bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/patterns/scan_for_repeat.rb

@@ -19,11 +19,6 @@ module Bioroebe
 
 class ScanForRepeat < ::Bioroebe::CommandlineApplication # === Bioroebe::ScanForRepeat
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -63,6 +58,7 @@ class ScanForRepeat < ::Bioroebe::CommandlineApplication # === Bioroebe::ScanFor
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
     # === @n_repeats
     # ======================================================================= #

data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb

@@ -21,11 +21,6 @@ class FetchFastaSequenceFromPdb < ::Bioroebe::CommandlineApplication # === Bioro
 
   require 'open-uri'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === URL_FOR_FASTA_ENTRIES_AT_THE_PDB
   # ========================================================================= #
@@ -59,10 +54,7 @@ class FetchFastaSequenceFromPdb < ::Bioroebe::CommandlineApplication # === Bioro
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @result
     # ======================================================================= #

data/lib/bioroebe/pdb/parse_mmCIF_file.rb

@@ -13,11 +13,6 @@ module Bioroebe
 
 class ParsemmCIFFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsemmCIFFile
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -44,10 +39,7 @@ class ParsemmCIFFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Parsem
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

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
     #
@@ -994,7 +986,9 @@ class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdb
               lightgreen(::Bioroebe.one_to_three(aminoacid_one_letter).upcase)+
               rev+
               ' - '+
-              steelblue(n_occurrences.to_s)
+              steelblue(
+                n_occurrences.to_s.rjust(2,' ')
+              )
       }
     end
   end

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"
+}

data/lib/bioroebe/python/protein_to_dna.py

@@ -0,0 +1,33 @@
+import sys
+import yaml
+
+USE_THIS_CODON_TABLE = \
+  '/home/x/programming/ruby/src/bioroebe/lib/bioroebe/yaml/codon_tables/1.yml'
+
+# =========================================================================== #
+# === protein_to_dna
+# =========================================================================== #
+def protein_to_dna(i):
+  output_string = ''
+  yaml_dataset = None
+  aminoacid_sequence = list(i)
+
+  with open(USE_THIS_CODON_TABLE) as file:
+    # The FullLoader parameter handles the conversion from YAML
+    # scalar values to Python the dictionary format
+    yaml_dataset = yaml.load(file, Loader=yaml.FullLoader)
+    yaml_dataset = { value: key for key, value in yaml_dataset.items() }
+
+  for this_aminoacid in aminoacid_sequence:
+    # Now we must obtain the DNA sequence.
+    # print(yaml_dataset[this_aminoacid])
+    output_string += yaml_dataset[this_aminoacid]
+    output_string += '-'
+
+  # print(yaml_dataset)
+  print(output_string[0: -1]) # Remove the last character.
+
+if __name__ == '__main__':
+  i = sys.argv[1]
+  protein_to_dna(i)
+# py protein_to_dna.py KKKLLL

data/lib/bioroebe/python/shell/shell.py

@@ -0,0 +1,19 @@
+#!/usr/bin/python 
+import sys
+
+# =========================================================================== #
+# === obtain_user_input
+# =========================================================================== #
+def obtain_user_input():
+  user_input = input("> ")
+  return user_input
+
+shall_we_continue = True
+
+while (shall_we_continue):
+  result = obtain_user_input
+  if result == "q":
+    shall_we_continue = False
+    # exit
+  else:
+    print(result)

data/lib/bioroebe/python/to_rna.py

@@ -0,0 +1,14 @@
+import sys
+    
+# =========================================================================== #
+# === to_rna
+#
+# This method will simply convert the given input, such as a 
+# nucleotide sequence, to RNA.
+# =========================================================================== #
+def to_rna(i):
+  converted = i.replace('T','U')
+  print(converted)
+
+to_rna(sys.argv[1])
+# py to_rna.py ATG

