bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/base/commandline_application/aminoacids.rb

@@ -1,33 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/base/commandline_application/aminoacids.rb'
-# =========================================================================== #
-module Bioroebe
-
-class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === return_array_of_one_letter_aminoacids
-  #
-  # This method will return a sorted Array of the one-letter aminoacids.
-  #
-  # Specifically, this may look like this:
-  #
-  #   ["A","C","D","E","F","G","H","I","K","L","M","N",
-  #    "O","P","Q","R","S","T","U","V","W","Y"]
-  #
-  # ========================================================================= #
-  def return_array_of_one_letter_aminoacids
-    AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.values.sort
-  end
-
-  # ========================================================================= #
-  # === all_aminoacids?
-  # ========================================================================= #
-  def all_aminoacids?
-    ::Bioroebe.all_aminoacids?
-  end
-
-end; end

data/lib/bioroebe/base/commandline_application/directory.rb

@@ -1,33 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/base/commandline_application/directory.rb'
-# =========================================================================== #
-module Bioroebe
-
-class CommandlineApplication < Base
-
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
-  # ========================================================================= #
-  # === change_directory                                             (cd tag)
-  #
-  # Use this to change the directory. The first argument should be the
-  # target directory in question.
-  #
-  # The second argument means that this method will be verbose.
-  # ========================================================================= #
-  def change_directory(
-      i = '$HOME'
-    )
-    # ======================================================================= #
-    # The verbose-flag set next is used to also report the current directory.
-    # ======================================================================= #
-    case i
-    when ':home', :home
-      i = :home_directory
-    end
-    ::Bioroebe.change_directory(i, :be_verbose)
-  end; alias cd change_directory # === cd
-
-end; end

data/lib/bioroebe/base/commandline_application/extract.rb

@@ -1,22 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/base/commandline_application/extract.rb' 
-# =========================================================================== #
-module Bioroebe
-
-class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === extract                                                 (extract tag)
-  #
-  # This method can be used to extract an archive, via a hardcoded
-  # call to "tar".
-  # ========================================================================= #
-  def extract(i)
-    require 'bioroebe/toplevel_methods/extract.rb'
-    ::Bioroebe.extract(i)
-  end
-
-end; end

