bioroebe 0.10.80 → 0.11.32

data/lib/bioroebe/shell/random.rb

@@ -1,289 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/random.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/constants/files_and_directories.rb'
-
-  # ========================================================================= #
-  # === random                                         (random tag, rand tag)
-  #
-  # This will generate a random DNA sequence or a random aminoacid
-  # sequence.
-  #
-  # The first argument tells us how many nucleotides or amino acids
-  # should be part of that sequence.
-  #
-  # If a second argument was given, we will generate AA. Otherwise we
-  # will generate DNA (which is the default).
-  #
-  # Usage examples:
-  #
-  #   random dna
-  #   random dna 20
-  #   random 2552
-  #   random 2552 aa
-  #
-  # ========================================================================= #
-  def random(
-      n_elements             = default_length?,
-      dna_or_amino_acid      = :dna,
-      do_report_the_sequence = false
-    )
-    # ====================================================================== #
-    # === First handle Arrays
-    # ====================================================================== #
-    if dna_or_amino_acid.is_a? Array
-      dna_or_amino_acid = dna_or_amino_acid.first
-    end
-    case n_elements.to_s
-    # ====================================================================== #
-    # === aminoacids
-    # ====================================================================== #
-    when 'aminoacids',
-         /^aa$/i
-      five_steps_array = [] # An array from 5 to 50, in 5 steps.
-      5.step(50, 5) { |entry| five_steps_array << entry }
-      n_elements = 200+five_steps_array.sample
-      dna_or_amino_acid = :aminoacids
-    # ====================================================================== #
-    # === do_not_show_the_string
-    # ====================================================================== #
-    when 'do_not_show_the_string'
-      dna_or_amino_acid = :dna
-      n_elements = default_length?
-      do_report_the_sequence = false
-    # ====================================================================== #
-    # === dna
-    # ====================================================================== #
-    when 'dna','' # This also handles nil.
-      n_elements = default_length?
-      if only_numbers?(dna_or_amino_acid)
-        n_elements = dna_or_amino_acid.to_i
-      end
-      dna_or_amino_acid = :dna
-    # ====================================================================== #
-    # === nil
-    # ====================================================================== #
-    when nil
-      n_elements = default_length? # defaults to 1000.
-    end
-    # ====================================================================== #
-    # If input has NOT only numbers alone:
-    # ====================================================================== #
-    if n_elements.to_s !~ /^\d+$/
-      n_elements = default_length?
-    end
-    dna_or_amino_acid = dna_or_amino_acid.to_s
-    # ====================================================================== #
-    # === Handle DNA or amino acid as input next
-    # ====================================================================== #
-    case dna_or_amino_acid
-    # ====================================================================== #
-    # === dna
-    # ====================================================================== #
-    when 'dna',
-         'd',
-         'default',
-         ''
-      # '' is also the default for this. 
-      erev 'Generating some DNA of length '+
-            simp(n_elements.to_s)+rev+'.'
-      if seq_object?.type?.nil?
-        seq_object?.is_DNA_now
-        require 'bioroebe/sequence/nucleotide_module/nucleotide_module.rb'
-        seq_object?.extend(Bioroebe::NucleotideModule)
-      else
-        unless seq_object?.respond_to? :n_random_dna
-          require 'bioroebe/sequence/nucleotide_module/nucleotide_module.rb'
-          seq_object?.extend(Bioroebe::NucleotideModule)
-        end
-      end
-      sequence = seq_object?.n_random_dna(n_elements)
-      set_dna_sequence(sequence)
-    # ====================================================================== #
-    # === aminoacids
-    # ====================================================================== #
-    when 'aminoacids',
-         'aminoacid',
-         'aa'
-      e 'Generating some ('+sfancy(n_elements.to_s)+rev+') AminoAcids next.'
-      _ = set_aminoacids(:generate, n_elements, :be_silent) # We are silent here because we report lateron anyway.
-      output = _
-    end
-    # ======================================================================= #
-    # Next, show this string if we also wish to report the sequence.
-    # ======================================================================= #
-    show_string(output) if do_report_the_sequence
-    return _ # Last but not least, return it.
-  end
-
-  # ========================================================================= #
-  # === generate_random_dna_sequence_with_variable_length_and_variable_composition
-  #
-  # This method will generate a random DNA sequence of variable
-  # length and composition.
-  # ========================================================================= #
-  def generate_random_dna_sequence_with_variable_length_and_variable_composition
-    e 'Input the desired length of your DNA string:'
-    length = $stdin.gets.chomp.to_i
-    e 'Input the percentage of Adenine, Thymin, Cytosine and Guanosine. You can'
-    e 'omit this, in which case we will default to 25% each.'
