bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/constants/constants.rb

@@ -0,0 +1,1349 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This file here also contains data particular to my home setup, the system
+# I use at home. It is thus not hugely relevant to other people, but
+# simplifies the job for me whenever I work on bio-related stuff in
+# general.
+#
+# This file may contain some handy remote URLs, as constants, such as
+# NCBI_GENE; we could also use local "URLs", although this is probably
+# no longer necessary.
+#
+# This .rb file used to contain several hardcoded constants. Since as of
+# September 2019 this older approach was slightly deprecated, mostly because
+# hardcoded constants do not allow for as much flexibility as method calls
+# do. Even if a method call is slightly slower, I found that in the long
+# run it greatly makes the resulting code easier to maintain, rather than
+# having to deal with hardcoded constants that may lead to inflexibility.
+# This happened to me in a restricted university setting, so I don't quite
+# fancy hardcoded constants anymore as much - at the least not for
+# important variables.
+# =========================================================================== #
+# require 'bioroebe/constants/constants.rb
+# Bioroebe.load_and_return_the_restriction_enzymes
+# Bioroebe.blosum_directory?
+# Bioroebe.filter_away_invalid_aminoacids
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/toplevel_methods/roebe.rb'
+  require 'bioroebe/log_directory/log_directory.rb'
+
+  # ========================================================================= #
+  # === array_failsave_requires
+  #
+  # Next we do some failsafe requires for the Bioroebe::Shell component
+  # specifically.
+  # ========================================================================= #
+  array_failsave_requires = %w(
+    convert_global_env
+  )
+  array_failsave_requires.each {|project|
+    begin
+      require project
+    rescue LoadError; end # Silent rescue.
+  }
+
+  # ========================================================================= #
+  # === Bioroebe::N
+  # ========================================================================= #
+  N = "\n"
+
+  # ========================================================================= #
+  # === Bioroebe::R
+  # ========================================================================= #
+  R = "\r"
+
+  # ========================================================================= #
+  # === TABULATOR
+  # ========================================================================= #
+  TABULATOR = "\t"
+
+  # ========================================================================= #
+  # === Bioroebe::ROW_TERMINATOR
+  #
+  # This constant is not often in use, though.
+  # ========================================================================= #
+  ROW_TERMINATOR = "#{TABULATOR}|\n"
+
+  # ========================================================================= #
+  # === E_BOX
+  #
+  # This constant was disabled in December 2020. It may have to be moved
+  # to .rb files that depend on it, if we still actually need it. If
+  # not then this comment will be removed at a later point anyway.
+  # ========================================================================= #
+  # E_BOX = 'CACGTG' # The "E Box".
+
+  # ========================================================================= #
+  # === BE_VERBOSE
+  # ========================================================================= #
+  BE_VERBOSE = true
+
+  # ========================================================================= #
+  # === TOKEN                                                     (TOKEN tag)
+  # ========================================================================= #
+  TOKEN = '|'
+  # ========================================================================= #
+  # === ARRAY_AMINOACIDS_THAT_CAN_BE_PHOSPHORYLATED
+  #
+  # Just list the aminoacids that can typically be phosphorylated.
+  # ========================================================================= #
+  ARRAY_AMINOACIDS_THAT_CAN_BE_PHOSPHORYLATED = %w(
+    S Y T
+  )
+
+  # ========================================================================= #
+  # === ENGLISH_LONG_NAMES_FOR_THE_AMINO_ACIDS
+  #
+  # We have to keep the long names for the amino acids in one
+  # constant, so that we can do queries lateron.
+  # ========================================================================= #
+  ENGLISH_LONG_NAMES_FOR_THE_AMINO_ACIDS = (%w( 
+    Alanine
+    Arginine
+    Asparagine
+    Cysteine
+    Glutamine
+    Glycine
+    Histidine
+    Isoleucine
+    Leucine
+    Lysine
+    Methionine
+    Phenylalanine
+    Proline
+    Serine
+    Threonine
+    Tryptophane
+    Tyrosine
+    Valine
+  ) << 'Aspartic acid' << 'Glutamic acid').sort
+
+  # ========================================================================= #
+  # === POSSIBLE_AMINO_ACIDS
+  #
+  # Which Aminoacids are possible/allowed? We will list them here:
+  #
+  #   ACDEFGHIKLMNPQRSTUVWY
+  #
+  # Note that this is distinct from the constant AMINO_ACIDS, which is
+  # instead loaded from a local .yml file. This constant includes
+  # all the 20 canonical aminoacids, whereas AMINO_ACIDS may also
+  # include pyrrolysine and selenocysteine.
+  # ========================================================================= #
+  POSSIBLE_AMINO_ACIDS = 'ACDEFGHIKLMNPQRSTVWY'
+    TWENTY_CANONICAL_AMINOACIDS = POSSIBLE_AMINO_ACIDS # === TWENTY_CANONICAL_AMINOACIDS
+
+  # ========================================================================= #
+  # === ARRAY_AMINO_ACIDS_ALPHABET
+  #
+  # This keeps an Array with all aminoacids, in one-letter format.
+  #
+  # So it is equivalent to:
+  #
+  #   ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"]
+  #
+  # ========================================================================= #
+  ARRAY_AMINO_ACIDS_ALPHABET = POSSIBLE_AMINO_ACIDS.chars
+
+  # ========================================================================= #
+  # === Bioroebe.all_aminoacids?
+  #
+  # This method will return all available aminoacids.
+  #
+  # Example:
+  #
+  #   Bioroebe.all_aminoacids? # => ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"]
+  #
+  # ========================================================================= #
+  def self.all_aminoacids?
+    ARRAY_AMINO_ACIDS_ALPHABET
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.filter_away_invalid_aminoacids
+  #
+  # Usage example:
+  #
+  #   Bioroebe.filter_away_invalid_aminoacids('ATMÜ') # => "ATM"
+  #
+  # ========================================================================= #
+  def self.filter_away_invalid_aminoacids(i)
+    array_that_is_allowed = all_aminoacids?
