2"
+ORIGIN      
+        1 cgtaacaagg tttccgtagg tgaacctgcg gaaggatcat tgttgagacc gccaaatata
+       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt cgccgctgtg
+      121 gtgaccgtga tttgccatcg agcctccttg ggagatttct tgatggcaat tgaacccttg
+      181 gcccggcgca gtttcgcgcc aagtcatatg agatagaacc ggcggagggc gtcgtcctcc
+      241 atggagcggg gagggccggc atgctccgtg cccccccatg aatttttctg acaactctcg
+      301 gcaacggacg taacaaggtt taaatgtgat aagcaggtgt gaattgcaga atcccgtgaa
+      361 ccatcgagtc tttgaacgca agttgcgccc gaggccatca ggttaagggc acgcctgcct
+      421 gggcgttgcg tgctgcatct ctcccattgc taaggttgaa cgggcatact gttcggccgg
+      481 cgcggatgag agtttggccc cttgttcttc ggtgcgatgg gtccaagacc tgggcttttg
+      541 acggtccaaa atccggcaag aggtggacgg acggtggctg cgacagagct gtcgtgcgaa
+      601 tgccctacgt tgtcgttttt gatgggccag aataaatccc ttttgaaccc cattggaggc
+      661 acgtcaaccc aatggggggt gacgggcatt tggttaaccc cggcaagtta aggcacccgt
+      721 taattttagg a
+//
+LOCUS       Z78508                   741 bp    DNA     linear   PLN 30-NOV-2006'
+
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
   def initialize(
-      commandline_arguments = ARGV,
+      commandline_arguments = nil,
       run_already           = true
     )
     reset
     set_commandline_arguments(
       commandline_arguments
     )
+    menu
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === :do_not_report_anything
+      # ===================================================================== #
+      when :do_not_report_anything
+        @internal_hash[:report_the_dataset] = false
+      end
+    end
     run if run_already
   end
 
   # ========================================================================= #
-  # === reset
+  # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
     super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @internal_hash
+    # ======================================================================= #
+    @internal_hash = {}
+    # ======================================================================= #
+    # === :work_on_this_file
+    # ======================================================================= #
+    @internal_hash[:work_on_this_file] = nil
+    # ======================================================================= #
+    # === :report_the_dataset
+    # ======================================================================= #
+    @internal_hash[:report_the_dataset] = true
+    # ======================================================================= #
+    # === :n_FASTA_entries_in_the_file
+    #
+    # This variable will keep track how many FASTA entries are in
+    # the genbank file at hand.
+    # ======================================================================= #
+    @internal_hash[:n_FASTA_entries_in_the_file] = 0
+    # ======================================================================= #
+    # === :dataset_from_all_FASTA_entries_as_a_hash
+    #
+    # This hash will contain all the FASTA sequences in the given
+    # genbank file at hand. This constitutes the main dataset of
+    # this clas.
+    # ======================================================================= #
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash] = {}
   end
 
   # ========================================================================= #
-  # === run
+  # === menu                                                       (menu tag)
   # ========================================================================= #
-  def run
-    _ = first_argument?
-    if _ and File.exist?(_)
-      dataset = File.readlines(_).select {|line|
-        line.start_with? '     '
-      }.map {|entry|
-        splitted = entry.strip.split(' ')
-        splitted.pop # Remove the last element.
-        splitted.join.strip
-      }
-      if dataset.is_a? Array
-        dataset = dataset.join
+  def menu(
+      i = commandline_arguments_containing_leading_hyphens?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # (case tag)
+      # ===================================================================== #
+      # === gparser --help
+      # ===================================================================== #
+      when /^-?-?help$/i
+        show_help
+        exit
+      # ===================================================================== #
+      # === gparser --test
+      #
+      # This entry point can be used to test the default TEST_STRING.
+      # ===================================================================== #
+      when /^-?-?test$/i,
+           /^-?-?test(-|_)?string$/i
+        analyse_this_dataset(TEST_STRING)
+        exit
       end
-      @sequence = dataset
     end
   end
 
