bioroebe 0.12.24 → 0.13.31

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

@@ -2,40 +2,679 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# require 'bioroebe/base/commandline_application/commandline_application.rb'
+# require 'bioroebe/requires/commandline_application.rb'
 # < ::Bioroebe::CommandlineApplication
 # =========================================================================== #
-require 'bioroebe/base/colours.rb'
-require 'bioroebe/base/prototype/prototype.rb'
-require 'bioroebe/base/misc.rb' # ← This file contains the is_palindrome? check.
+require 'bioroebe/base/base.rb'
 
 module Bioroebe
 
 class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
 
-  require 'bioroebe/base/commandline_application/aminoacids.rb'
-  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
-  require 'bioroebe/base/commandline_application/directory.rb'
-  require 'bioroebe/base/commandline_application/extract.rb'
-  require 'bioroebe/base/commandline_application/misc.rb'
-  require 'bioroebe/base/commandline_application/opn.rb'
-  require 'bioroebe/base/commandline_application/reset.rb'
-  require 'bioroebe/base/commandline_application/warnings.rb'
-  require 'bioroebe/base/commandline_application/write_what_into.rb'
-
-  require 'bioroebe/constants/nucleotides.rb'
-  require 'bioroebe/constants/misc.rb'
-  require 'bioroebe/constants/urls.rb'
-
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/toplevel_methods/cliner.rb'
-  require 'bioroebe/toplevel_methods/log_directory.rb'
-  require 'bioroebe/toplevel_methods/open_reading_frames.rb'
+  alias ee print
+
+  require 'bioroebe/configuration/configuration.rb'
+
+  begin
+    require 'opn'
+  rescue LoadError; end
 
+  require 'bioroebe/constants/constants.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+
+  require 'bioroebe/base/colours_for_base/colours_for_base.rb'
   include Bioroebe::ColoursForBase
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
   include Bioroebe::CommandlineArguments
 
   require 'bioroebe/base/base_module/base_module.rb'
   include Bioroebe::BaseModule
 
+  # ========================================================================= #
+  # === reset
+  #
+  # We only define two instance variables here.
+  # ========================================================================= #
+  def reset
+    super()
+    reset_the_internal_hash
+    infer_the_namespace
+    # ======================================================================= #
+    # === @commandline_arguments
+    # ======================================================================= #
+    @commandline_arguments = []
+    # ======================================================================= #
+    # === :be_verbose
+    #
+    # By default, CommandlineApplication will report a lot of stuff.
+    # ======================================================================= #
+    set_be_verbose
+    # ======================================================================= #
+    # === :use_colours
+    # ======================================================================= #
+    enable_colours
+  end
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === write_what_into
+  #
+  # This method can be used to write into a (local) file.
+  # ========================================================================= #
+  def write_what_into(what, into)
+    ::Bioroebe.write_what_into(what, into)
+  end; alias save_file write_what_into # === save_file
+
+  # ========================================================================= #
+  # === append_what_into
+  # ========================================================================= #
+  def append_what_into(what, into)
+    ::Bioroebe.append_what_into(what, into)
+  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
+
+  # ========================================================================= #
+  # === OLD_VERBOSE_VALUE
+  #
+  # Keep an old reference to the VERBOSE flag.
+  # ========================================================================= #
+  OLD_VERBOSE_VALUE = $VERBOSE
+
+  $VERBOSE = nil
+
+  # ========================================================================= #
+  # === disable_warnings
+  # ========================================================================= #
+  def disable_warnings
+    $VERBOSE = nil
+  end
+
+  # ========================================================================= #
+  # === enable_warnings
+  # ========================================================================= #
+  def enable_warnings
+    $VERBOSE = OLD_VERBOSE_VALUE
+  end
+
+  $VERBOSE = OLD_VERBOSE_VALUE # Reinstate the old verbosity level here.
+
+  # ========================================================================= #
+  # === one_to_three
+  # ========================================================================= #
+  def one_to_three(i)
+    ::Bioroebe.one_to_three(i)
+  end
+
+  # ========================================================================= #
+  # === extract                                                 (extract tag)
+  #
+  # This method can be used to extract an archive, via a hardcoded
+  # call to "tar".
+  # ========================================================================= #
+  def extract(i)
+    ::Bioroebe.extract(i)
+  end
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === stop_codons?
+  # ========================================================================= #
+  def stop_codons?(i)
+    require 'bioroebe/codons/codons.rb'
+    ::Bioroebe.stop_codons?(i)
+  end
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === codon_table_dataset?
+  # ========================================================================= #
+  def codon_table_dataset?
+    require 'bioroebe/codons/codon_table.rb'
+    ::Bioroebe.codon_table_dataset?
+  end
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === strict_filter_away_invalid_aminoacids
+  # ========================================================================= #
+  def strict_filter_away_invalid_aminoacids(i)
+    ::Bioroebe.strict_filter_away_invalid_aminoacids(i)
+  end
+
+  # ========================================================================= #
+  # === partner_nucleotide
+  # ========================================================================= #
+  def partner_nucleotide(i)
+    ::Bioroebe.partner_nucleotide(i)
+  end; alias return_dna_match partner_nucleotide # === return_dna_match
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === 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)
+    require 'bioroebe/sequence/sequence.rb'
+    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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === set_runmode
+  #
+  # Three runmodes are allowed here:
+  #
+  #   :GUI
+  #   :commandline
+  #   :www
+  #
+  # :www is for use in cgi and similar world wide web settings.
+  # ========================================================================= #
+  def set_runmode(
+      i = :commandline
+    )
+    @internal_hash[:runmode] = i
+  end
+
+  # ========================================================================= #
+  # === runmode?
+  # ========================================================================= #
+  def runmode?
+    @internal_hash[:runmode]
+  end
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === opnerev
+  # ========================================================================= #
+  def opnerev(i = '')
+    opnn; erev i
+  end; alias opne opnerev # === opne
+
 end; end