data/lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py

@@ -0,0 +1,137 @@
+# =========================================================================== #
+# Filename: convert_dna_to_aminoacid_sequence.py
+# =========================================================================== #
+import pprint
+import sys
+import re
+
+# =========================================================================== #
+# pp for simpler debugging.
+# =========================================================================== #
+pp = pprint.PrettyPrinter(indent = 4)
+
+# =========================================================================== #
+# === ConvertDNAtoAminoacidSequence
+#
+# This class does not do much other than map from CODON to Aminoacid
+# sequence really.
+# =========================================================================== #
+class ConvertDNAtoAminoacidSequence:
+
+  # ========================================================================= #
+  # === HASH_CODON_TO_AMINOACID
+  #
+  # This will map from eukaryotes (aka humans).
+  # ========================================================================= #
+  HASH_CODON_TO_AMINOACID = {
+    'TAA': '*', # Stop Codon.
+    'TGA': '*', # Stop Codon.
+    'TAG': '*', # Stop Codon.
+    'START': 'ATG', # This is the main one in Eukaryotes.
+    'TTT': 'F', # Phenylalanine.
+    'TCT': 'S', # Serine.
+    'TAT': 'Y', # Tyrosine.
+    'TGT': 'C', # Cysteine.
+    'TTC': 'F', # Phenylalanine.
+    'TCC': 'S', # Serine.
+    'TAC': 'Y', # Tyrosine.
+    'TGC': 'C', # Cysteine.
+    'TTA': 'L', # Leucine.
+    'TCA': 'S', # Serine.
+    'TTG': 'L', # Leucine.
+    'TCG': 'S', # Serine.
+    'TGG': 'W',# Tryptophane.
+    'CTT': 'L', # Leucine.
+    'CCT': 'P', # Proline.
+    'CAT': 'H', # Histidine.
+    'CGT': 'R', # Arginine.
+    'CTC': 'L', # Leucine.
+    'CCC': 'P', # Proline.
+    'CAC': 'H', # Histidine.
+    'CGC': 'R', # Arginine.
+    'CTA': 'L', # Leucine.
+    'CCA': 'P', # Proline.
+    'CAA': 'Q', # Glutamine.
+    'CGA': 'R', # Arginine.
+    'CTG': 'L', # Leucine.
+    'CCG': 'P', # Proline.
+    'CAG': 'Q', # Glutamine.
+    'CGG': 'R', # Arginine.
+    'AAG': 'K', # Lysine.
+    'AAA': 'K', # Lysine.
+    'ATT': 'I', # Isoleucin.
+    'ACT': 'T', # Threonine.
+    'AAT': 'N', # Asparagin.
+    'AGT': 'S', # Serine.
+    'ATC': 'I', # Isoleucin.
+    'ACC': 'T', # Threonine.
+    'AAC': 'N', # Asparagin.
+    'AGC': 'S', # Serine.
+    'ATA': 'I', # Isoleucin.
+    'ACA': 'T', # Threonine.
+    'AGA': 'R', # Arginine.
+    'ATG': 'M', # Methionin. This is also the start-codon.
+    'ACG': 'T', # Threonine.
+    'AGG': 'R', # Arginine.
+    'GTT': 'V', # Valine.
+    'GCT': 'A', # Alanine.
+    'GAT': 'D', # Aspartic Acid.
+    'GGT': 'G', # Glycine.
+    'GTC': 'V', # Valine.
+    'GCC': 'A', # Alanine.
+    'GAC': 'D', # Aspartic Acid.
+    'GGC': 'G', # Glycine.
+    'GTA': 'V', # Valine.
+    'GCA': 'A', # Alanine.
+    'GAA': 'E', # Glutamic Acid.
+    'GGA': 'G', # Glycine.
+    'GTG': 'V', # Valine.
+    'GCG': 'A', # Alanine.
+    'GAG': 'E', # Glutamic Acid.
+    'GGG': 'G'  # Glycine.
+  } 
+
+  # ========================================================================= #
+  # === __init__
+  #
+  # Our constructor. We will store the sequence onto the string
+  # called string_fasta_sequence.
+  # ========================================================================= #
+  def __init__(self, this_sequence = 'ATGCATCGCATCATGCATCA'):
+    if type(this_sequence) == list:
+      this_sequence = ''.join(this_sequence)
+    self.sequence = this_sequence
+    self.scan_for_codons()
+
+  # ========================================================================= #
+  # === scan_for_codons()
+  # ========================================================================= #