+  # ========================================================================= #
+  # === work_on_which_file?
+  # ========================================================================= #
+  def work_on_which_file?
+    @internal_hash[:work_on_this_file]
+  end
+
+  # ========================================================================= #
+  # === report_the_dataset?
+  # ========================================================================= #
+  def report_the_dataset?
+    @internal_hash[:report_the_dataset]
+  end
+
+  # ========================================================================= #
+  # === set_work_on_this_file
+  # ========================================================================= #
+  def set_work_on_this_file(
+      i = first_argument?
+    )
+    @internal_hash[:work_on_this_file] = i
+  end
+
+  # ========================================================================= #
+  # === analyse_this_dataset
+  # ========================================================================= #
+  def analyse_this_dataset(dataset)
+    use_this_regex =
+      /ORIGIN[\/\-\.\s0-9a-zA-Z]+VERSION\s*[\.0-9A-Z]+/ # See: https://rubular.com/r/0q7rFIUflX7yzw
+    scanned = dataset.scan(use_this_regex)
+    @internal_hash[:n_FASTA_entries_in_the_file] = scanned
+    discover_the_corresponding_FASTA_entries_from_this_dataset(scanned)
+    consider_reporting_our_findings_to_the_user
+  end; alias determine_dataset analyse_this_dataset # === determine_dataset
+
+  # ========================================================================= #
+  # === dataset?
+  # ========================================================================= #
+  def dataset?
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash]
+  end; alias main_dataset? dataset? # === main_dataset?
+
+  # ========================================================================= #
+  # === sequences?
+  # ========================================================================= #
+  def sequences?
+    dataset?.values
+  end
+
   # ========================================================================= #
   # === sequence?
   # ========================================================================= #
   def sequence?
-    @sequence
+    sequences?.first
   end; alias coding_sequence? sequence? # === coding_sequence?
        alias cds              sequence? # === cds
 
+  # ========================================================================= #
+  # === discover_the_corresponding_FASTA_entries_from_this_dataset
+  # ========================================================================= #
+  def discover_the_corresponding_FASTA_entries_from_this_dataset(i)
+    regex_to_use_for_the_id = /VERSION\s*([\.A-Za-z0-9]+)/
+    if i.is_a? Array
+      i.each {|this_dataset|
+        this_dataset =~ regex_to_use_for_the_id
+        use_this_id = $1.to_s.dup
+        use_this_FASTA_sequence = this_dataset.scan(
+          /^\s*\d{1,100}([\sa-zA-Z]+)/
+        ).flatten.join(' ').delete(" \n")
+        use_this_FASTA_sequence.upcase! if UPCASE_THE_SEQUENCE
+        @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash][use_this_id] = use_this_FASTA_sequence
+      }
+    end
+  end
+
+  # ========================================================================= #
+  # === verbose_check_whether_the_file_exists
+  # ========================================================================= #
+  def verbose_check_whether_the_file_exists
+    _ = @internal_hash[:work_on_this_file]
+    if _ and File.exist?(_)
+      true
+    else
+      opnn; e 'No file exists at '+sfile(_)
+      false
+    end
+  end
+
+  # ========================================================================= #
+  # === consider_reporting_our_findings_to_the_user              (report tag)
+  # ========================================================================= #
+  def consider_reporting_our_findings_to_the_user
+    if report_the_dataset? and dataset? and !dataset?.empty?
+      main_dataset?.each_pair {|key, value|
+        e steelblue("#{key}:")
+        e lightblue(value)
+        e
+      }
+    end
+  end; alias report             consider_reporting_our_findings_to_the_user # === report
+       alias report_the_dataset consider_reporting_our_findings_to_the_user # === report_the_dataset
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    set_work_on_this_file(first_argument?)
+    # ======================================================================= #
+    # First check whether the given file exists or not:
+    # ======================================================================= #
+    if verbose_check_whether_the_file_exists
+      original_dataset = File.read(@internal_hash[:work_on_this_file]) # Just store it completely.
+      if original_dataset.include?('ORIGIN') and original_dataset.include?('VERSION ')
+        analyse_this_dataset(original_dataset)
+      else
+        opnn; e 'No keywords ORIGIN and VERSION were found in this file.'
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GenbankParser[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME
-  _ = Bioroebe::GenbankParser.new(ARGV)
-  pp _.id
-  pp _.sequence?
-end # genbankparser *genbank
+  alias e puts
+  genbank_parser = Bioroebe::GenbankParser.new(ARGV)
+  # genbank_parser = Bioroebe::GenbankParser.new('/home/Temp/bioroebe/ls_orchid.gbk')
+  e genbank_parser.sequence?
+  # e _.id
+end # genbankparser *genbank
+    # genbankparser
+    # genbankparser sample_file.genbank
+    # genbankparser --test