-    e 'Use a / as delimiter please, as in '+
-      orange('30 / 30 / 20 / 20')+rev+'.'
-    e
-    print 'Adenine / Thymin / Cytosine / Guanosine: '
-    composition = $stdin.gets.chomp
-    if composition.include? '/'
-      splitted = composition.split('/').
-                 map(&:strip).map(&:to_f)
-    else
-      splitted = [25,25,25,25]
-    end
-    # ======================================================================= #
-    # Next, we fill in our pool of nucleotides.
-    # ======================================================================= #
-    pool_of_nucleotides = []
-    # ======================================================================= #
-    # Next, we must determine how many we will use. The percentage value
-    # tells us this.
-    # The entries are e. g. 35%. So we first must calculate how much is
-    # 1%, then we multiply this.
-    # ======================================================================= #
-    n_A = (length.to_f / 100) * splitted[0].to_f
-    n_T = (length.to_f / 100) * splitted[1].to_f
-    n_C = (length.to_f / 100) * splitted[2].to_f
-    n_G = (length.to_f / 100) * splitted[3].to_f
-    pool_of_nucleotides << (['A'] * n_A)
-    pool_of_nucleotides << (['T'] * n_T)
-    pool_of_nucleotides << (['C'] * n_C)
-    pool_of_nucleotides << (['G'] * n_G)
-    pool_of_nucleotides.flatten!
-    _ = ''.dup # This is the return string.
-    _ << pool_of_nucleotides.shuffle.join
-    return _
-  end
-
-  # ========================================================================= #
-  # === return_random_nucleotide
-  #
-  # Here we return a random nucleotide.
-  # ========================================================================= #
-  def return_random_nucleotide
-    Bioroebe.return_random_nucleotide
-  end; alias add_nucleotide return_random_nucleotide # === add_nucleotide
-
-  # ========================================================================= #
-  # === random_dna_sequence
-  #
-  # Generate a random DNA sequence. Note that this will return a String -
-  # if you wish to put this onto a Sequence object then you have to
-  # handle this situation on your own.
-  #
-  # The argument shall be how many DNA nucleotides you want to have.
-  # ========================================================================= #
-  def random_dna_sequence(
-      length = 250
-    )
-    ::Bioroebe.generate_random_dna_sequence(length)
-  end
-
-  # ========================================================================= #
-  # === random_insert
-  #
-  # Use this method to do a random insert into your main DNA sequence.
-  #
-  # The input should be a nucleotide sequence such as ATGCCA, but it can
-  # also be a number - see the examples below for that.
-  #
-  # Note that this method will insert the given input into ONE random
-  # position of our main sequence.
-  #
-  # To use this, try:
-  #
-  #   random 15; rinsert ATTGGGCCC
-  #   random 15; rinsert 5
-  #   random 15; rinsert 15
-  #
-  # ========================================================================= #
-  def random_insert(i)
-    i = i.join if i.is_a? Array
-    i.delete!(' ')
-    if i =~ /\d+$/ # If it has at the least one number.
-      _ = ''
-      i.to_i.times { _ << return_random_nucleotide }
-      e "The #{simp(i.to_i.to_s)}#{rev} nucleotides to be added "\
-        "will be `#{sfancy(_)}#{rev}`."
-      i = _
-    end
-    # ======================================================================= #
-    # We need to determine the insert position. The insert_position can
-    # be 0 zoo.
-    # ======================================================================= #
-    insert_position = rand(sequence?.size)
-    n_nucleotides = i.size.to_s
-    e 'Inserting '+sfancy(n_nucleotides.to_s)+rev+' nucleotides at '\
-      'nucleotide position '+simp(insert_position.to_s)+rev+'.'
-    old_size = @sequence.size
-    @sequence[insert_position+1, 0] = i
-    e 'The old size was '+sfancy(old_size.to_s)+rev+'. The new '\
-      'size is '+sfancy(@sequence.size.to_s)+rev+'.'
-  end
-
-  # ========================================================================= #
-  # === create_n_random_amino_acids
-  # ========================================================================= #
-  def create_n_random_amino_acids(n = 1000)
-    set_aminoacids :random, n, :be_verbose
-  end
-
-  # ========================================================================= #
-  # === set_aminoacids
-  #
-  # Simply delegate to set_aminoacids.