data/lib/bioroebe/base/commandline_application/misc.rb

@@ -1,502 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-module Bioroebe
-
-class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
-
-  require 'bioroebe/sequence/sequence.rb'
-  require 'bioroebe/configuration/configuration.rb'
-  require 'bioroebe/constants/files_and_directories.rb'
-  require 'bioroebe/base/commandline_application/reset.rb'
-
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  # ========================================================================= #
-  # === one_to_three
-  # ========================================================================= #
-  def one_to_three(i)
-    ::Bioroebe.one_to_three(i)
-  end
-
-  require 'bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb'
-  # ========================================================================= #
-  # === trailing_three_prime
-  # ========================================================================= #
-  def trailing_three_prime(
-      i                 = '',
-      get_rid_of_spaces = false,
-      use_hyphen        = false
-    )
-    ::Bioroebe.trailing_three_prime(i, get_rid_of_spaces, use_hyphen)
-  end
-
-  require 'bioroebe/codons/codons.rb'
-  # ========================================================================= #
-  # === stop_codons?
-  # ========================================================================= #
-  def stop_codons?(i)
-    ::Bioroebe.stop_codons?(i)
-  end
-
-  require 'bioroebe/codons/codon_table.rb'
-  # ========================================================================= #
-  # === codon_table_dataset?
-  # ========================================================================= #
-  def codon_table_dataset?
-    ::Bioroebe.codon_table_dataset?
-  end
-
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
-  # ========================================================================= #
-  # === ensure_that_the_base_directory_exists
-  #
-  # Common functionality to ensure that the necessary base directories
-  # exist on the target computer system.
-  # ========================================================================= #
-  def ensure_that_the_base_directories_exist
-    ::Bioroebe.ensure_that_the_base_directories_exist
-  end
-
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  # ========================================================================= #
-  # === strict_filter_away_invalid_aminoacids
-  # ========================================================================= #
-  def strict_filter_away_invalid_aminoacids(i)
-    ::Bioroebe.strict_filter_away_invalid_aminoacids(i)
-  end
-
-  require 'bioroebe/toplevel_methods/nucleotides.rb'
-  # ========================================================================= #
-  # === partner_nucleotide
-  # ========================================================================= #
-  def partner_nucleotide(i)
-    ::Bioroebe.partner_nucleotide(i)
-  end; alias return_dna_match partner_nucleotide # === return_dna_match
-
-  require 'bioroebe/toplevel_methods/taxonomy.rb'
-  # ========================================================================= #
-  # === taxonomy_download_directory?
-  # ========================================================================= #
-  def taxonomy_download_directory?
-    ::Bioroebe.taxonomy_download_directory?
-  end
-
-  # ========================================================================= #
-  # === codons_for?
-  #
-  # See documentation for Bioroebe.codons_for? in the file
-  # codons.rb, so it belongs to the above require statement.
-  # ========================================================================= #
-  def codons_for?(i)
-    ::Bioroebe.codons_for?(i)
-  end
-
-  require 'bioroebe/toplevel_methods/chunked_display.rb'
-  # ========================================================================= #
-  # === return_chunked_display
-  # ========================================================================= #
-  def return_chunked_display(i)
-    ::Bioroebe.chunked_display(i)
-  end
-
-  # ========================================================================= #
-  # === return_cheerful_person
-  # ========================================================================= #
-  def return_cheerful_person
-    '\\o/'
-  end; alias cheerful_person return_cheerful_person # === cheerful_person
-
-  # ========================================================================= #
-  # === to_rna
-  # ========================================================================= #
-  def to_rna(i)
-    i.tr('T','U')
-  end
-
-  require 'bioroebe/codons/start_codons.rb'
-  # ========================================================================= #
-  # === start_codon?
-  # ========================================================================= #
-  def start_codon?
-    ::Bioroebe.start_codon?
-  end
-
-  # ========================================================================= #
-  # === return_all_possible_start_codons
-  #
-  # This method will return all possible start codons. The code itself is
-  # defined in the file "bioroebe/codons/start_codons.rb", so the
-  # method here is grouped with the above .rb file (the require statement
-  # above here).
-  # ========================================================================= #
-  def return_all_possible_start_codons
-    ::Bioroebe.start_codons?
-  end
-
-  # ========================================================================= #
-  # === is_this_a_start_codon?
-  #
-  # Note that the method-call defind in this method will return the start
-  # codon as a DNA variant, so the given input should be in the form of
-  # DNA rather than RNA.
-  # ========================================================================= #
-  def is_this_a_start_codon?(i)
-    ::Bioroebe.start_codons?.include? i
-  end
-
-  # ========================================================================= #
-  # === is_this_a_stop_codon?
-  #
-  # Query method to determine whether the given input is a stop codon or
-  # whether it is not.
-  # ========================================================================= #
-  def is_this_a_stop_codon?(i)
-    ::Bioroebe.stop_codons?.include? i
-  end
-
-  require 'bioroebe/toplevel_methods/cat.rb'
-  # ========================================================================= #
-  # === cat
-  # ========================================================================= #