data/lib/bioroebe/parsers/gff.rb

@@ -68,11 +68,6 @@ module Parser
 
 class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === INPUT_FILE
   #
@@ -112,10 +107,7 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @input_file
     # ======================================================================= #

data/lib/bioroebe/pdb/parse_pdb_file.rb

@@ -114,11 +114,6 @@ module Bioroebe
 
 class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdbFile
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_PDB_FILE
   # ========================================================================= #
@@ -171,10 +166,7 @@ class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdb
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @do_create_a_fasta_file
     #

data/lib/bioroebe/project/project.rb

@@ -248,7 +248,7 @@ module Taxonomy
   # ========================================================================= #
   def self.project_base_dir?
     "#{::Bioroebe.project_base_directory?}taxonomy/"
-  end
+  end; self.instance_eval { alias base_dir? project_base_dir? } # === Bioroebe::Taxonomy.base_dir?
 
   # ========================================================================= #
   # === Bioroebe::Taxonomy.project_yaml_dir?

data/lib/bioroebe/python/README.md

@@ -0,0 +1 @@
+This directory will contain some python-specific code.

data/lib/bioroebe/python/gui/gtk3/all_in_one.css

@@ -0,0 +1,4 @@
+window {
+  font-size: 28px;
+  border: 2px solid black;
+}

data/lib/bioroebe/python/gui/gtk3/all_in_one.py

@@ -0,0 +1,59 @@
+import gi
+#import cairo
+#from gi.repository import PangoCairo
+
+gi.require_version("Gtk", "3.0")
+from gi.repository import Gtk, Gdk, GLib
+
+gi.require_version('Pango', '1.0')
+from gi.repository import Pango
+
+class MyWindow(Gtk.Window):
+
+  def __init__(self):
+    super().__init__(title="Hello World")
+
+    self.set_title("Bioroebe - all in one")
+    self.set_default_size(1400, 800)
+    
+    #self.override_font(Pango.FontDescription("Times New Roman Italic 20"))
+    # ^^^ this is deprecated
+    outer_vbox = Gtk.Box.new(Gtk.Orientation.VERTICAL, spacing = 5)
+
+    top_hbox = Gtk.Box.new(Gtk.Orientation.HORIZONTAL, spacing = 5)
+    
+    label = Gtk.Label(label="Time: ")
+    label.set_halign(Gtk.Align.END) # Right-align.
+    top_hbox.add(label)
+    outer_vbox.add(top_hbox)
+
+    self.button = Gtk.Button(label="Click Here")
+    self.button.connect("clicked", self.on_button_clicked)
+    outer_vbox.add(self.button)
+    # Bioroebe.return_current_day_month_year()
+
+    self.add(outer_vbox)
+    self.apply_css()
+
+  def apply_css(self):
+    screen = Gdk.Screen.get_default()
+    css_provider = Gtk.CssProvider()
+    try:
+      css_provider.load_from_path('all_in_one.css')
+      context = Gtk.StyleContext()
+      context.add_provider_for_screen(screen, css_provider,
+                      Gtk.STYLE_PROVIDER_PRIORITY_USER)
+    except GLib.Error as e:
+      print(f"Error in theme: {e} ")
+
+  def en(self, i = ""):
+    print(i)
+
+  def on_button_clicked(self, widget):
+    self.en("Hello there.")
+
+win = MyWindow()
+win.move(0, 0)
+win.connect("destroy", Gtk.main_quit)
+win.show_all()
+Gtk.main()