-  # ========================================================================= #
-  def set_random_aminoacids
-    set_aminoacids :random
-  end
-
-  # ========================================================================= #
-  # === generate_random_protein_sequence_with_variable_length_and_variable_composition
-  #
-  # Use this method to generate a random protein sequence with variable
-  # length and variable composition.
-  # ========================================================================= #
-  def generate_random_protein_sequence_with_variable_length_and_variable_composition
-    _ = {} # This is our hash.
-    e 'You can generate a random protein sequence next. First, input the'
-    print 'target length of the protein in question: '
-    length = $stdin.gets.chomp.to_i
-    e
-    e 'Next, you have to input the percentage for the respective amino '\
-      'acids, separated via the token '+orange('/')+rev+'.'
-    e
-    e 'This can be quite tedious though. Unfortunately, there is not a'
-    e 'much simpler way possible on the commandline, so here we go:'
-    e
-    print 'Glycine Alanine Valine: '
-    glycine_alanine_valine   = $stdin.gets.chomp
-    glycine, alanine, valine = glycine_alanine_valine.split('/').map(&:strip)
-    _['glycine'] = glycine
-    _['alanine'] = alanine
-    _['valine'] = valine
-    e 'The length of the target protein is '+simp(length.to_s)+'.'
-e swarn('!!! THE ABOVE CODE ^^^ IS UNFINISHED !!!!!')+rev
-  end
-
-  # ========================================================================= #
-  # === return_random_aminoacid
-  # ========================================================================= #
-  def return_random_aminoacid
-    Bioroebe.return_random_aminoacid
-  end
-
-end; end

data/lib/bioroebe/shell/reset.rb

@@ -1,335 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/reset.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/raw_sequence/raw_sequence.rb'
-  require 'bioroebe/nucleotides/show_nucleotide_sequence.rb'
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset(
-      be_verbose = true
-    )
-    super()
-    # ======================================================================= #
-    # First we try to enable the configuration.
-    # ======================================================================= #
-    enable_configuration
-    reset_to_initial_state(be_verbose)
-    set_default_length # Set the default length of 1000 here.
-    # ======================================================================= #
-    # Make sure that the base directories exist.
-    # ======================================================================= #
-    ensure_that_the_base_directories_exist
-    if defined? DEFAULT_DNA_INPUT_YAML_FILE # Main DNA string.
-      set_string(DEFAULT_DNA_INPUT_YAML_FILE)
-    end
-  end
-
-  require 'bioroebe/sequence/sequence.rb'
-  # ========================================================================= #
-  # === initialize_main_sequence
-  #
-  # Initialize a Sequence-object on startup. We use the length 150
-  # for now.
-  # ========================================================================= #  
-  def initialize_main_sequence
-    @internal_hash[:array_dna_sequence] << Bioroebe::Sequence.new(250)
-  end; alias reset_string initialize_main_sequence # === reset_string
-
-  # ========================================================================= #
-  # === reset_to_initial_state
-  # ========================================================================= #
-  def reset_to_initial_state(
-      be_verbose = true
-    )
-    # ======================================================================= #
-    # === @internal_hash
-    #
-    # The internal Hash can be used to store internal behaviour variables
-    # rather than spawn so many different instance variables.
-    #
-    # It should be defined very early in this method.
-    # ======================================================================= #
-    @internal_hash = {}
-    # ======================================================================= #
-    # === :first_argument
-    #
-    # This variable refers to the first argument passed into a method,
-    # from the menu.rb file.
-    # ======================================================================= #
-    @internal_hash[:first_argument] = nil
-    # ======================================================================= #
-    # === :show_nucleotide_sequence
-    # ======================================================================= #
-    @internal_hash[:show_nucleotide_sequence] = ::Bioroebe::ShowNucleotideSequence.new(
-      '', :do_not_run_yet
-    )
-    # ======================================================================= #
-    # === :array_aminoacid_sequence
-    #
-    # This variable should be an empty Array, aka [], initially, so that we
-    # can distinguish the case when the user has added data onto that
-    # Array.
