bioroebe 0.10.80 → 0.12.12

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/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 +1,42 @@
+#!/usr/bin/python3
+import sys
+
+class Bioroebe(object):
+
+  # =========================================================================== #
+  # === is_palindrome
+  # =========================================================================== #
+  def is_palindrome(i):
+    result = False
+    reverse_string = i[::-1]
+
+    hash = {
+      "A": "T",
+      "T": "A",
+      "G": "C",
+      "C": "G"
+    }
+
+    for nucleotide in i:
+      print(nucleotide)
+      if hash[nucleotide] == reverse
+      result
+# THIS IS INCOMPLETE AS OF JULY 2022.
+    return result
+
+if __name__ == '__main__':
+
+  if len(sys.argv) > 1:
+    i = sys.argv[1]
+  else:
+    i = "malayalam"
+
+  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

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

@@ -0,0 +1,37 @@
+#!/usr/bin/python3
+# =========================================================================== #
+import sys
+import re
+
+class Bioroebe(object):
+
+  # ========================================================================= #
+  # === Bioroebe.three_delimiter
+  #
+  # This method will, applied onto a String, add the '|' token
+  # after 3 positions.
+  #
+  # Example: 
+  #
+  #    Bioroebe.three_delimiter('ATGGGGATGTAGGTA') # => "ATG|GGG|ATG|TAG|GTA"
+  #
+  # ========================================================================= #
+  def three_delimiter(i):
+
+    if isinstance(i, list):
+      i = ' '.join(str(e) for e in i)
+
+    i = re.sub(r'(...)', r'\1-', i)
+
+    if i[-1] == '-': # Chop of the last character if it is a '-' token.
+      i = i[:-1]
+
+    return i 
+
+if __name__ == '__main__':
+  if len(sys.argv) > 1:
+    i = sys.argv[1]
+    print(Bioroebe.three_delimiter(i))
+  else:
+    print("Please provide an argument to this method.")
+# py three_delimiter.py ATGGGGATGTAGGTA

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

@@ -0,0 +1,43 @@
+#!/usr/bin/python3
+import sys
+from datetime import datetime
+
+class Bioroebe(object):
+
+  # ========================================================================= #
+  # === Bioroebe.return_current_day_month_year()
+  #
+  # This method will return a String such as "09.07.2022".
+  # ========================================================================= #
+  def return_current_day_month_year():
+    day   = str(datetime.now().day).rjust(2, '0')
+    month = str(datetime.now().month).rjust(2, '0')
+    year  = str(datetime.now().year)
+    return day+'.'+month+'.'+year
+
+  # ========================================================================= #
+  # === Bioroebe.return_current_hours_minutes_seconds()
+  #
+  # This method will return a String such as "20:44:20".
+  # ========================================================================= #
+  def return_current_hours_minutes_seconds():
+    hours   = str(datetime.now().hour).rjust(2, '0')
+    minutes = str(datetime.now().minute).rjust(2, '0')
+    seconds = str(datetime.now().second).rjust(2, '0')
+    return hours+':'+minutes+':'+seconds
+
+  # ========================================================================= #
+  # === Bioroebe.show_time_now
+  #
+  # This method will show the current time. It will do so only if the
+  # verbosity-variable has been set to true.
+  # ========================================================================= #
+  def show_time_now(be_verbose = True):
+    time = Bioroebe.return_current_hours_minutes_seconds()
+    if be_verbose:
+      print("Showing the current time: "+time)
+
+if __name__ == '__main__':
+  print(Bioroebe.return_current_day_month_year())
+  print(Bioroebe.return_current_hours_minutes_seconds())
+  Bioroebe.show_time_now()

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

@@ -0,0 +1,21 @@
+from re import sub
+import sys
+
+# =========================================================================== #
+# === camel_case
+# =========================================================================== #
+def camel_case(i):
+  i = sub(r"(_|-)+", " ", i).title().replace(" ", "")
+  return ''.join(
+    [
+      i[0].upper(),
+      i[1:]
+    ]
+  )
+
+if __name__ == "__main__":
+  print(
+    camel_case(
+      sys.argv[1]
+    )
+  ) # py to_camelcase.py abcDef

data/lib/bioroebe/requires/require_the_bioroebe_project.rb

@@ -159,4 +159,6 @@ require 'bioroebe/requires/require_all_codon_files.rb'
 # And the sinatra-interface:
 # =========================================================================== #
 # require 'bioroebe/requires/require_the_bioroebe_sinatra_components.rb'
-require 'bioroebe/www/sinatra/sinatra.rb'
+require 'bioroebe/www/sinatra/sinatra.rb'
+
+require 'bioroebe/sequence/protein.rb'