+    return i.chars.select {|entry| array_that_is_allowed.include? entry }.join
+  end
+
+  # ========================================================================= #
+  # === all_aminoacids?
+  # ========================================================================= #
+  def all_aminoacids?
+    ::Bioroebe.all_aminoacids?
+  end
+
+  # ========================================================================= #
+  # === VERTICAL_UNICODE_BAR
+  # ========================================================================= #
+  VERTICAL_UNICODE_BAR = '|'
+
+  # ========================================================================= #
+  # === AMINOACID_FAMILIES
+  # ========================================================================= #
+  AMINOACID_FAMILIES = {
+    'citratzyklus' => {
+      # Alpha-Ketoglutarat: EPQR
+      'alpha-ketoglutarat' => %w( E P Q R ),
+      # Oxalacetat: DMN-KTI
+      'oxalacetat' => %w( D N K M T I ),
+    },
+    'glykolyse' => {
+      'pyruvat' => %w( A V L ),                 # AVL
+      '3-phosphoglycerinsäure' => %w( S G C ), # SGC
+      },
+      'chorismat' => {
+        'aromatische_familie' => %w( F Y W )       # FYW
+      },
+      'ribose-5-p' => {
+        'histidinol' => %w( H ) # Histidine.
+      },
+  }
+
+  # ========================================================================= #
+  # === Bioroebe.aminoacid_families?
+  #
+  # Feedback which aminoacid-families we know of.
+  #
+  # Usage example:
+  #
+  #   pp Bioroebe.aminoacid_families?; ''
+  #
+  # ========================================================================= #
+  def self.aminoacid_families?
+    AMINOACID_FAMILIES
+  end; self.instance_eval { alias aa_families? aminoacid_families? } # === Bioroebe.aa_families?
+
+  # ========================================================================= #
+  # === VALID_WAYS_TO_EXIT
+  #
+  # All ways to exit will be recorded here.
+  #
+  # If you need to use more ways, simply append to this Array.
+  #
+  # This constant may have to be moved into the bio-shell part eventually.
+  # ========================================================================= #
+  VALID_WAYS_TO_EXIT = %w(
+    quit q exit qq :q qt
+    bye
+    rda
+    r2
+    tq
+    sq
+    exit_program
+    exitprogram
+  )
+
+  # ========================================================================= #
+  # === NAMES_ENTRIES
+  #
+  # This used to belong to the Taxonomy submodule.
+  # ========================================================================= #
+  NAMES_ENTRIES = 'names.sql'
+
+  # ========================================================================= #
+  # === NODES_ENTRIES
+  #
+  # This used to belong to the Taxonomy submodule.
+  # ========================================================================= #
+  NODES_ENTRIES = 'nodes.sql'
+
+  # ========================================================================= #
+  # === FASTA_ENTRIES
+  #
+  # This used to belong to the Taxonomy submodule.
+  # ========================================================================= #
+  FASTA_ENTRIES = 'fasta.sql'
+
+  # ========================================================================= #
+  # === SHALL_WE_LOG_LAST_UPDATE
+  #
+  # This constant exists specifically for the taxonomy-component of
+  # the Bioroebe project.
+  # ========================================================================= #
+  SHALL_WE_LOG_LAST_UPDATE = true
+
+  # ========================================================================= #
+  # === Bioroebe.taxonomy_ncbi_database_last_update_log_file
+  #
+  # This constant is used specifically for the taxonomy-component of the
+  # Bioroebe project.
+  # ========================================================================= #
+  def self.taxonomy_ncbi_database_last_update_log_file
+    "#{::Bioroebe.log_dir?}taxonomy_ncbi_database_last_update.log"
+  end
+
+  # ========================================================================= #
+  # === NAME_OF_BIO_SHELL
+  #
+  # This constant can be used as the default prompt for the bioshell
+  # component.
+  # ========================================================================= #
+  NAME_OF_BIO_SHELL = 'BIO SHELL> '
+
+  # ========================================================================= #
+  # === DEFAULT_DNA_SEQUENCE
+  #
+  # This is a default "test" DNA sequence, in the sense that it can be
+  # used to quickly test functionality within the bioroebe project.
+  #
+  # It was added in May 2020, but it may be that we have to remove
+  # it at a later time, or move it into a separate .yml file. For
+  # the time being, though, it will reside here.
+  # ========================================================================= #
+  DEFAULT_DNA_SEQUENCE =
+    'CGGCCCGATTTGGGTTTCGGAGCGATCGAAATACCAGCACTACCATGAATTCTAT'\
+    'ATGGCTGCCGTTCACAGCCTTAATTTTAGGCTTTCCACCTGATCACTCTTTAATC'\
+    'TCCATTGTTTCTGGTACGCAGAAATTGACGCTTCCCATTCATTCACGGCTAAAAT'\
+    'CAAGGATTCCACCAGAATCGCGGGCCGCGTGGGTGCGCCGTCGACCTCCTCGGCC'\
+    'AAATAAGAACGGGCAGGTAAGAGACTAGGGTACTCAAGAT'
+
+  # ========================================================================= #
+  # === DEFAULT_LENGTH_FOR_DNA
+  #
+  # How long our DNA-generated strings should be by default.
+  #
+  # This may be used by some scripts, so it provides a default value
+  # for use in these scripts.
+  #
+  # 150 nucleotides are the current default.
+  # ========================================================================= #
+  DEFAULT_LENGTH_FOR_DNA = 150
+
+  # ========================================================================= #
+  # === FIELD_TERMINATOR
+  # ========================================================================= #
+  FIELD_TERMINATOR = "#{TABULATOR}|#{TABULATOR}"
+    MAIN_DELIMITER = DELIMITER = FIELD_TERMINATOR # An alias to the above.
+
+  # ========================================================================= #
+  # === USERS_X
+  # ========================================================================= #
+  USERS_X = '/home/x/'
+    HOME_DIRECTORY_OF_USER_X = USERS_X # === HOME_DIRECTORY_OF_USER_X
+
+  # ========================================================================= #
+  # === RUBY_SRC
+  #
+  # This constant is only useful on my home directory. Most other users
+  # will not need it, ever.