-  def cat(i)
-    ::Bioroebe.cat(i)
-  end
-
-  # ========================================================================= #
-  # === without_extname
-  #
-  # This method will return a filename without the extname.
-  # ========================================================================= #
-  def without_extname(i)
-    _ = File.extname(i)
-    return i.gsub(/#{_}/, '')
-  end
-
-  # ========================================================================= #
-  # === only_numbers?
-  #
-  # This method will return true if the input consists of only numbers.
-  # Otherwise, false will be returned.
-  # ========================================================================= #
-  def only_numbers?(i)
-    i = i.to_s
-    i =~ /^\d+$/
-  end
-
-  # ========================================================================= #
-  # === pad_with_double_quotes
-  #
-  # Pad the input with "" quotes.
-  # ========================================================================= #
-  def pad_with_double_quotes(i)
-    return "\"#{i}\""
-  end
-
-  # ========================================================================= #
-  # === pad_with_single_quotes
-  #
-  # Pad the input with '' quotes, unless it has them already.
-  # ========================================================================= #
-  def pad_with_single_quotes(i)
-    _ = ''.dup
-    _ << "'"
-    _ << i.to_s.delete("'")
-    _ << "'"
-    return _
-  end
-
-  # ========================================================================= #
-  # === one_letter_to_long_name
-  #
-  # The purpose of this method is really simple:
-  #
-  # - Take the one-letter abbreviation of an amino acid, and find
-  #   the corresponding long name of the aminoacid.
-  #
-  # ========================================================================= #
-  def one_letter_to_long_name(one_letter_code)
-    inverted = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.invert
-    inverted[one_letter_code.upcase]
-  end
-
-  require 'bioroebe/toplevel_methods/editor.rb'
-  # ========================================================================= #
-  # === editor?
-  #
-  # Which editor we will use.
-  # ========================================================================= #
-  def editor?
-    Bioroebe.editor?
-  end
-
-  # ========================================================================= #
-  # === cp                                                 (cp tag, copy tag)
-  #
-  # Copy some files via this method here.
-  # ========================================================================= #
-  def cp(
-      from, to = return_pwd
-    )
-    e "Now copying #{sfile(from.to_s)} to #{sfile(to.to_s)}."
-    FileUtils.cp(from.to_s, to.to_s)
-  end; alias copy cp # === copy
-
-  # ========================================================================= #
-  # === at_home?
-  # ========================================================================= #
-  def at_home?
-    if ENV['IS_ROEBE']
-      true
-    else
-      false
-    end
-  end; alias is_roebe? at_home? # === is_roebe?
-
-  # ========================================================================= #
-  # === remove_trailing_ansii_escape_code
-  # ========================================================================= #
-  def remove_trailing_ansii_escape_code(i)
-    return ::Colours.remove_trailing_ansii_escape_code(i) if use_colours?
-    i
-  end
-
-  # ========================================================================= #
-  # === download_dir?
-  # ========================================================================= #
-  def download_dir?
-    ::Bioroebe.download_dir?
-  end
-
-  require 'bioroebe/toplevel_methods/complement.rb'
-  # ========================================================================= #
-  # === complement                                           (complement tag)
-  #
-  # Usage example:
-  #
-  #   x = Bioroebe::Sequence.new('ATGGCA').complement # => "TACCGT"
-  #
-  # ========================================================================= #
-  def complement(i)
-    ::Bioroebe.complement(i)
-  end; alias return_the_complementary_nucleotide_sequence_to complement # === return_the_complementary_nucleotide_sequence_to
-       alias complementary_dna_strand                        complement # === complementary_dna_strand
-       alias complementary_dna_sequence                      complement # === complementary_dna_sequence
-
-  # ========================================================================= #
-  # === esystem
-  #
-  # Run an external program - and output the result.
-  # ========================================================================= #
-  def esystem(i)
-    ::Bioroebe.esystem(i)
-  end
-
-  # ========================================================================= #
-  # === log_directory?
-  # ========================================================================= #
-  def log_directory?
-    ::Bioroebe.log_directory?
-  end; alias log_dir? log_directory? # === log_dir?
-
-  # ========================================================================= #
-  # === was_or_were
-  # ========================================================================= #
-  def was_or_were(i = 1)
-    if i == 1
-      'was'
-    else
-      'were'
-    end
-  end
-
-  require 'bioroebe/toplevel_methods/misc.rb'
-  # ========================================================================= #
-  # === return_ubiquitin_sequence
-  # ========================================================================= #
-  def return_ubiquitin_sequence(i)
-    ::Bioroebe.return_ubiquitin_sequence(i)
-  end
-
-  # ========================================================================= #
-  # === leading_five_prime
-  #
-  # The first argument should be the input sequence; or, alternatively,
-  # if you only need the "5' " header then you can omit it altogether.
-  # ========================================================================= #
-  def leading_five_prime(
-      i                 = '',
-      get_rid_of_spaces = false,
-      use_hyphen        = false
-    )
-    ::Bioroebe.leading_five_prime(i, get_rid_of_spaces, use_hyphen)
-  end
-
-  # ========================================================================= #
-  # === ccliner
-  # ========================================================================= #
-  def ccliner(
-      n_times = :default_n_times
-    )
-    ee rev; cliner(:default_token, n_times)
