bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/shell/chop_and_cut.rb

@@ -1,281 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/chop_and_cut.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === chop                                                       (chop tag)
-  #
-  # We use this method to get rid of some nucleotides, from the 3'
-  # end of a nucleotide sequence (aka the "right hand side" of it) by
-  # default.
-  #
-  # The first argument to this method tells us how many nucleotides are
-  # to be removed.
-  #
-  # The second argument determines whether to chop from the right side
-  # (the 3' side) or from the left side (the 5' side).
-  # ========================================================================= #
-  def chop(
-      i = 1,
-      chop_from_left_or_right_hand_side = :default # The default is the 3' end.
-    ) # Default will be to chop off one nucleotide.
-    if is_the_main_sequence_frozen?
-      report_that_the_main_sequence_is_frozen
-      return
-    end
-    i = i.first if i.is_a? Array
-    if i == '?'
-      e 'chop allows us to remove nucleotides from the main sequence.'
-      return
-    end
-    i = 1 if i.nil? # Assign to the default then.
-    i = i.to_i # Need a number past this point.
-    if i == 0
-      erev 'Please add a number, such as 1, or any other value.'
-    else
-      case chop_from_left_or_right_hand_side
-      # ===================================================================== #
-      # === :right
-      # ===================================================================== #
-      when :right,
-           :default
-        which_end = "3'"
-      # ===================================================================== #
-      # === :left
-      # ===================================================================== #
-      when :left
-        which_end = "5'"
-      end
-      if dna_sequence_object?.size > 0
-        erev "We will now remove some characters (#{simp(i.to_s)}#{rev}"\
-             ") from the #{which_end} end of our main string."
-      end
-      if dna_sequence_object?.size == 0
-        erev 'Can not remove anything as the sequence is empty.'
-      elsif i > dna_sequence_object?.size
-        erev 'We can not remove that many characters, thus we will'
-        erev 'simply remove all characters now.'
-        reset_string 
-      else
-        # =================================================================== #
-        # Finally do the manipulation. We need to honour from which
-        # side we will be operating on.
-        # =================================================================== #
-        case chop_from_left_or_right_hand_side
-        # =================================================================== #
-        # === :default
-        # =================================================================== #
-        when :default,
-             :right
-          # ================================================================= #
-          # We also store the chopped-away sequence, but we have to be
-          # mindful here since the sequence-object counts the nucleotides
-          # differently than ruby counts Arrays.
-          # ================================================================= #
-          @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[(-i)+1, i-1].dup
-          seq_object?[-i, i] = ''
-        # =================================================================== #
-        # === :left
-        # =================================================================== #
-        when :left
-          @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, i].dup
-          seq_object?[0, i+1] = ''
-        end
-      end
-      unless dna_sequence_object?.size == 0
-        erev "#{rev}The new length of the main string is now: "\
-             "#{simp(dna_sequence_object?.size.to_s)}#{rev}."
-      end
-      show_dna_sequence
-    end
-  end; alias remove_n_nucleotides chop # === remove_n_nucleotides
-
-  # ========================================================================= #
-  # === cut_sequence_in_slices_of
-  #
-  # This method cuts the sequence into slices of n, where n is the
-  # argument to this method.
-  #
-  # So if you input 10 as argument, then we will put the nucleotides
-  # into chunks of 10 nucleotides per row.
-  #
-  # Usage examples:
-  #
-  #   cut_sequence_in_slices_of 5
-  #   cut_sequence_in_slices_of 6
-  #   cut_sequence_in_slices_of 7
-  #
-  # ========================================================================= #
-  def cut_sequence_in_slices_of(threshold = '9')
-    _ = dna_sequence_object?
-    matches = _.scan(/.{#{threshold}}/)
-    matches.each {|entry|
-      erev '  '+entry
-    }
-  end
-
-  # ========================================================================= #
-  # === left_chop
-  # ========================================================================= #
-  def left_chop(i)
-    chop(i, :left)
-  end
-
-  # ========================================================================= #
-  # === cut_at
-  #
-  # Use this method to chop off or rather cut at a DNA sequence.
-  # ========================================================================= #
-  def cut_at(
-      this_sequence = 'GAATTC',
-      be_verbose    = true
-    )
-    main_sequence = dna_sequence_object?
-    this_sequence = this_sequence.join.strip if this_sequence.is_a? Array
-    if be_verbose
-      erev "We will chop away (at) the sequence #{simp(this_sequence)}#{rev}."
-      erev 'Note that the sequences all originated from the larger '\
-           'parent sequence.'
-    end
-    results = main_sequence.split(/#{this_sequence}/)
-    results.each {|sequence|
-      _ = properly_spaced_dna(sequence)
-      _ << (' ('+sequence.size.to_s+' nucleotides)').rjust(110 - sequence.size)
-      erev _
-    }
-  end
-
-  # ========================================================================= #
-  # === restore_the_last_chop_operation
-  #
-  # This method will "restore" the last chop operation.
-  #
-  # Presently it will only append onto the 3' area but in the future
-  # this may change, depending on whether we will store the position
-  # as well.
-  # ========================================================================= #
-  def restore_the_last_chop_operation
-    if @internal_hash[:array_these_sequences_were_chopped_away].empty?
-      erev 'Can not restore the last chop-operation as we have not yet'
-      erev 'chopped away any nucleotide from the main sequence.'
-    else
-      this_sequence = @internal_hash[:array_these_sequences_were_chopped_away].pop
-      erev 'Now adding the sequence '+
-           format_this_nucleotide_sequence(
-             this_sequence
-           )
-      erev 'to our main sequence.'
-      main_sequence?.append(this_sequence)
-    end
-  end
-
-  # ========================================================================= #
-  # === chop_to
-  #
-  # This method will chop up to the first occurence of the given input
-  # sequence.
-  #
-  # If the given input sequence can not be found, no change is made.
-  # ========================================================================= #
-  def chop_to(i)
-    if i.is_a? Array
-      i = i.first
-    end
-    case i
-    when 'start'
-      i = 'ATG'
-    end
-    _ = nucleotide_sequence?
-    if i.include? 'U'
-      # ===================================================================== #
-      # Convert Uracil to Thymine next.
-      # ===================================================================== #
-      erev "The given input sequence includes at the least one "\
-           "#{sfancy('U')}#{rev}, which we will convert to #{sfancy('T')}#{rev}."
-      i.tr!('U','T')
-    end
-    if _.include? i
-      # ===================================================================== #
-      # Ok, we found the search sequence, so now we can chop off the
-      # unnecessary sequences.
-      # ===================================================================== #
-      position = _.index(i)
-      erev "Chopping away #{sfancy(position.to_s)}#{rev} nucleotides from "\
-           "the left-hand side (5' end) next."
-      @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, position+1]
-      seq_object?[0, position+1] = ''
-      show_dna_sequence
-    else
-      erev 'No modification can be made as our target nucleotide sequence'
-      erev "does not include the given search string #{sfancy(i)}."
-    end
-  end
-
-  # ========================================================================= #
-  # === cut                                                         (cut tag)
-  #
-  # This method will cut away some part from the DNA string.
-  # ========================================================================= #
-  def cut(i)
-    i = i.to_i
-    @sequence[-i,i] = ''
-    show_dna_sequence
-  end
-
-  # ========================================================================= #
-  # === cutseq
-  #
-  # This can be used to modify the sequence object. It will cut some
-  # segment out from the nucleotide.
-  #
-  # Usage examples:
-  #
-  #   random 30; cutseq 5 8
-  #   random 30; cutseq 5-8
-  #
-  # ========================================================================= #
-  def cutseq(i = [1,3])
-    if i.is_a? Array
-      if i.size == 1 and i.first.is_a? String and i.first.include?('-')
-        i = [i.first.split('-')].flatten
-      end
-      if i.empty? # In this case we will ask the user for input.
-        erev 'No argument was provided. Please input the start nucleotide position next:'
-        start_position = $stdin.gets.chomp.to_i
-        erev 'Next, input the end nucleotide position:'
-        end_position   = $stdin.gets.chomp
-      elsif i.size > 1
-        start_position = i.first
-        end_position   = i.last
-      end
-    end
-    # ======================================================================= #
-    # === Handle +3 relational position given
-    # ======================================================================= #
-    if end_position.is_a? String and end_position.include?('+')
-      end_position = start_position + end_position.delete('+').to_i
-    end
-    n_nucleotides_will_be_deleted = (end_position.to_i - start_position.to_i)+1
-    # ======================================================================= #
-    # Notify the user what we will do next.
-    # ======================================================================= #
-    erev 'Next cutting away '+simp(n_nucleotides_will_be_deleted.to_s)+
-          rev+' nucleotides.'
-    sequence_object?[start_position, end_position] = ''
-  end
-
-  # ========================================================================= #
-  # === cut_with_enzyme
-  # ========================================================================= #
-  def cut_with_enzyme(i)
-    i = i.join(' ').strip if i.is_a? Array
-    pp sequence_object?.cut_with_enzyme(i)
-  end
-
-end; end