+  # ========================================================================= #
+  RUBY_SRC =
+    "#{USERS_X}programming/ruby/src/"
+
+  # ========================================================================= #
+  # === BIOROEBE_AT_HOME
+  # ========================================================================= #
+  BIOROEBE_AT_HOME = "#{RUBY_SRC}bioroebe/lib/bioroebe/"
+
+  # ========================================================================= #
+  # === LOCALHOST
+  # ========================================================================= #
+  LOCALHOST = 'http://localhost/'
+
+  # ========================================================================= #
+  # === PATH_TO_THE_RELION_BINARY
+  #
+  # This constant can be set to determine where relion resides. It is
+  # mostly an ad-hoc constant.
+  # ========================================================================= #
+  PATH_TO_THE_RELION_BINARY =
+    '/opt/RELION/relion-1.3/bin/relion'
+
+  # ========================================================================= #
+  # === ARRAY_REGISTERED_ACTIONS
+  #
+  # ARRAY_REGISTERED_ACTIONS becomes @registered_actions.
+  # ========================================================================= #
+  ARRAY_REGISTERED_ACTIONS = %w(
+    to_rna
+    to_dna
+    rest
+    pubmed
+    blosum
+    restriction
+    translate
+    quit
+    shorten_aminoacid
+  )
+
+  # ========================================================================= #
+  # === FILE_BIO_LANG
+  # ========================================================================= #
+  FILE_BIO_LANG =
+    "#{USERS_X}data/personal/yaml/bio_lang/bio_lang.md"
+
+  # ========================================================================= #
+  # === AC_ELEMENT
+  # ========================================================================= #
+  # AC_ELEMENT = 4_565 # n nucleotides found in the AC zea mais element.
+
+  # ========================================================================= #
+  # === BIOSHELL_FILE
+  # ========================================================================= #
+  BIOSHELL_FILE = ConvertGlobalEnv[
+    '$BIORUBY/shell/shell.rb'
+  ] if Object.const_defined?(:ConvertGlobalEnv)
+
+  # ========================================================================= #
+  # === EMAIL
+  #
+  # My email address - not too terribly useful for other people,
+  # but nonetheless it may be useful to display it, in particular
+  # for GUI-related components of the bioroebe-project and simple
+  # feedback in the long run.
+  # ========================================================================= #
+  EMAIL = 'shevy@inbox.lt'
+
+  # ========================================================================= #
+  # === REGEX_FOR_N_GLYCOSYLATION_PATTERN
+  #
+  # See rubular at:
+  #
+  #   https://rubular.com/r/D95Cq7oR5x
+  #
+  # ========================================================================= #
+  REGEX_FOR_N_GLYCOSYLATION_PATTERN =
+    /(?=(N[^P][ST][^P]))/
+
+  # ========================================================================= #
+  # === REGEX_PROSITE_FOR_ANY_AMINOACID
+  # ========================================================================= #
+  REGEX_PROSITE_FOR_ANY_AMINOACID =
+    /x\((\d+)\)/
+
+  # ========================================================================= #
+  # === Bioroebe::STOP_CODONS
+  #
+  # The STOP codons that can be found in Humans, in RNA format.
+  # ========================================================================= #
+  STOP_CODONS = %w(
+    UAA UAG UGA
+  )
+
+  # ========================================================================= #
+  # === Bioroebe::RNA_NUCLEOTIDES
+  #
+  # This will refer to an Array including all four RNA nucleotides,
+  # that is A, U, G and C.
+  # ========================================================================= #
+  RNA_NUCLEOTIDES = %w( A U G C )
+    ALLOWED_RNA_NUCLEOTIDES = RNA_NUCLEOTIDES # === ALLOWED_RNA_NUCLEOTIDES
+
+  # ========================================================================= #
+  # === Bioroebe::POSSIBLE_RNA_NUCLEOTIDES
+  #
+  # This is a bit different to RNA_NUCLEOTIDES in that N is also a part
+  # of it. It is not entirely clear whether this array here is kept,
+  # though.
+  # ========================================================================= #
+  POSSIBLE_RNA_NUCLEOTIDES = %w(
+    A U G C N
+  )
+
+  # ========================================================================= #
+  # === Bioroebe::DNA_NUCLEOTIDES
+  #
+  # This is the variant without N.
+  # ========================================================================= #
+  DNA_NUCLEOTIDES = %w( A T G C )
+
+  # ========================================================================= #
+  # === Bioroebe::HASH_DNA_NUCLEOTIDES
+  #
+  # Since as of 20.04.2014, Uracil is also part of this Hash. While this
+  # is, strictly speaking, not absolutely correct, it does simplify some
+  # downstream code. However had, this may possibly be re-evaluated in 
+  # the future.
+  #
+  # This Hash may be helpful when the user wishes to find a complement to
+  # a nucleotide. There is a method that does the same, but this Hash
+  # should be faster than a method call, so use it in particular if 
+  # you need to focus more on speed.
+  # ========================================================================= #
+  HASH_DNA_NUCLEOTIDES = {
+    'A' => 'T',
+    'T' => 'A',
+    'G' => 'C',
+    'C' => 'G',
+    'U' => 'A'
+  }
+
+  # ========================================================================= #
+  # === Bioroebe.this_nucleotide_pairs_with?
+  # ========================================================================= #
+  def self.this_nucleotide_pairs_with?(i)
+    HASH_DNA_NUCLEOTIDES[i.to_s.upcase]
+  end
+
+  # ========================================================================= #
+  # === POSSIBLE_DNA_NUCLEOTIDES
+  #
+  # This constant will keep all possible DNA nucleotides.
+  #
+  # N is also a valid entry, 'Yarrowia_lipolytica_genome.fa' includes it.
+  # However had, 
+  #
+  # Only these sequences are allowed in DNA.