-    # ======================================================================= #
-    @internal_hash[:array_aminoacid_sequence] = []
-    # ======================================================================= #
-    # === :array_rna_sequence
-    #
-    # This can be populated with sequence objects such as:
-    #
-    #   Bioroebe::Sequence.new(''.dup, :rna)
-    #
-    # ======================================================================= #
-    @internal_hash[:array_rna_sequence] = []
-    # ======================================================================= #
-    # === :array_dna_sequence
-    # ======================================================================= #
-    @internal_hash[:array_dna_sequence] = []
-    # ======================================================================= #
-    # === @use_working_directory_as_prompt
-    # ======================================================================= #
-    @internal_hash[:use_working_directory_as_prompt] = false
-    # ======================================================================= #
-    # === @debug
-    #
-    # Determine whether we will debug or whether we will not
-    # ======================================================================= #
-    @internal_hash[:debug] = SHALL_WE_DEBUG
-    # ======================================================================= #
-    # === @array_sequences
-    # ======================================================================= #
-    @internal_hash[:array_sequences] = []
-    # ======================================================================= #
-    # === @all_arguments
-    # ======================================================================= #
-    @internal_hash[:all_arguments] = []
-    # ======================================================================= #
-    # === :remaining_arguments
-    # ======================================================================= #
-    @internal_hash[:remaining_arguments] = []
-    # ======================================================================= #
-    # === :registered_actions
-    # ======================================================================= #
-    @internal_hash[:registered_actions] = ARRAY_REGISTERED_ACTIONS
-    # ======================================================================= #
-    # === :the_main_sequence_is_frozen
-    # ======================================================================= #
-    @internal_hash[:the_main_sequence_is_frozen] = false
-    # ======================================================================= #
-    # === :file_dna_string_saved
-    #
-    # Where to store our DNA string by default.
-    # ======================================================================= #
-    @internal_hash[:file_dna_string_saved] = "#{log_dir?}dna_string_saved.yml"
-    # ======================================================================= #
-    # === :array_jumper_directories
-    # ======================================================================= #
-    @internal_hash[:array_jumper_directories] = []
-    # ======================================================================= #
-    # === :array_fasta
-    # ======================================================================= #
-    @internal_hash[:array_fasta] = []
-    # ======================================================================= #
-    # === :raw_sequence
-    # ======================================================================= #
-    @internal_hash[:raw_sequence] = Bioroebe::RawSequence.new
-    # ======================================================================= #
-    # === :use_xsel
-    #
-    # This method will determine whether we will use the external
-    # program "xsel". By default, at the least on my home system,
-    # I prefer to make use of xsel.
-    # ======================================================================= #
-    @internal_hash[:use_xsel] = true
-    # ======================================================================= #
-    # === :silent_startup
-    #
-    # This variable keeps track as to whether we will display a welcome
-    # message on startup or whether we will not.
-    # ======================================================================= #
-    @internal_hash[:silent_startup] = false
-    # ======================================================================= #
-    # === exit_the_shell_how
-    #
-    # The next variable has two valid modes:
-    #
-    #   :instantly
-    #   :exit_gracefully
-    #
-    # The first is the default; the second can be used if the Bioshell
-    # is embedded into another program.
-    # ======================================================================= #
-    @internal_hash[:exit_the_shell_how] = :instantly
-    # ======================================================================= #
-    # === search_for
-    #
-    # This is the sequence we wish to find, in a given nucleotide sequence.
-    # By default this will be nil.
-    # ======================================================================= #
-    @internal_hash[:search_for] = nil
-    # ======================================================================= #
-    # === analyse_the_local_dataset_on_startup
-    #
-    # If this setting is set to true then, on startup, the bioshell
-    # will report some information about the local dataset (FASTA
-    # files and pdb files).
-    # ======================================================================= #
-    @internal_hash[:analyse_the_local_dataset_on_startup] = true
-    # ======================================================================= #
-    # === user_input
-    # ======================================================================= #
-    @internal_hash[:user_input] = nil
-    # ======================================================================= #
-    # === array_history
-    #
-    # This array will keep track of the input-history, aka the commands
-    # that the user has used.
-    # ======================================================================= #
-    @internal_hash[:array_history] = []
-    # ======================================================================= #
-    # === remove_last_character_if_it_is_a_question_mark
-    #
-    # If this variable is set to true then we will remove the last
-    # input character - at the least if it is a '?'.
-    # ======================================================================= #
-    @internal_hash[:remove_last_character_if_it_is_a_question_mark] = false
-    # ======================================================================= #
-    # === prompt_to_use
-    #
-    # This variable keeps track as to which prompt is to be used.
-    # ======================================================================= #
-    @internal_hash[:prompt_to_use] = :default
-    # ======================================================================= #
-    # === use_xsel
-    # ======================================================================= #
-    @internal_hash[:use_xsel] = false
-    # ======================================================================= #
-    # === search_for
-    # ======================================================================= #
-    @internal_hash[:search_for] = nil
-    # ======================================================================= #
-    # === coding_area
-    # ======================================================================= #
-    @internal_hash[:coding_area] = nil # This can keep track of the real coding area.
