bioroebe 0.10.80

data/lib/bioroebe/aminoacids/codon_percentage.rb

@@ -0,0 +1,189 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::CodonPercentage
+#
+# This small class can be used to load the frequencies of the codon
+# table into a hash-like object.
+#
+# Usage example from within ruby code:
+#
+#   Bioroebe::CodonPercentage.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/aminoacids/codon_percentage.rb'
+# Bioroebe::CodonPercentage.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::CodonPercentage
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @internal_hash
+    # ======================================================================= #
+    @internal_hash = {}
+    # ======================================================================= #
+    # === :dataset
+    # ======================================================================= #
+    @internal_hash[:dataset] = nil
+  end
+
+  # ========================================================================= #
+  # === []
+  #
+  # This method was added primarily to make this class respond similar
+  # to a regular Hash in ruby.
+  # ========================================================================= #
+  def [](this_codon)
+    this_codon = this_codon.to_s.tr('T','U')
+    @internal_hash[:dataset][this_codon]
+  end
+
+  # ========================================================================= #
+  # === try_to_load_this_codon_frequency
+  # ========================================================================= #
+  def try_to_load_this_codon_frequency(
+      i = '9606_Homo_sapiens.yml'
+    )
+    case i # case tag
+    # ======================================================================= #
+    # === :homo_sapiens
+    #
+    # This is the default codon-frequency table.
+    # ======================================================================= #
+    when :homo_sapiens,
+         :humans,
+         :human,
+         :default,
+         1
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_HOMO_SAPIENS
+    # ======================================================================= #
+    # === :ecoli
+    # ======================================================================= #
+    when :ecoli,
+         :e_coli,
+         2
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_E_COLI
+    # ======================================================================= #
+    # === :yeast
+    # ======================================================================= #
+    when :yeast,
+         3
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_SACCHAROMYCES_CEREVISIAE
+    # ======================================================================= #
+    # === :cat
+    #
+    # This entry point is for the domestic cat.
+    # ======================================================================= #
+    when :cat,
+         4
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_FELIS_CATUS
+    # ======================================================================= #
+    # === :arabidopsis
+    #
+    # This entry point is for Arabidopsis thaliana.
+    # ======================================================================= #
+    when :arabidopsis
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_ARABIDOPSIS_THALIANA
+    # ======================================================================= #
+    # === :drosophila
+    #
+    # This entry point is for the fruit fly.
+    # ======================================================================= #
+    when :drosophila,
+         :the_fly,
+         :fly
+      i = ::Bioroebe::CodonTablesFrequencies::FILE_DROSOPHILA_MELANOGASTER
+    # else
+    # else use the number ID.
+    end
+    set_use_this_codon_table(Bioroebe.directory_frequencies?+File.basename(i))
+    if File.exist? @internal_hash[:use_this_codon_table]
+      @internal_hash[:dataset] = YAML.load_file(@internal_hash[:use_this_codon_table])
+    else
+      no_file_exists_at(file)
+    end
+  end
+
+  # ========================================================================= #
+  # === set_use_this_codon_table
+  # ========================================================================= #
+  def set_use_this_codon_table(i)
+    @internal_hash[:use_this_codon_table] = i
+  end
+
+  # ========================================================================= #
+  # === codon_table?
+  # ========================================================================= #
+  def codon_table?
+    @internal_hash[:use_this_codon_table]
+  end; alias use_this_codon_table? codon_table? # === use_this_codon_table?
+
+  # ========================================================================= #
+  # === name_of_the_codon_table?
+  # ========================================================================= #
+  def name_of_the_codon_table?
+    File.basename(codon_table?)
+  end
+
+  # ========================================================================= #
+  # === dataset?
+  # ========================================================================= #
+  def dataset?
+    @internal_hash[:dataset]
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    # ======================================================================= #
+    # The :human variant is the default codon table to use.
+    # ======================================================================= #
+    try_to_load_this_codon_frequency(:human)
+    # try_to_load_this_codon_frequency(:drosophila) # <- This here could be used for testing.
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::CodonPercentage[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::CodonPercentage.new(ARGV)
+end