+  #
+  # To scope to this, do:
+  #
+  #   Bioroebe::POSSIBLE_DNA_NUCLEOTIDES
+  #
+  # ========================================================================= #
+  POSSIBLE_DNA_NUCLEOTIDES = %w(
+    A T G C N
+  ); ARRAY_VALID_DNA_SEQUENCES = POSSIBLE_DNA_NUCLEOTIDES # === ARRAY_VALID_DNA_SEQUENCES
+
+  # ========================================================================= #
+  # === Bioroebe.return_random_nucleotide
+  #
+  # This method will randomly return either 'A', 'T', 'C' or 'G'.
+  # ========================================================================= #
+  def self.return_random_nucleotide
+    (POSSIBLE_DNA_NUCLEOTIDES - ['N']).sample # This constant holds A T G and C.
+  end; self.instance_eval { alias random_nucleotide return_random_nucleotide } # === Bioroebe.random_nucleotide
+
+  # ========================================================================= #
+  # === Bioroebe.allowed_dna_nucleotides?
+  #
+  # This will return an Array with valid DNA nucleotides.
+  # ========================================================================= #
+  def self.allowed_dna_nucleotides?
+    POSSIBLE_DNA_NUCLEOTIDES - ['N']
+  end; self.instance_eval { alias dna? allowed_dna_nucleotides? } # === Bioroebe.dna?
+
+  # ========================================================================= #
+  # === Bioroebe.return_DNA_nucleotides
+  # ========================================================================= #
+  def self.return_DNA_nucleotides
+    return DNA_NUCLEOTIDES
+  end
+
+  # ========================================================================= #
+  # === FTP_NCBI_TAXONOMY_DATABASE
+  #
+  # This constant refers to the taxonomy-database from NCBI. This is the
+  # file that can be downloaded from the NCBI homepage (actually, the
+  # ftp-listing).
+  #
+  # Take note that this database, in .tar.gz format, is about 50 MB in 
+  # size or even larger these days. So only download it if you really 
+  # need it locally.
+  # ========================================================================= #
+  FTP_NCBI_TAXONOMY_DATABASE =
+    'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz'
+
+  # ========================================================================= #
+  # === URL_TO_TAXONOMY_ARCHIVE
+  #
+  # An "alias" to the above ^^^ constant.
+  # ========================================================================= #
+  URL_TO_TAXONOMY_ARCHIVE = FTP_NCBI_TAXONOMY_DATABASE
+
+  # ========================================================================= #
+  # === NCBI_NUCCORE
+  # ========================================================================= #
+  NCBI_NUCCORE =
+    'https://www.ncbi.nlm.nih.gov/nuccore/'
+
+  # ========================================================================= #
+  # === NCBI_GENE
+  # ========================================================================= #
+  NCBI_GENE =
+    'https://www.ncbi.nlm.nih.gov/gene/'
+
+  # ========================================================================= #
+  # === FILE_HYDROPATHY_TABLE
+  # ========================================================================= #
+  FILE_HYDROPATHY_TABLE =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}hydropathy_table.yml"
+
+  # ========================================================================= #
+  # === FILE_NUCLEAR_LOCALIZATION_SEQUENCES
+  # ========================================================================= #
+  FILE_NUCLEAR_LOCALIZATION_SEQUENCES =
+    "#{project_yaml_directory?}nuclear_localization_sequences.yml"
+
+  # ========================================================================= #
+  # === FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS
+  # ========================================================================= #
+  FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS =
+    "#{project_yaml_directory?}configuration/default_colours_for_the_aminoacids.yml"
+
+  # ========================================================================= #
+  # === FILE_BROWSER
+  # ========================================================================= #
+  FILE_BROWSER =
+    "#{project_yaml_directory?}configuration/browser.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINOACIDS_MOLECULAR_FORMULA
+  # ========================================================================= #
+  FILE_AMINOACIDS_MOLECULAR_FORMULA =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_molecular_formula.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINOACIDS_THREE_TO_ONE
+  # ========================================================================= #
+  FILE_AMINOACIDS_THREE_TO_ONE = 
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_three_to_one.yml"
+
+  # ========================================================================= #
+  # === FILE_WEIGHT_OF_COMMON_PROTEINS
+  # ========================================================================= #
+  FILE_WEIGHT_OF_COMMON_PROTEINS = 
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}weight_of_common_proteins.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_long_name_to_one_letter.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_MOLECULAR_FORMULA
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_MOLECULAR_FORMULA =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_molecular_formula.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_MASS_TABLE
+  #
+  #   bl $BIOROEBE_YAML/aminoacids/amino_acids_monoisotopic_mass_table.yml
+  #
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_MASS_TABLE =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_monoisotopic_mass_table.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS
+  # ========================================================================= #
+  FILE_AMINO_ACIDS =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids.yml"
+
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids
+  # ========================================================================= #
+  def self.file_amino_acids
+    FILE_AMINO_ACIDS
+  end
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_ABBREVIATIONS
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_ABBREVIATIONS =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_abbreviations.yml"
+
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids_abbreviations
+  # ========================================================================= #
+  def self.file_amino_acids_abbreviations
+    FILE_AMINO_ACIDS_ABBREVIATIONS
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_ABBREVIATIONS
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_ABBREVIATIONS
+    begin
+      # $BIOROEBE/amino_acids_abbreviations.yml
+      AMINO_ACIDS_ABBREVIATIONS = YAML.load_file(FILE_AMINO_ACIDS_ABBREVIATIONS)
+    rescue Psych::SyntaxError => error
+      pp error
+      AMINO_ACIDS_ABBREVIATIONS = {}
+    end
+  end
+
+  # ========================================================================= #
+  # === DIRECTORY_CODON_TABLES_FREQUENCIES
+  #
+  # This constant may point to a directory such as:
+  #
+  #   /home/Programs/Ruby/2.7.0/lib/ruby/site_ruby/2.7.0/bioroebe/codon_tables/frequencies/
+  #
+  # ========================================================================= #
+  DIRECTORY_CODON_TABLES_FREQUENCIES =
+    "#{CODON_TABLES_DIRECTORY}frequencies/"
+
+  # ========================================================================= #
+  # === Bioroebe.directory_frequencies?
+  #
+  # Preferentially use this method past the year 2022 - it is a tiny bit
+  # more flexible than the above constant.