-    # ======================================================================= #
-    # === misc_sequence
-    # ======================================================================= #
-    @internal_hash[:misc_sequence] = nil # This can store a misc DNA or RNA sequence.
-    # ======================================================================= #
-    # === fasta_file
-    #
-    # This used to be a standalone @hash variable, but during the
-    # rewrite in April 2020 this was integrated into @internal_hash.
-    # ======================================================================= #
-    @internal_hash[:fasta_file] = {}
-    # ======================================================================= #
-    # === @array_all_downloads
-    # ======================================================================= #
-    @internal_hash[:array_all_downloads] = [] # Must be an Array.
-    # ======================================================================= #
-    # === @use_working_directory_as_prompt
-    # ======================================================================= #
-    @internal_hash[:use_working_directory_as_prompt] = true
-    # ======================================================================= #
-    # === @mode
-    #
-    # @mode can be either :dna or :rna or :aminoacid
-    # ======================================================================= #
-    @internal_hash[:mode] = :dna
-    # ======================================================================= #
-    # === @array_these_sequences_were_chopped_away
-    #
-    # Keep an Array that can be used to keep track of which sequences
-    # were chopped away. Whenever we perform a chop-related action we
-    # will store that sequence in an Array.
-    # ======================================================================= #
-    @internal_hash[:array_these_sequences_were_chopped_away] = []
-    # ======================================================================= #
-    # === @save_file
-    # ======================================================================= #
-    @internal_hash[:save_file] = BIOSHELL_SAVE_FILE
-    # ======================================================================= #
-    # === create_directories_on_startup_of_the_shell
-    #
-    # If this variable is set to true then the bio-shell will create
-    # some directories on startup. The user can modify this from
-    # the commandline, though, and specifically disable it.
-    # ======================================================================= #
-    @internal_hash[:create_directories_on_startup_of_the_shell] = true
-    # ======================================================================= #
-    # === show_the_leader
-    # ======================================================================= #
-    @internal_hash[:show_the_leader]  = true # Show the 5' leader.
-    # ======================================================================= #
-    # === show_the_trailer
-    # ======================================================================= #
-    @internal_hash[:show_the_trailer] = true # Show the 3' trailer.
-    # ======================================================================= #
-    # === array_timer_snapshots
-    # ======================================================================= #
-    @internal_hash[:array_timer_snapshots] = [] # This Array keeps track of the time.
-    # ======================================================================= #
-    # === may_we_show_the_startup_information
-    #
-    # This variable determines whether the startup-information may be
-    # shown, on start-up of the bioshell. By default this will be true
-    # typically, but a config-variable may overrule this.
-    # ======================================================================= #
-    @internal_hash[:may_we_show_the_startup_information] = true
-    if @config and @config.respond_to? :may_we_show_the_startup_information
-      @internal_hash[:may_we_show_the_startup_information] = @config.may_we_show_the_startup_information
-    end
-    # ======================================================================= #
-    # === @use_colours
-    #
-    # Let's enable the colours.
-    # ======================================================================= #
-    enable_colours(:be_quiet)
-    initialize_clipboard
-    # ======================================================================= #
-    # === @sequence
-    #
-    # We set @sequence to a new instance of Bioroebe::Sequence next.
-    # ======================================================================= #
-    initialize_main_sequence
-# ======================================================================= #
-    # === Setting towards a default padding
-    #
-    # Next comes left-padding, defaulting to '  '. This should come after
-    # the clipboard has been initialized, and after @internal_hash has
-    # been populated.
-    # ======================================================================= #
-    set_padding :default
-    set_sequence_2
-    set_sequence_3
-    set_sequence_4
-    set_sequence_5
-    set_sequence_6
-    ::Bioroebe.clear_array_colourize_this_aminoacid
-    # ======================================================================= #
-    # === Determine whether silent startup is active
-    #
-    # Next, determine whether we will show a small startup-message or
-    # whether we shall not show it. By default this should be false -
-    # but if a file called 'use_silent_startup.yml' exists then we
-    # will use that file.
-    # ======================================================================= #
-    if File.exist? FILE_USE_SILENT_STARTUP
-      dataset = YAML.load_file(FILE_USE_SILENT_STARTUP)
-      if dataset.is_a?(Hash) and dataset.has_key?('use_silent_startup')
-        @internal_hash[:silent_startup] = dataset['use_silent_startup']
-      end
-    else # else it is 
-      @internal_hash[:silent_startup] = false
-    end
-  end
-
-end; end