data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb

@@ -0,0 +1,110 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ColourizeHydrophilicAndHydrophobicAminoacids
+#
+# This class will colourize the given aminoacid sequence.
+#
+# The code was inspired from:
+#
+#   https://www.biophp.org/minitools/reduce_protein_alphabet/demo.php
+#
+# =========================================================================== #
+# require 'bioroebe/colourize_hydrophilic_and_hydrophobic_aminoacids.rb'
+# =========================================================================== #
+require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
+class ColourizeHydrophilicAndHydrophobicAminoacids < Base # === Bioroebe::ColourizeHydrophilicAndHydrophobicAminoacids
+
+  # ========================================================================= #
+  # === ARRAY_HYROPHILIC_AMINOACIDS
+  # ========================================================================= #
+  ARRAY_HYROPHILIC_AMINOACIDS = %w(
+    A G T S N Q D E H R K P
+  )
+
+  # ========================================================================= #
+  # === ARRAY_HYDROPHOBIC_AMINOACIDS
+  # ========================================================================= #
+  ARRAY_HYDROPHOBIC_AMINOACIDS = %w(
+    C M F I L V W Y
+  )
+
+  # ========================================================================= #
+  # === COLOUR_FOR_HYDROPHILIC_AMINOACIDS
+  # ========================================================================= #
+  COLOUR_FOR_HYDROPHILIC_AMINOACIDS = :royalblue # Is blue originally.
+
+  # ========================================================================= #
+  # === COLOUR_FOR_HYDROPHOBIC_AMINOACIDS
+  # ========================================================================= #
+  COLOUR_FOR_HYDROPHOBIC_AMINOACIDS = :orangered # Is red originally.
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      this_sequence = ARGV,
+      run_already   = true
+    )
+    reset
+    set_this_sequence(this_sequence)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === set_this_sequence
+  # ========================================================================= #
+  def set_this_sequence(i)
+    if i.is_a? Array
+      i = i.join
+    end
+    @this_sequence = i
+  end
+
+  # ========================================================================= #
+  # === this_sequence?
+  # ========================================================================= #
+  def this_sequence?
+    @this_sequence
+  end; alias input? this_sequence? # === input?
+
+  # ========================================================================= #
+  # === output_colourized_sequence
+  # ========================================================================= #
+  def output_colourized_sequence
+    _ = input?.chars.map {|aminoacid|
+      if    ARRAY_HYROPHILIC_AMINOACIDS.include? aminoacid
+        ::Colours.send COLOUR_FOR_HYDROPHILIC_AMINOACIDS, aminoacid
+      elsif ARRAY_HYDROPHOBIC_AMINOACIDS.include? aminoacid
+        ::Colours.send COLOUR_FOR_HYDROPHOBIC_AMINOACIDS, aminoacid
+      else
+        aminoacid # else we will simply return it without any special colour.
+      end
+    }
+    _ = _.join # Join it back into a String.
+    e _
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    output_colourized_sequence
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ColourizeHydrophilicAndHydrophobicAminoacids.new(ARGV)
+end # colourizehydrophilicaminoacid QTNLRWSVIVSILNPHLEILPRNGRDQ*KIRGLGNCFWERPLVSACQRRT