+  # ========================================================================= #
+  def self.directory_frequencies?(
+      codon_tables_directory = CODON_TABLES_DIRECTORY
+    )
+    "#{codon_tables_directory}frequencies/"
+  end
+
+  # ========================================================================= #
+  # === FILE_NUCLEOTIDES
+  # ========================================================================= #
+  FILE_NUCLEOTIDES =
+    "#{project_yaml_directory?}nucleotides/nucleotides.yml"
+
+  # ========================================================================= #
+  # === NUCLEOTIDES
+  # ========================================================================= #
+  if File.exist? FILE_NUCLEOTIDES
+    NUCLEOTIDES = YAML.load_file(FILE_NUCLEOTIDES)
+  else
+    NUCLEOTIDES = nil
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_statistics?
+  #
+  # This file can normally be found here:
+  #
+  #   $BIOROEBE/yaml/statistics.yml
+  #
+  # ========================================================================= #
+  def self.file_statistics?
+    "#{Bioroebe.log_dir?}statistics.yml"
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.fasta_dir?
+  # ========================================================================= #
+  def self.fasta_dir?
+    "#{Bioroebe.log_dir?}fasta/"
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_fastq_quality_schemes
+  #
+  # This constant will point to a location such as this one here:
+  #
+  #   /Programs/Ruby/2.6.4/lib/ruby/site_ruby/2.6.0/bioroebe/yaml/fastq_quality_schemes.yml
+  #
+  # ========================================================================= #
+  def self.file_fastq_quality_schemes
+    "#{project_yaml_directory?}fasta_and_fastq/fastq_quality_schemes.yml"
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_talens
+  # ========================================================================= #
+  def self.file_talens
+    "#{project_yaml_directory?}talens.yml"
+  end
+
+  # ========================================================================= #
+  # === FILE_GFP_SEQUENCE
+  # ========================================================================= #
+  FILE_GFP_SEQUENCE = 
+    "#{project_yaml_directory?}sequences/"\
+    "JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta"
+
+  # ========================================================================= #
+  # === FILE_RESTRICTION_ENZYMES
+  #
+  # bl $BIOROEBE/yaml/restriction/enzymes/restriction_enzymes.yml
+  # ========================================================================= #
+  FILE_RESTRICTION_ENZYMES =
+    "#{project_yaml_directory?}restriction_enzymes/restriction_enzymes.yml"
+
+  # ========================================================================= #
+  # === FILE_COLOURIZE_FASTA_SEQUENCES
+  #
+  # This constants points to the .yml file that will hold information
+  # in how to colourize the FASTA sequences.
+  # ========================================================================= #
+  FILE_COLOURIZE_FASTA_SEQUENCES =
+    "#{project_yaml_directory?}configuration/colourize_fasta_sequences.yml"
+
+  # ========================================================================= #
+  # === FILE_BLOSUM45
+  # ========================================================================= #
+  FILE_BLOSUM45 = "#{BLOSUM_DIRECTORY}/blosum45.yml"
+
+  # ========================================================================= #
+  # === FILE_BLOSUM50
+  # ========================================================================= #
+  FILE_BLOSUM50 = "#{BLOSUM_DIRECTORY}/blosum50.yml"
+
+  # ========================================================================= #
+  # === FILE_BLOSUM62
+  # ========================================================================= #
+  FILE_BLOSUM62 = "#{BLOSUM_DIRECTORY}/blosum62.yml"
+
+  # ========================================================================= #
+  # === FILE_BLOSUM80
+  # ========================================================================= #
+  FILE_BLOSUM80 = "#{BLOSUM_DIRECTORY}/blosum80.yml"
+
+  # ========================================================================= #
+  # === FILE_BLOSUM90
+  # ========================================================================= #
+  FILE_BLOSUM90 = "#{BLOSUM_DIRECTORY}/blosum90.yml"
+
+  # ========================================================================= #
+  # === BLOSUM_MATRIX
+  # ========================================================================= #
+  FILE_BLOSUM_MATRIX = "#{BLOSUM_DIRECTORY}blosum_matrix.yml"
+
+  # ========================================================================= #
+  # === Bioroebe.blosum_matrix
+  # ========================================================================= #
+  def self.blosum_matrix(i = FILE_BLOSUM_MATRIX)
+    YAML.load_file(i)
+  end
+
+  # ========================================================================= #
+  # === HYDROPATHY_TABLE
+  # ========================================================================= #
+  if File.exist? FILE_HYDROPATHY_TABLE
+    HYDROPATHY_TABLE =
+      YAML.load_file(
+        FILE_HYDROPATHY_TABLE
+      )
+  end
+
+  # ========================================================================= #
+  # === FILE_CHROMOSOME_NUMBERS
+  # ========================================================================= #
+  FILE_CHROMOSOME_NUMBERS =
+    "#{project_yaml_directory?}chromosomes/chromosome_numbers.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_FREQUENCY
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_FREQUENCY =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_frequency.yml"
+
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids_frequency
+  # ========================================================================= #
+  def self.file_amino_acids_frequency
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_frequency.yml"
+  end
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_RESTE_YAML
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_RESTE_YAML =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_reste.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_THREE_TO_ONE
+  #
+  # We'll keep the keys downcased.
+  #
+  #   bl $RUBY_SRC/bioroebe/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml
+  #
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_THREE_TO_ONE =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_three_to_one.yml"
+
+  # ========================================================================= #
+  # === FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE
+  #
+  # This will point to the file amino_acids_average_mass_table.yml.
+  # ========================================================================= #
+  FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE =
+    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_average_mass_table.yml"
+
+  # ========================================================================= #
+  # === FILE_NUCLEOTIDES_WEIGHT
+  #
+  # The path to the file that holds the weight of the nucleotides.
+  # ========================================================================= #
+  FILE_NUCLEOTIDES_WEIGHT =
+    "#{project_yaml_directory?}nucleotides/nucleotides_weight.yml"
+
+  # ========================================================================= #
+  # === UNICODE_HORIZONTAL_BAR
+  # ========================================================================= #
+  UNICODE_HORIZONTAL_BAR = '―'
+
+  # ========================================================================= #
+  # === Bioroebe.load_and_return_the_restriction_enzymes
+  #
+  # This method will load, and then return the restriction enzymes that
+  # are bundled within the bioroebe-project.
