bioroebe 0.10.80 → 0.11.12

data/lib/bioroebe/shell/prompt.rb

@@ -1,107 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/prompt.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/constants/misc.rb'
-
-  # ========================================================================= #
-  # === use_which_prompt?
-  # ========================================================================= #
-  def use_which_prompt?
-    @internal_hash[:prompt_to_use]
-  end
-
-  # ========================================================================= #
-  # === set_use_this_prompt
-  #
-  # This method can be used to set the prompt of the bio-shell.
-  # ========================================================================= #
-  def set_use_this_prompt(i = NAME_OF_BIO_SHELL)
-    case i # case tag
-    # ======================================================================= #
-    # === NONE
-    # ======================================================================= #
-    when /^NONE$/i,
-         'empty',
-         :empty
-      i = "\n"
-      do_not_use_working_directory_as_prompt
-    # ======================================================================= #
-    # === pwd
-    # ======================================================================= #
-    when 'pwd', :cwd, nil 
-      i = return_default_prompt
-      do_use_working_directory_as_prompt
-    # ======================================================================= #
-    # === REVERT
-    # ======================================================================= #
-    when /^REVERT$/i,
-         /^DEFAULT$/i,
-         :default
-      i = NAME_OF_BIO_SHELL
-      do_not_use_working_directory_as_prompt
-    end
-    @internal_hash[:prompt_to_use] = i
-  end; alias set_prompt set_use_this_prompt # === set_prompt
-
-  # ========================================================================= #
-  # === return_pwd
-  # ========================================================================= #
-  def return_pwd
-    ("#{Dir.pwd}/").squeeze('/')
-  end; alias return_default_prompt return_pwd # === return_default_prompt
-
-  # ========================================================================= #
-  # === obtain_current_prompt
-  #
-  # This is essentially a getter-method over the instance variable
-  # called @internal_hash[:prompt_to_use].
-  # ========================================================================= #
-  def obtain_current_prompt
-    if @internal_hash[:use_working_directory_as_prompt]
-      @internal_hash[:prompt_to_use] = return_pwd
-    end
-    @internal_hash[:prompt_to_use]
-  end
-
-  # ========================================================================= #
-  # === obtain_current_prompt_while_honouring_colours
-  # ========================================================================= #
-  def obtain_current_prompt_while_honouring_colours
-    _ = obtain_current_prompt
-    if _ and use_colours?
-      _ = "#{Colours::TEAL}#{_}#{rev}"
-    end
-    return _
-  end
-
-  # ========================================================================= #
-  # === restore_default_prompt
-  # ========================================================================= #
-  def restore_default_prompt
-    set_prompt :default
-  end
-
-  # ========================================================================= #
-  # === use_working_directory_as_prompt
-  #
-  # Use this method if you wish to use the working-directory as your prompt.
-  # ========================================================================= #
-  def do_use_working_directory_as_prompt
-    @internal_hash[:use_working_directory_as_prompt] = true
-  end; alias use_working_directory_as_prompt do_use_working_directory_as_prompt # === use_working_directory_as_prompt
-
-  # ========================================================================= #
-  # === do_not_use_working_directory_as_prompt
-  # ========================================================================= #
-  def do_not_use_working_directory_as_prompt
-    @internal_hash[:use_working_directory_as_prompt] = false
-  end
-
-end; end

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