+  def scan_for_codons(self):
+    codons = re.findall('...', self.sequence)
+    for codon in codons:
+      # ===================================================================== #
+      # Check whether the given input is included in the main hash.
+      # ===================================================================== #
+      if codon in self.HASH_CODON_TO_AMINOACID:
+        match = self.HASH_CODON_TO_AMINOACID[codon]
+        print(match, end='')
+    print()
+
+# =========================================================================== #
+# py convert_dna*py ATGCAC
+# =========================================================================== #
+if __name__ == '__main__':
+
+  if len(sys.argv) > 1:
+    i = sys.argv[1:]
+    ConvertDNAtoAminoacidSequence(i)
+  else:
+    # ======================================================================= #
+    # Next testing 6 sequences:
+    # ======================================================================= #
+    ConvertDNAtoAminoacidSequence('ATGGGCCCGTGCGCGGGGAGCGCGCGATCGCGCGCGGGCGCGAGGGCGACGACGACGCGGTGGAGGTCTTGTCGCGACGGGCGTTGGCGGGGAAGGCGGTGACGCTCGCGGCGGCGCTCGCGGCGTGGCCGGCGGATAAGCGGGCGCTGGCGGAGGGATCGATCGAGAGCGAGTACTGGGAGCGCGTGGAGCTGCCGCTCGAACCTGGGGTCATTCTTCTGGATATCGCGTTCGTGAACGAACAGCGTGGATTTTTGCTCGGGACGAGGCAGACGATCTTGGAGACGACGAACGGTGGGAAGACGTGGGACGCGCGGGATCTGACGGGTTTGTTGGACGACGACGTGAATTATCGGTTCAACAGCGTGTCGTTCGCCGGCGAAGAGGGCTGGATCATCGGTAAACCGGCGGTGCTGTTGCACACTGTGGACGGCGGTAAGAACTGGGAACGCGTTGGTTTGAGTCCGAGACTTCCGGGCGCCCCGTTGTTGGTCACGGCGGTGAAGGACAACGGCACGGCGGAGATGGTCACCGACGAGGGCGCCATTTACTTCACCAAGGACGCCGCGCGCAACTGGAAGGCTGCCGTCGAAGAGACCGTCTCCGCGACGCTCAACCGAACGGTAAGCTCCGGTATCACCGGTGCCTCGTACTACACGGGCACCTTCTCCACCGTCTCGCGCAACGACAAGGGCGAATACCTCGGCCTGAGCTCTCGCGGTAACTTCTACATGACCTGGGCCCCGGGTCAGGCTTACTGGCAACCGCACAACAGAACTTCGGCCAGACGCGTGCAAAGCATGGGCTGGCGCAAAGATGGCGGGGTCTGGGAACTCACTCGCGGCGGTGGCGTCTTCCAGTCTCAAGACATCGGTCTTCCGGAGGAAGATTCGGAGTTCGTCGAGGCAAAAATCGGCTCGCGCGGTTTCGGCCTCCTTGATCTCGGAAGCGATCCAAAGGGTAACACGTACTGGGCCGTCGGAGGTTCGGGCAGCGTCTTCTACTCCACGGATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')
+    ConvertDNAtoAminoacidSequence('ATGGTCACCGACGAGGGCGCCATTTACTTCACCAAGGACGCCGCGCGCAACTGGAAGGCTGCCGTCGAAGAGACCGTCTCCGCGACGCTCAACCGAACGGTAAGCTCCGGTATCACCGGTGCCTCGTACTACACGGGCACCTTCTCCACCGTCTCGCGCAACGACAAGGGCGAATACCTCGGCCTGAGCTCTCGCGGTAACTTCTACATGACCTGGGCCCCGGGTCAGGCTTACTGGCAACCGCACAACAGAACTTCGGCCAGACGCGTGCAAAGCATGGGCTGGCGCAAAGATGGCGGGGTCTGGGAACTCACTCGCGGCGGTGGCGTCTTCCAGTCTCAAGACATCGGTCTTCCGGAGGAAGATTCGGAGTTCGTCGAGGCAAAAATCGGCTCGCGCGGTTTCGGCCTCCTTGATCTCGGAAGCGATCCAAAGGGTAACACGTACTGGGCCGTCGGAGGTTCGGGCAGCGTCTTCTACTCCACGGATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')
+    ConvertDNAtoAminoacidSequence('ATGACCTGGGCCCCGGGTCAGGCTTACTGGCAACCGCACAACAGAACTTCGGCCAGACGCGTGCAAAGCATGGGCTGGCGCAAAGATGGCGGGGTCTGGGAACTCACTCGCGGCGGTGGCGTCTTCCAGTCTCAAGACATCGGTCTTCCGGAGGAAGATTCGGAGTTCGTCGAGGCAAAAATCGGCTCGCGCGGTTTCGGCCTCCTTGATCTCGGAAGCGATCCAAAGGGTAACACGTACTGGGCCGTCGGAGGTTCGGGCAGCGTCTTCTACTCCACGGATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')
+    ConvertDNAtoAminoacidSequence('ATGGGCTGGCGCAAAGATGGCGGGGTCTGGGAACTCACTCGCGGCGGTGGCGTCTTCCAGTCTCAAGACATCGGTCTTCCGGAGGAAGATTCGGAGTTCGTCGAGGCAAAAATCGGCTCGCGCGGTTTCGGCCTCCTTGATCTCGGAAGCGATCCAAAGGGTAACACGTACTGGGCCGTCGGAGGTTCGGGCAGCGTCTTCTACTCCACGGATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')
+    ConvertDNAtoAminoacidSequence('ATGGCGGGGTCTGGGAACTCACTCGCGGCGGTGGCGTCTTCCAGTCTCAAGACATCGGTCTTCCGGAGGAAGATTCGGAGTTCGTCGAGGCAAAAATCGGCTCGCGCGGTTTCGGCCTCCTTGATCTCGGAAGCGATCCAAAGGGTAACACGTACTGGGCCGTCGGAGGTTCGGGCAGCGTCTTCTACTCCACGGATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')
+    ConvertDNAtoAminoacidSequence('ATGGCGGCAAAAGCTGGAAGCGCGACCGCGGCACCGATAACGTCGCGGCCAACCTCTACAACGTCAAGTTCCAATCTGAGACGCAAGGTTTCATCCTCGGTAACGACGGTGTTTTGTTGCGCTACATCGGTCGCAGCCCGAAGTGA')