+  # ========================================================================= #
+  def self.load_and_return_the_restriction_enzymes
+    YAML.load_file(FILE_RESTRICTION_ENZYMES)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_restriction_enzymes
+  # ========================================================================= #
+  def self.file_restriction_enzymes
+    FILE_RESTRICTION_ENZYMES
+  end
+
+  # ========================================================================= #
+  # === file_restriction_enzymes
+  # ========================================================================= #
+  def file_restriction_enzymes
+    ::Bioroebe.file_restriction_enzymes
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.blosum_directory?
+  # ========================================================================= #
+  def self.blosum_directory?
+    "#{project_yaml_directory?}blosum/"
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_MOLECULAR_FORMULA
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_MOLECULAR_FORMULA
+    AMINO_ACIDS_MOLECULAR_FORMULA = YAML.load_file(
+      FILE_AMINO_ACIDS_MOLECULAR_FORMULA
+    )
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_RESTE
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_RESTE_YAML
+    hash = {}
+    begin
+      _ = YAML.load_file(FILE_AMINO_ACIDS_RESTE_YAML)
+      # ======================================================================= #
+      # As of August 2015, we will keep the keys downcased.
+      # ======================================================================= #
+      _.each_pair {|key, value|
+        key = key.dup if key.frozen?
+        key.downcase!
+        hash[key] = value
+      }
+      AMINO_ACIDS_RESTE = hash
+    rescue Psych::SyntaxError
+      AMINO_ACIDS_RESTE = {}
+    end
+  else
+    AMINO_ACIDS_RESTE = {}
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
+  #
+  # Load up the dataset stored in the file
+  # amino_acids_long_name_to_one_letter.yml.
+  # ========================================================================= #
+  _ = FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
+  if File.exist? _
+    AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER = YAML.load_file(_)
+  else
+    puts "No file exists at #{_}."
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_MASS_TABLE
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_MASS_TABLE # bl $BIOROEBE/yaml/amino_acids_mass_table.yml
+    AMINO_ACIDS_MASS_TABLE = YAML.load_file(FILE_AMINO_ACIDS_MASS_TABLE)
+  else # Else hardcode the AminoAcid table here. This may no longer be necessary, though.
+    AMINO_ACIDS_MASS_TABLE = {
+      'A' =>  71.03711, 'C' => 103.00919, 'D' => 115.02694,
+      'E' => 129.04259, 'F' => 147.06841, 'G' =>  57.02146,
+      'H' => 137.05891, 'I' => 113.08406, 'K' => 128.09496,
+      'L' => 113.08406, 'M' => 131.04049, 'N' => 114.04293,
+      'P' =>  97.05276, 'Q' => 128.05858, 'R' => 156.10111,
+      'S' =>  87.03203, 'T' => 101.04768, 'V' =>  99.06841,
+      'W' => 186.07931, 'Y' => 163.06333
+    }
+  end; AMINO_ACIDS_AVERAGE_MONOISOTOPIC_TABLE = AMINO_ACIDS_MASS_TABLE # An alias.
+
+  # ========================================================================= #
+  # Next determine some important constants.
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS
+    # ======================================================================= #
+    # === Bioroebe::AMINO_ACIDS
+    #
+    # Currently listing 21 AminoAcids from amino_acids.yml
+    #
+    #   bl $BIOROEBE/yaml/aminoacids/amino_acids.yml
+    #
+    # ======================================================================= #
+    AMINO_ACIDS = YAML.load_file(
+      FILE_AMINO_ACIDS
+    )
+    # ======================================================================= #
+    # === ::Bioroebe::AMINO_ACIDS_ENGLISH
+    # ======================================================================= #
+    FILE_AMINO_ACIDS_ENGLISH = YAML.load_file("#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_english.yml")
+      AMINO_ACIDS_ENGLISH = FILE_AMINO_ACIDS_ENGLISH # === AMINO_ACIDS_ENGLISH
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.aminoacids?
+  #
+  # Note that this will return a Hash that looks like this:
+  #
+  #   {"A"=>{"ala"=>"alanine", "d
+  #
+  # ========================================================================= #
+  def self.aminoacids?
+    AMINO_ACIDS
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_AVERAGE_MASS_TABLE
+  #
+  # And here is the average mass table.
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE # bl $BIOROEBE/yaml/aminoacids/amino_acids_average_mass_table.yml
+    AMINO_ACIDS_AVERAGE_MASS_TABLE = YAML.load_file(FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE)
+  else # Else simply hardcode the AminoAcid table here.
+    AMINO_ACIDS_AVERAGE_MASS_TABLE = {
+      'A' =>  71.0788,
+      'C' => 103.1388,
+      'D' => 115.0886,
+      'E' => 129.1155,
+      'F' => 147.1766,
+      'G' =>  57.0519,
+      'H' => 137.1411,
+      'I' => 113.1594,
+      'K' => 128.1741,
+      'L' => 113.1594,
+      'M' => 131.1926,
+      'N' => 114.1038,
+      'P' =>  97.1167,
+      'Q' => 128.1307,
+      'R' => 156.1875,
+      'S' =>  87.0782,
+      'T' => 101.1051,
+      'V' =>  99.1326,
+      'W' => 186.2132,
+      'Y' => 163.1760
+    }
+  end
+
+  # ========================================================================= #
+  # === AMINO_ACIDS_THREE_TO_ONE
+  #
+  # An "alias" to this constant exists, named AA_THREE_TO_ONE.
+  #
+  #   bl $BIOROEBE/yaml/aminoacids/amino_acids_three_to_one.yml
+  #
+  # ========================================================================= #
+  if File.exist? FILE_AMINO_ACIDS_THREE_TO_ONE
+    hash = {}
+    YAML.load_file(
+      FILE_AMINO_ACIDS_THREE_TO_ONE
+    ).each {|key, value|
+      hash[key.to_s.downcase] = value
+    }
+    AMINO_ACIDS_THREE_TO_ONE = hash
+             # AA_THREE_TO_ONE = AMINO_ACIDS_THREE_TO_ONE # Legacy pointer. Is mildly deprecated.