data/lib/bioroebe/sequence/alignment.rb

@@ -28,6 +28,8 @@ module Bioroebe
 
 class Alignment < ::Bioroebe::CommandlineApplication # === Bioroebe::Alignment
 
+  require 'bioroebe/misc/ruler.rb'
+
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -122,9 +124,12 @@ class Alignment < ::Bioroebe::CommandlineApplication # === Bioroebe::Alignment
   # ========================================================================= #
   def print_consensus_sequence
     e
-    erev 'The consensus sequence, derived from the above matrix, is:'
+    n_nucleotides = @array_G.size
+    erev 'The consensus sequence ('+steelblue(n_nucleotides.to_s)+
+         rev+' nucleotides), '\
+         'derived from the above matrix, is:'
     e
-    print '  '
+    sequence_that_will_be_displayed = ''.dup
     @array_G.size.times {|index|
       hash = {}
       hash['A'] = @array_A[index]
@@ -132,8 +137,12 @@ class Alignment < ::Bioroebe::CommandlineApplication # === Bioroebe::Alignment
       hash['C'] = @array_C[index]
       hash['G'] = @array_G[index]
       _ = hash.max_by {|key, value| value }
-      print mediumslateblue(_[0])+rev # Print each individual character here.
+      sequence = _[0]
+      sequence_that_will_be_displayed << sequence
     }
+    ruler_result = Bioroebe.return_ruler(sequence_that_will_be_displayed)
+    e '  '+ruler_result+rev
+    print '  '+mediumslateblue(sequence_that_will_be_displayed)+rev # Print each individual character here.
     e Colours.rev
     e
   end
@@ -159,7 +168,8 @@ class Alignment < ::Bioroebe::CommandlineApplication # === Bioroebe::Alignment
   # === print_row_for
   # ========================================================================= #
   def print_row_for(
-      i = 'A', array = @array_A
+      i     = 'A',
+      array = @array_A
     )
     print "#{rev}  #{i}: " # First output the identifier, e. g. "A" or "T" and so forth.
     array.each {|entry| # entry is a Float.

data/lib/bioroebe/sequence/dna.rb

@@ -83,6 +83,7 @@ class DNA < ::Bioroebe::Sequence # === Bioroebe::DNA
   end; alias to_RNA to_rna # === to_RNA
        alias to_T   to_rna # === to_T
 
+  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
   # ========================================================================= #
   # === to_aminoacids
   #

data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb

@@ -72,13 +72,6 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     i.tr('U','T')
   end
 
-  # ========================================================================= #
-  # === to_dna
-  # ========================================================================= #
-  def to_dna
-    seq?.tr('U','T')
-  end; alias dna to_dna # === dna
-
   # ========================================================================= #
   # === n_random_dna
   #
@@ -258,24 +251,6 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     ::Bioroebe.codon_to_aminoacid(codon)
   end; alias translate_aminoacid_into_dna codon_to_aminoacid # === translate_aminoacid_into_dna
 
-  # ========================================================================= #
-  # === to_dna
-  #
-  # This method will convert a RNA sequence into a DNA sequence.
-  #
-  # It will return the translation.
-  #
-  # bio; puts Bioroebe.new.to_dna('actgggcgagagklklklklk')
-  # ========================================================================= #
-  def to_dna(
-      i = sequence?, upcase_me = true
-    )
-    if is_RNA?
-      i = sequence? if i.nil?
-      ::Bioroebe.to_dna(i, upcase_me)
-    end
-  end; alias dna to_dna # === dna
-
   # ========================================================================= #
   # === random
   #
@@ -397,6 +372,34 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     end
   end; alias gc_percent gc_percentage # === gc_percent
 
+  # ========================================================================= #
+  # === to_dna
+  #
+  # This method will convert a RNA sequence into a DNA sequence.
+  #
+  # It will return the translation.
+  #
+  # Usage example:
+  #
+  #   require 'bioroebe'; puts Bioroebe::DNA.new('actgggcgagaguuuuUUUUUU').to_dna
+  #
+  # ========================================================================= #
+  def to_dna(
+      i         = sequence?,
+      upcase_me = true
+    )
+    i = sequence? if i.nil?
+    i = ::Bioroebe.to_dna(i, upcase_me)
+    return i
+  end; alias dna to_dna # === dna
+
+  # ========================================================================= #
+  # === to_dna
+  # ========================================================================= #
+  # def to_dna
+  #   seq?.tr('U','T')
+  # end; alias dna to_dna # === dna
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/sequence/protein.rb