-  end
-
-  require 'bioroebe/toplevel_methods/cliner.rb'
-  # ========================================================================= #
-  # === cliner                                                   (cliner tag)
-  # ========================================================================= #
-  def cliner(
-      use_this_token = :default_token,
-      how_many_times = :default_n_times,
-      &block
-    )
-    case how_many_times
-    # ======================================================================= #
-    # === :default_n_times
-    # ======================================================================= #
-    when :default_n_times
-      how_many_times = 80
-    end
-    ::Bioroebe.cliner(
-      use_this_token,
-      how_many_times,
-      &block
-    )
-  end
-
-  # ========================================================================= #
-  # === colourize_this_dna_sequence
-  #
-  # This method can be used to colourize a DNA sequence.
-  # ========================================================================= #
-  def colourize_this_dna_sequence(i)
-    if i.is_a? ::Bioroebe::Sequence
-      i = i.to_s
-    end
-    _ = ''.dup
-    if use_colours?
-      _ << remove_trailing_escape_code(
-        ::Colours.send(USE_THIS_COLOUR_FOR_DNA)
-      )
-    end
-    _ << i
-    _ << rev if use_colours?
-  end; alias colourize_dna_sequence        colourize_this_dna_sequence # === colourize_dna_sequence
-       alias colourize_nucleotides         colourize_this_dna_sequence # === colourize_nucleotides
-       alias colourize_nucleotide_sequence colourize_this_dna_sequence # === colourize_nucleotide_sequence
-
-  # ========================================================================= #
-  # === remove_numbers
-  #
-  # This method will chop off numbers.
-  # ========================================================================= #
-  def remove_numbers(i)
-    return i.delete('[0-9]')
-  end
-
-  # ========================================================================= #
-  # === load_bioroebe_yaml_file
-  #
-  # This method can be used to more easily load up a yaml file residing
-  # in the main yaml/ directory of Bioroebe.
-  #
-  # If a Symbol is passed as input, then this will be assumed to correspond
-  # to some existing yaml file there.
-  # ========================================================================= #
-  def load_bioroebe_yaml_file(
-      i = :agarose
-    )
-    case i # case tag
-    when :agarose
-      i = 'agarose/agarose_concentrations.yml'
-    end
-    # ======================================================================= #
-    # Aggregate it together with the BIOROEBE_YAML constant.
-    # ======================================================================= #
-    this_file = "#{yaml_directory?}#{i}"
-    if File.exist? this_file
-      return YAML.load_file(this_file)
-    else
-      nil
-    end
-  end
-
-  # ========================================================================= #
-  # === three_to_one
-  #
-  # This method will "convert" from the three-letter amino acid code to
-  # the one-letter amino acid code. So, for instance, "Lys" will become
-  # "L".
-  # ========================================================================= #
-  def three_to_one(i)
-    ::Bioroebe.three_to_one(i)
-  end; alias three_aminoacid_letter_code_to_one_aminoacid_letter_code three_to_one # === three_aminoacid_letter_code_to_one_aminoacid_letter_code
-       alias three_letters_to_one_letter                              three_to_one # === three_letters_to_one_letter
-
-  require 'bioroebe/toplevel_methods/open_in_browser.rb'
-  # ========================================================================= #
-  # === open_in_browser
-  # ========================================================================= #
-  def open_in_browser(this_url)
-    ::Bioroebe.open_in_browser(this_url)
-  end; alias open_in_browser_tab open_in_browser # === open_in_browser_tab
-
-  require 'bioroebe/toplevel_methods/verbose.rb'
-  # ========================================================================= #
-  # === verbose_truth
-  #
-  # Delegate towards the module Bioroebe::VerboseTruth here.
-  # ========================================================================= #
-  def verbose_truth(i)
-    ::Bioroebe::VerboseTruth[i]
-  end
-
-  # ========================================================================= #
-  # === codon_to_aminoacid
-  # ========================================================================= #
-  def codon_to_aminoacid(i)
-    unless Bioroebe.respond_to? :codon_to_aminoacid
-      require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
-    end
-    ::Bioroebe.codon_to_aminoacid(i).to_s
-  end; alias nucleotides_to_aminoacid codon_to_aminoacid # === nucleotides_to_aminoacid
-       alias codons_to_aminoacid      codon_to_aminoacid # === codons_to_aminoacid
-
-  # ========================================================================= #
-  # === be_verbose?
-  # ========================================================================= #
-  def be_verbose?
-    @internal_hash[:be_verbose]
-  end; alias verbose? be_verbose? # === be_verbose?
-
-  # ========================================================================= #
-  # === be_silent
-  # ========================================================================= #
-  def be_silent
-    @internal_hash[:be_verbose] = false
-  end; alias be_quiet          be_silent # === be_quiet
-       alias set_be_silent     be_silent # === set_be_silent
-       alias set_be_quiet      be_silent # === set_be_quiet
-       alias do_not_be_verbose be_silent # === do_not_be_verbose
-
-  # ========================================================================= #
-  # === set_be_verbose
-  # ========================================================================= #
-  def set_be_verbose(i = true)
-    case i
-    # ======================================================================= #
-    # === :be_verbose
-    # ======================================================================= #
-    when :be_verbose,
-         :default
-      i = true
-    # ======================================================================= #
-    # === :be_quiet
-    # ======================================================================= #
-    when :be_quiet
-      i = false
-    end
-    @internal_hash[:be_verbose] = i
-  end
-
-end; end