+             # ^^^ Disabled as of 25.03.2020. Use the longer variant instead. 
+  end
+
+  # ========================================================================= #
+  # === NUCLEAR_LOCALIZATION_SEQUENCES
+  #
+  # We must be careful and check whether it exists or not.
+  # ========================================================================= #
+  _ = FILE_NUCLEAR_LOCALIZATION_SEQUENCES
+  if File.exist? _
+    begin
+      NUCLEAR_LOCALIZATION_SEQUENCES = YAML.load_file(_)
+      # ======================================================================= #
+      # === Bioroebe::ARRAY_NLS_SEQUENCES
+      #
+      # All NLS sequences should be registered here.
+      # ======================================================================= #
+      ARRAY_NLS_SEQUENCES = NUCLEAR_LOCALIZATION_SEQUENCES.values.map {|entry|
+        entry = entry[0, entry.index(' ')] if entry.include? ' '
+        entry.delete!('[') if entry.include? '['
+        entry.delete!(']') if entry.include? ']'
+        entry
+      }
+    rescue Psych::SyntaxError => error
+      pp error
+      ARRAY_NLS_SEQUENCES = []
+    end
+  else
+    NUCLEAR_LOCALIZATION_SEQUENCES = ''
+    ARRAY_NLS_SEQUENCES = []
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.random_aminoacid?
+  #
+  # This method will return a random aminoacid.
+  #
+  # A number can be passed to this method, which specifies how many
+  # random aminoacids are to be returned, e. g. 20 as argument refers
+  # to 20 aminoacids that will be generated here.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.random_aminoacid? 20 # => "UAVHYQQESWUYAOVESEIY"
+  #
+  # ========================================================================= #
+  def self.random_aminoacid?(optional_return_n_aminoacids = 1)
+    case optional_return_n_aminoacids
+    when 1
+      AMINO_ACIDS.keys.sample # This should be a bit faster.
+    else
+      optional_return_n_aminoacids.to_i.times.map {
+        AMINO_ACIDS.keys.sample
+      }.join.strip
+    end
+  end; self.instance_eval { alias random_aminoacid        random_aminoacid? } # === Bioroebe.random_aminoacid
+       self.instance_eval { alias return_random_aminoacid random_aminoacid? } # === Bioroebe.return_random_aminoacid
+
+  # ========================================================================= #
+  # === Bioroebe.return_array_of_common_aminoacids
+  # ========================================================================= #
+  def self.return_array_of_common_aminoacids
+    AMINO_ACIDS.keys - ['O'] - ['U']
+  end
+
+  # ========================================================================= #
+  # === FILE_ALU_ELEMENTS
+  # ========================================================================= #
+  # FILE_ALU_ELEMENTS =
+  #   "#{project_yaml_directory?}alu_elements.yml"
+
+  # ========================================================================= #
+  # === Bioroebe.file_molecular_weight
+  # ========================================================================= #
+  def self.file_molecular_weight
+    "#{project_yaml_directory?}aminoacids/molecular_weight.yml"
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids_long_name_to_one_letter
+  #
+  # This method will return a String such as:
+  #
+  #   "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml"
+  #
+  # ========================================================================= #
+  def self.file_amino_acids_long_name_to_one_letter
+    "#{project_yaml_directory?}aminoacids/amino_acids_long_name_to_one_letter.yml"
+  end
+
+module CodonTablesFrequencies # === Bioroebe::CodonTablesFrequencies
+
+  # ========================================================================= #
+  # === Bioroebe::CodonTablesFrequencies::FILE_HOMO_SAPIENS
+  #
+  # Note that before the rewrite in September 2019, there was another
+  # old constant referring to this entry here, called
+  # CODON_TABLE_FOR_HOMO_SAPIENS. That latter constant was removed in
+  # 2019, to simplify the code and make it overall more consistent.
+  # ========================================================================= #
+  # bl $RUBY_BIOROEBE/codon_tables/frequencies/9606_Homo_sapiens.yml
+  # ========================================================================= #
+  FILE_HOMO_SAPIENS =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "9606_Homo_sapiens.yml"
+
+  # ========================================================================= #
+  # === FILE_E_COLI
+  #
+  # This is for the bacterium E. coli.
+  # ========================================================================= #
+  FILE_E_COLI =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "83333_Escherichia_coli_K12.yml"
+
+  # ========================================================================= #
+  # === FILE_SACCHAROMYCES_CEREVISIAE
+  #
+  # This is for the yeast Saccharomyces cerevisiae.
+  # ========================================================================= #
+  FILE_SACCHAROMYCES_CEREVISIAE =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "4932_Saccharomyces_cerevisiae.yml"
+
+  # ========================================================================= #
+  # === FILE_FELIS_CATUS
+  #
+  # This is for the domestic cat.
+  # ========================================================================= #
+  FILE_FELIS_CATUS =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "9685_Felis_catus.yml"
+
+  # ========================================================================= #
+  # === FILE_ARABIDOPSIS_THALIANA
+  #
+  # This is for Arabidopsis thaliana.
+  # ========================================================================= #
+  FILE_ARABIDOPSIS_THALIANA =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "3702_Arabidopsis_thaliana.yml"
+
+  # ========================================================================= #
+  # === FILE_DROSOPHILA_MELANOGASTER
+  #
+  # This is for the fruit fly.
+  # ========================================================================= #
+  FILE_DROSOPHILA_MELANOGASTER =
+    "#{::Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES}"\
+    "7227_Drosophila_melanogaster.yml"
+
+end # === end Bioroebe::CodonTablesFrequencies
+
+# =========================================================================== #
+# === Bioroebe::Postgresql
+#
+# This file stores any required information to login into a postgresql
+# database. This can be on your home system or as part of a cluster.