data/lib/bioroebe/aminoacids/create_random_aminoacids.rb

@@ -0,0 +1,221 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::CreateRandomAminoacids
+#
+# This class will create "random" aminoacids, e. g. as String representation.
+#
+# The input to this class should be a number such as 20 - then this class
+# will yield 20 random aminoacids.
+#
+# Usage examples:
+#
+#   Bioroebe::CreateRandomAminoacids.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/aminoacids/create_random_aminoacids.rb'
+# Bioroebe.create_random_aminoacids(125)
+# Bioroebe::CreateRandomAminoacids.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class CreateRandomAminoacids < ::Bioroebe::CommandlineApplication # === Bioroebe::CreateRandomAminoacids
+
+  # ========================================================================= #
+  # === CREATE_N_AMINOACIDS
+  #
+  # This is the default length, e. g. we will create 50 random
+  # aminoacids by default.
+  # ========================================================================= #
+  CREATE_N_AMINOACIDS = 150
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      how_many_aminoacids = CREATE_N_AMINOACIDS,
+      split_at            = nil,
+      be_verbose          = false,
+      run_already         = true,
+      &block
+    )
+    reset
+    set_commandline_arguments(
+      how_many_aminoacids
+    )
+    set_how_many_aminoacids(
+      how_many_aminoacids
+    )
+    @be_verbose = be_verbose
+    @split_at = split_at
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      when :do_report
+        @shall_we_report = true
+        @be_verbose = true
+      end
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @shall_we_report
+    # ======================================================================= #
+    @shall_we_report = false
+  end
+
+  # ========================================================================= #
+  # === set_how_many_aminoacids
+  # ========================================================================= #
+  def set_how_many_aminoacids(
+      i = CREATE_N_AMINOACIDS
+    )
+    if i.is_a? Array
+      i = i.first
+    end
+    i = CREATE_N_AMINOACIDS if i.nil?
+    @how_many_aminoacids = i.to_i
+  end
+
+  # ========================================================================= #
+  # === determine_the_amino_acid_sequence
+  # ========================================================================= #
+  def determine_the_amino_acid_sequence
+    use_these_keys_for_the_aminoacids = TWENTY_CANONICAL_AMINOACIDS.split(//)
+    amino_acid_sequence = ''.dup
+    @how_many_aminoacids.times {|aminoacid|
+      amino_acid_sequence << use_these_keys_for_the_aminoacids.sample # return a random character.
+      unless @split_at.nil?
+        amino_acid_sequence << "\n" if (aminoacid + 1) % split_at == 0
+      end
+    }
+    set_amino_acid_sequence(
+      amino_acid_sequence
+    )
+  end
+
+  # ========================================================================= #
+  # === set_amino_acid_sequence
+  # ========================================================================= #
+  def set_amino_acid_sequence(i)
+    @amino_acid_sequence = i
+  end
+
+  # ========================================================================= #
+  # === amino_acid_sequence?
+  # ========================================================================= #
+  def amino_acid_sequence?
+    @amino_acid_sequence
+  end; alias amino_acid_sequence amino_acid_sequence? # === amino_acid_sequence()
+       alias sequence?           amino_acid_sequence? # === sequence?
+
+  # ========================================================================= #
+  # === report
+  # ========================================================================= #
+  def report
+    if @shall_we_report
+      if use_colours?
+        erev @amino_acid_sequence
+      else
+        e @amino_acid_sequence
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === run_everything
+  # ========================================================================= #
+  def run_everything
+    determine_the_amino_acid_sequence
+    report if @be_verbose
+    return @amino_acid_sequence
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = return_commandline_arguments_starting_with_hyphens
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # case tag
+      # ===================================================================== #
+      # === randomAA 35 --disable-colours
+      # ===================================================================== #
+      when /^-?-?disable(-|_)?colours/i,
+           /^-?-?no(-|_)?colours/i
+        disable_colours
+      end
+    end
+  end
+
+  # ========================================================================= #
+  #  === run                                                       (run tag)
+  # ========================================================================= #
+  def run
+    menu
+    run_everything
+  end
+
+end
+
+  # ========================================================================= #
+  # === Bioroebe.create_random_aminoacids
+  #
+  # This method will create a random chain of aminoacids.
+  #
+  # The first argument to this method shall denote how many aminoacids
+  # are to be generated, e. g. 25 would mean to create "25 aminoacids".
+  #
+  # If the second argument, called `split_at`, is not nil and is
+  # a number, then this method we add a newline into the 
+  # returned String.
+  #
+  # This method will return a String, consisting of the random
+  # aminoacids.
+  #
+  # Usage Examples:
+  #
+  #   Bioroebe.create_random_aminoacids 125
+  #   Bioroebe.create_random_aminoacids  25 # => "SQHWVGGGVSRCWLMWAPECMYVWW"
+  #   Bioroebe.create_random_aminoacids  15 # => "CLKHMLMGLVAEEKA"
+  #   Bioroebe.random_aminoacids(5) # => "STRRM"
+  #   Bioroebe.random_aminoacids(8) # => "TRTQHSNN"s
+  #
+  # ========================================================================= #
+  def self.create_random_aminoacids(
+      how_many_aminoacids = CREATE_N_AMINOACIDS,
+      split_at            = nil,
+      be_verbose          = false,
+      &block
+    )
+    _ = ::Bioroebe::CreateRandomAminoacids.new(
+          how_many_aminoacids,
+          split_at,
+          be_verbose,
+          &block
+        )
+    return _.amino_acid_sequence # ← And return the aminoacid sequence here.
+  end; self.instance_eval { alias generate_aminoacid  create_random_aminoacids } # === Bioroebe.generate_aminoacid
+       self.instance_eval { alias generate_aminoacids create_random_aminoacids } # === Bioroebe.generate_aminoacids
+       self.instance_eval { alias random_aminoacids   create_random_aminoacids } # === Bioroebe.random_aminoacids
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::CreateRandomAminoacids.new(ARGV) { :do_report }
+end # createrandomaminoacids 22