data/lib/bioroebe/python/gui/gtk3/widget1.py

@@ -0,0 +1,20 @@
+import gi
+
+gi.require_version("Gtk", "3.0")
+from gi.repository import Gtk
+
+class MyWindow(Gtk.Window):
+  def __init__(self):
+    super().__init__(title="Hello World")
+
+    self.button = Gtk.Button(label="Click Here")
+    self.button.connect("clicked", self.on_button_clicked)
+    self.add(self.button)
+
+  def on_button_clicked(self, widget):
+    print("Hello World")
+
+win = MyWindow()
+win.connect("destroy", Gtk.main_quit)
+win.show_all()
+Gtk.main()

data/lib/bioroebe/python/gui/tkinter/all_in_one.py

@@ -0,0 +1,91 @@
+import sys
+import os
+import importlib
+
+from tkinter import *
+from tkinter import ttk
+from tkinter.ttk import Label
+from tkinter import messagebox
+
+sys.path.append(".")
+
+# sys.path.append("../../") # Adds higher directory to python modules path.
+
+# from ../.. import protein_to_dna
+# module_name = "../../protein_to_dna"
+# importlib.import_module(module_name, package='Bioroebe')
+
+# sys.path.append(os.path.abspath("/home/x/programming/ruby/src/bioroebe/lib/bioroebe/python/"))
+# from protein_to_dny import *
+
+class App:
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = "Bioroebe: all in one"
+
+  # ========================================================================= #
+  # === FONT_TO_USE
+  # ========================================================================= #
+  FONT_TO_USE = 'Hack' # 'Arial'
+
+  # ========================================================================= #
+  # === FONT_SIZE_TO_USE
+  # ========================================================================= #
+  FONT_SIZE_TO_USE = 28
+
+  # ========================================================================= #
+  # === SMALLER_FONT_SIZE_TO_USE
+  # ========================================================================= #
+  SMALLER_FONT_SIZE_TO_USE = 22
+
+  # ========================================================================= #
+  # === __init__
+  # ========================================================================= #
+  def __init__(self, master):
+    # Instantiating master i.e toplevel Widget
+    self.master = master
+    self.create_and_add_header()
+    self.create_and_add_the_button_for_the_protein_to_DNA_conversion()
+
+  # ========================================================================= #
+  # === do_the_conversion_from_protein_to_DNA
+  # ========================================================================= #
+  def do_the_conversion_from_protein_to_DNA(self):
+     messagebox.showinfo("Message","Hey There! I hope you are doing well.")
+
+  # ========================================================================= #
+  # === create_and_add_the_button_for_the_protein_to_DNA_conversion()
+  # ========================================================================= #
+  def create_and_add_the_button_for_the_protein_to_DNA_conversion(self):
+    Button(self.master,
+      text="Convert from protein sequence to DNA sequence",
+      font = (App.FONT_TO_USE, App.SMALLER_FONT_SIZE_TO_USE),
+      command = lambda: self.do_the_conversion_from_protein_to_DNA()
+    ).pack(pady = 5)
+
+  # ========================================================================= #
+  # === create_and_add_header
+  # ========================================================================= #
+  def create_and_add_header(self):
+    # Creating second label
+    # This label has a font-family of Arial
+    # and font-size of 25
+    Label(self.master,
+      text = "Protein to DNA conversion:",
+      font = (App.FONT_TO_USE, App.FONT_SIZE_TO_USE) # Changing font-size here
+    ).pack(padx = 12, pady = 12, anchor = "w") # Align to the left side.
+
+if __name__ == "__main__":
+  root = Tk()
+  root.title(App.TITLE) # Setting the title of the window
+  root.geometry("1400x800") # Set width and height - aka the geometry/dimensions.
+  app = App(root) # Calling our App
+  root.mainloop() # Mainloop which will cause this toplevel to run infinitely
+
+# frm = ttk.Frame(root, padding = 12)
+# frm.grid()
+# ttk.Label(frm, text="Hello World!").grid(column=0, row=0)
+# ttk.Button(frm, text="Quit", command=root.destroy).grid(column=1, row=0)
+# root.mainloop()

data/lib/bioroebe/python/mymodule.py

@@ -0,0 +1,8 @@
+def greeting(name):
+  print("Hello, " + name)
+
+person1 = {
+  "name": "John",
+  "age": 36,
+  "country": "Norway"
+}