+#
+# The below command is equivalent to the following command-line:
+#
+#     psql --host=bunuel.imp.univie.ac.at --port=5471 --username=robert --dbname=robert_db --quiet
+#
+# =========================================================================== #
+# POSTGRE_LOGIN_COMMAND = '
+#   psql --host=bunuel.imp.univie.ac.at --port=5471 --username=robert --dbname=robert_db --quiet
+# '.delete("\n").strip
+# =========================================================================== #
+module Postgresql # === Bioroebe::Postgresql
+
+  # ========================================================================= #
+  # === Bioroebe::Postgresql
+  #
+  # The following constants can be modified to account for different
+  # password, username, dbname and so forth.
+  # ========================================================================= #
+
+  # ========================================================================= #
+  # === POSTGRE_HOST
+  # ========================================================================= #
+  POSTGRE_HOST        = 'bunuel.imp.univie.ac.at'
+
+  # ========================================================================= #
+  # === POSTGRE_PORT
+  # ========================================================================= #
+  POSTGRE_PORT        = '5471'
+
+  # ========================================================================= #
+  # === POSTGRE_USERNAME
+  # ========================================================================= #
+  POSTGRE_USERNAME    = 'robert'
+
+  # ========================================================================= #
+  # === POSTGRE_DBNAME
+  # ========================================================================= #
+  POSTGRE_DBNAME      = 'robert_db'
+
+  # ========================================================================= #
+  # === POSTGRE_EXTRA_FLAGS  
+  # ========================================================================= #
+  POSTGRE_EXTRA_FLAGS = '--quiet'
+
+  # ========================================================================= #
+  # === POSTGRE_PASSWORD
+  # ========================================================================= #
+  POSTGRE_PASSWORD    = 'robert123'
+
+  # ========================================================================= #
+  # === POSTGRE_LOGIN_COMMAND
+  #
+  # This constant will become the full postgre login command.
+  # ========================================================================= #
+  POSTGRE_LOGIN_COMMAND = ('
+    psql --host='+POSTGRE_HOST+' --port='+POSTGRE_PORT+
+    ' --username='+POSTGRE_USERNAME+
+    ' --dbname='+POSTGRE_DBNAME+
+    ' '+POSTGRE_EXTRA_FLAGS+'
+  '.delete("\n").strip).strip
+  POSTGRE_LOGIN_COMMAND_HOME = POSTGRE_LOGIN_COMMAND
+
+  # ========================================================================= #
+  # === POSTGRE_LOGIN_COMMAND_NO_HEADERS
+  #
+  # Here we use --tuples-only.
+  # ========================================================================= #
+  POSTGRE_LOGIN_COMMAND_NO_HEADERS = POSTGRE_LOGIN_COMMAND+' 
+    --tuples-only  
+  '.delete("\n").squeeze(' ') # --quiet
+
+  # ========================================================================= #
+  # === POSTGRE_DROP_NODES_COMMAND
+  # ========================================================================= #
+  POSTGRE_DROP_NODES_COMMAND = DROP_TABLE_NODES = 'DROP TABLE nodes;'
+  POSTGRE_DROP_NAMES_COMMAND = DROP_TABLE_NAMES = 'DROP TABLE names;'
+  DROP_TABLE_FASTA = 'DROP TABLE fasta;'
+
+  # ========================================================================= #
+  # === Bioroebe::Postgresql::POSTGRE_DROP_FASTA_COMMAND
+  # ========================================================================= #
+  POSTGRE_DROP_FASTA_COMMAND = DROP_FASTA_TABLE = DROP_TABLE_FASTA
+
+end # === end Bioroebe::Postgresql
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  alias e puts
+  e
+  e 'The allowed DNA nucleotides are:'
+  e
+  e '  '+Bioroebe.allowed_dna_nucleotides?.join(', ')
+  e
+  e 'The base directory for the Bioroebe project can be found at: '+
+    Bioroebe.base_directory?
+  e Bioroebe.user_home_directory?
+  _ = "wget #{Bioroebe::FTP_NCBI_TAXONOMY_DATABASE}"
+  e _; e '(We could invoke the above, but this is currently disabled.)' # system _
+  e
+  # ========================================================================= #
+  # Past this points we will test file-constants:
+  # ========================================================================= #
+  include Bioroebe
+  e FILE_FASTQ_QUALITY_SCHEMES
+  pp NUCLEOTIDES
+  e 'Restriction enzymes can be found here: '+
+    FILE_RESTRICTION_ENZYMES
+  e FILE_HYDROPATHY_TABLE
+  pp HYDROPATHY_TABLE
+  e '='*80
+  e FILE_AMINO_ACIDS_FREQUENCY
+  e FILE_NUCLEOTIDES_WEIGHT
+  e FILE_AMINOACIDS_MOLECULAR_FORMULA
+  e FILE_AMINOACIDS_THREE_TO_ONE
+  e '='*80
+  pp AMINO_ACIDS
+  e '='*80
+  pp AMINO_ACIDS_AVERAGE_MASS_TABLE
+  e '='*80
+  pp AMINO_ACIDS_THREE_TO_ONE
+  e '='*80
+  pp Bioroebe::DEFAULT_DNA_SEQUENCE
+  # ========================================================================= #
+  # Show where the taxonomy-component is stored at:
+  # ========================================================================= #
+  e "The log file for the taxonomy-component is at: "\
+    "#{Bioroebe.taxonomy_ncbi_database_last_update_log_file}"  
+  # ========================================================================= #
+  # Past this point we will test Postgresql specific parts:
+  # ========================================================================= #
+  include Bioroebe::Postgresql
+  e POSTGRE_LOGIN_COMMAND
+  e POSTGRE_LOGIN_COMMAND_HOME
+  e POSTGRE_LOGIN_COMMAND_NO_HEADERS
+  e POSTGRE_DROP_NODES_COMMAND
+  e POSTGRE_DROP_NAMES_COMMAND
+  e POSTGRE_DROP_FASTA_COMMAND
+  e
+  e Bioroebe::CodonTablesFrequencies::FILE_DROSOPHILA_MELANOGASTER
+  e
+  pp Bioroebe.aa_families?
+  e
+end