data/lib/bioroebe/python/toplevel_methods/esystem.py

@@ -0,0 +1,12 @@
+import subprocess
+
+# =========================================================================== #
+# === esystem
+# =========================================================================== #
+def esystem(i):
+  print(i)
+  process = subprocess.run(i)
+  
+# This is our shell command, executed in subprocess.
+
+esystem("ls")

data/lib/bioroebe/python/toplevel_methods/open_in_browser.py

@@ -0,0 +1,20 @@
+#!/usr/bin/python3
+import sys
+import os
+
+class Bioroebe(object):
+
+  # =========================================================================== #
+  # === open_in_browser
+  # =========================================================================== #
+  def open_in_browser(
+      this_url,
+      use_this_browser = 'firefox'
+    ):
+    cmd = use_this_browser+" -new-tab "+this_url
+    print(cmd)
+    os.system(cmd)
+
+if __name__ == '__main__':
+  i = sys.argv[1]
+  Bioroebe.open_in_browser(i) # py open_in_browser.py "derstandard.at"

data/lib/bioroebe/python/toplevel_methods/palindromes.py

@@ -0,0 +1,52 @@
+#!/usr/bin/python3
+import sys
+
+class Bioroebe(object):
+
+  # =========================================================================== #
+  # === is_palindrome
+  # =========================================================================== #
+  def is_palindrome(i):
+    """
+    This method takes a sequence and converts it to all lowercase letters
+    while ignoring punctuation marks and whitespaces. If it matches the
+    reverse spelling then it is a palindrome. Returns true if matched,
+    false otherwise.
+    """
+    if type(i) == list:
+      i = ''.join(i) 
+
+    result = False # Our result-value.
+    reverse_string = i[::-1].lower()
+
+    # hash = {
+    #   "A": "T",
+    #   "T": "A",
+    #   "G": "C",
+    #   "C": "G"
+    # }
+    phrase_letters = [c for c in i.lower() if c.isalpha()]
+    phrase_letters = ''.join(phrase_letters)
+    # print(phrase_letters) # Debug.
+    # print(reverse_string)
+    return (phrase_letters == reverse_string)
+
+if __name__ == '__main__':
+
+  if len(sys.argv) > 1:
+    i = sys.argv[1:]
+  else:
+    i = "malayalam"
+
+  if type(i) == list:
+    i = ''.join(i)
+
+  ans = Bioroebe.is_palindrome(i)
+
+  if ans:
+    print(f"Yes, {i} is a palindrome.")
+  else:
+    print(f"No, {i} is NOT a palindrome.")
+
+# py palindromes.py "OTTO"
+# py palindromes.py "GAATTC"

data/lib/bioroebe/python/toplevel_methods/rds.py

@@ -0,0 +1,13 @@
+#!/usr/bin/python3
+import re
+import sys
+
+# =========================================================================== #
+# === rds
+# =========================================================================== #
+def rds(i):
+  return re.sub('//', '/', i)
+
+if __name__ == '__main__':
+  i = sys.argv[1]
+  print(rds(i)) # py rds.py "foobar//barfoo"

data/lib/bioroebe/python/toplevel_methods/shuffleseq.py

@@ -0,0 +1,23 @@
+#!/usr/bin/python3
+# =========================================================================== #
+import sys
+import random
+
+# =========================================================================== #
+# === shuffleseq
+#
+# This method will take the input string and simply re-arrange it as-is.
+# =========================================================================== #
+def shuffleseq(i):
+  l = list(i)
+  random.shuffle(l)
+  result = ''.join(l)
+  return result
+
+if __name__ == '__main__':
+  if len(sys.argv) > 1:
+    i = sys.argv[1]
+    print(shuffleseq(i))
+  else:
+    print("Please provide an argument to this method.")
+# py shuffleseq.py ATTTTTTTT