@@ -4,7 +4,12 @@
 # =========================================================================== #
 # === Bioroebe::Protein
 #
-# This is a typical sequence of aminoacids.
+# This is a typical sequence of aminoacids. It is not 100% certain whether
+# this class will be retained, but for the time being it will be. Note
+# that peptides should also use this class - while the name may not be
+# 100% accurate (smaller proteins are typically called peptides or
+# oligopeptides) I feel that this is a distinction that does not really
+# make a whole lot of sense.
 # =========================================================================== #
 # require 'bioroebe/sequence/protein.rb'
 # =========================================================================== #
@@ -94,6 +99,9 @@ class Protein < ::Bioroebe::Sequence # === Bioroebe::Protein
   # This method will return true if there are at the least two
   # cysteines in the aminoacid sequence of this protein.
   #
+  # If anyone knows of a better algorithm to determine whether
+  # a protein can REALLY create a disulfide bond let me know.
+  #
   # Usage example:
   #
   #   Bioroebe::Protein.new('MLKLKNASCCEEE').can_form_disulfide_bonds? # => true
@@ -146,7 +154,7 @@ class Protein < ::Bioroebe::Sequence # === Bioroebe::Protein
     chars.each {|this_aminoacid|
       sum += weight_of(this_aminoacid)
     }
-    sum
+    return sum
   end; alias molecular_weight? weight? # === molecular_weight?
 
   # ========================================================================= #
@@ -230,10 +238,99 @@ class Protein < ::Bioroebe::Sequence # === Bioroebe::Protein
     return result
   end
 
+  # ========================================================================= #
+  # === can_be_stained_via_coomassie?
+  #
+  # Determine whether a protein can be stained in a coomassie
+  # staining. This is just a simple, fairly dumb check and
+  # NOT guaranteed to be correct. If anyone has a better
+  # way to check for this let me know.
+  # ========================================================================= #
+  def can_be_stained_via_coomassie?
+    disallowed_aminoacids = %w( K H R W F Y)
+    sequence = sequence?
+    return sequence.chars.uniq.any? {|this_aminoacid|
+      disallowed_aminoacids.include? this_aminoacid
+    }
+  end
+
+  # ========================================================================= #
+  # === aliphatic_index
+  #
+  # This method will calculate the aliphatic acid of an aminoacid,
+  # aka a Protein.
+  #
+  # Usage example:
+  #
+  #    require 'bioroebe'; Bioroebe::Protein.new('MVKSYDRYEYEDCLGIVNSKSSNCVFLNNA').aliphatic_index # => 71.33333
+  #
+  # ========================================================================= #
+  def aliphatic_index(
+      a = 2.9,
+      b = 3.9
+    )
+   composition = {}
+   composition.default = 0
+   chars = sequence?.chars
+   chars.each { |entry| composition[entry] += 1} 
+   (
+     composition['A'] + 
+     a * composition['V'].to_f + 
+     b * (composition['I'] + composition['L'])
+   ).to_f / length.to_f * 100
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Protein.one_to_three
+  #
+  # Usage example:
+  #
+  #   Bioroebe::Protein.one_to_three('A') # => "Ala"
+  #
+  # ========================================================================= #
+  def self.one_to_three(this_aminoacid = 'A')
+    if this_aminoacid.is_a? Array
+      this_aminoacid = this_aminoacid.join(' ').strip
+    end
+    return ::Bioroebe.one_to_three(this_aminoacid)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Protein.name
+  #
+  # Usage example:
+  #
+  #   Bioroebe::Protein.name('A') # => "alanine"
+  #
+  # ========================================================================= #
+  def self.name(this_aminoacid = 'A')
+    Bioroebe.return_long_name_of_this_aminoacid(this_aminoacid).downcase
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Protein.to_1
+  #
+  # This will convert from the long name of an aminoacid, such as 'alanine',
+  # to the short one-letter abbreviation.
+  #
+  # Usage example:
+  #
+  #   Bioroebe::Protein.to_1('alanine') # => "A"
+  #
+  # ========================================================================= #
+  def self.to_1(this_aminoacid = 'alanine')
+    if this_aminoacid.is_a? Array
+      this_aminoacid = this_aminoacid.join(' ').strip
+    end
+    this_aminoacid.downcase!
+    dataset = YAML.load_file(Bioroebe.file_amino_acids_long_name_to_one_letter)
+    return dataset[this_aminoacid]
+  end
+
 end
 
 # =========================================================================== #
-# This "alias" was added in May 2022.
+# The following "alias" was added in May 2022.
 # =========================================================================== #
 Aminoacids = Protein
 
@@ -267,6 +364,7 @@ end
 
 if __FILE__ == $PROGRAM_NAME
   require 'colours/autoinclude'
+  require 'bioroebe/toplevel_methods/verbose.rb'
   protein = Bioroebe::Protein.new(ARGV)
   e protein.weight?
   e Colours.rev+'For the aminoacid sequence:'
@@ -277,5 +375,9 @@ if __FILE__ == $PROGRAM_NAME
   e
   e "  #{Colours.royalblue(protein.to_rna)}"
   e
+  e 'Can this protein be stained via coomassie brilliant blue?:'
+  e
+  e "  #{lightblue(Bioroebe::VerboseTruth[protein.can_be_stained_via_coomassie?])}"
+  e
 end # protein MAC
     # protein MACCCCAAAAAKKKKLLLLL