data/lib/bioroebe/base/commandline_application/opn.rb

@@ -1,47 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/base/commandline_application/opn.rb'
-# =========================================================================== #
-module Bioroebe
-
-class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
-
-  require 'bioroebe/base/namespace.rb'
-  require 'bioroebe/configuration/configuration.rb'
-
-  begin
-    require 'opn'
-  rescue LoadError; end
-  
-  # ========================================================================= #
-  # === use_opn?
-  # ========================================================================= #
-  def use_opn?
-    ::Bioroebe.use_opn?
-  end
-
-  # ========================================================================= #
-  # === opnn
-  # ========================================================================= #
-  def opnn(
-      i = namespace?,
-      &block
-    )
-    if use_opn?
-      if i.is_a? String
-        i = { namespace: i }
-      end
-      Opn.opn(i, &block)
-    end
-  end
-
-  # ========================================================================= #
-  # === opne
-  # ========================================================================= #
-  def opne(i = '')
-    opnn; erev i
-  end
-
-end; end

data/lib/bioroebe/base/commandline_application/reset.rb

@@ -1,42 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/base/commandline_application/reset.rb'
-# =========================================================================== #
-module Bioroebe
-
-module CommandlineArguments # === Bioroebe::CommandlineApplication
-
-  require 'bioroebe/base/namespace.rb'
-
-  # ========================================================================= #
-  # === reset
-  #
-  # We only define two instance variables here.
-  # ========================================================================= #
-  def reset
-    super()
-    reset_the_internal_hash
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    # @namespace = Bioroebe::Base::NAMESPACE
-    infer_the_namespace
-    # ======================================================================= #
-    # === @commandline_arguments
-    # ======================================================================= #
-    @commandline_arguments = []
-    # ======================================================================= #
-    # === :be_verbose
-    #
-    # By default, CommandlineApplication will report a lot of stuff.
-    # ======================================================================= #
-    set_be_verbose
-    # ======================================================================= #
-    # === @use_colours
-    # ======================================================================= #
-    @use_colours = true
-  end
-
-end; end