data/lib/bioroebe/shell/constants.rb

@@ -1,166 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/constants.rb'
-# =========================================================================== #
-module Bioroebe # === Bioroebe::Shell
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # Right now we will only add the chemistry_paradise gem, if it is available.
-  # ========================================================================= #
-  array_failsave_requires = %w(
-    chemistry_paradise
-  )
-  array_failsave_requires.each {|project|
-    begin
-      require project
-    rescue LoadError; end # Silent rescue.
-  }
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === TRUNCATE_AT_N_ELEMENTS
-  #
-  # If we display nucleotide strings, then by default, these may be very
-  # long. So the following constant will act as a threshold.
-  # ========================================================================= #
-  TRUNCATE_AT_N_ELEMENTS = 2000
-
-  # ========================================================================= #
-  # === VALID_WAYS_TO_EXIT
-  #
-  # All ways to exit will be recorded here.
-  #
-  # If you need to use more ways, simply append to this Array.
-  #
-  # This constant may have to be moved into the bio-shell part eventually.
-  # ========================================================================= #
-  VALID_WAYS_TO_EXIT = %w(
-    quit q exit qq :q qt
-    bye
-    rda
-    r2
-    tq
-    sq
-    exit_program
-    exitprogram
-  )
-
-  # ========================================================================= #
-  # === DEFAULT_PADDING
-  # ========================================================================= #
-  DEFAULT_PADDING = '  ' # This is left-padding.
-
-  # ========================================================================= #
-  # === MAIN_EDITOR
-  #
-  # Which editor to use.
-  # ========================================================================= #
-  if ENV['IS_ROEBE']
-    MAIN_EDITOR = 'bluefish'
-  else # else assume that we may be on windows. 
-    MAIN_EDITOR = 'notepad++.exe'
-  end; MY_EDITOR = MAIN_EDITOR # === MY_EDITOR
-
-  # ========================================================================= #
-  # === HOME_DIRECTORY_OF_USER_X
-  #
-  # Hardcoded path - only useful on my home setup, though.
-  # ========================================================================= #
-  HOME_DIRECTORY_OF_USER_X = '/home/x/'
-
-  # ========================================================================= #
-  # === RUBY_SRC
-  #
-  # Hardcoded. This is only useful on my home system.
-  # ========================================================================= #
-  if ENV['RSRC']
-    RUBY_SRC = "#{ENV['RSRC']}/"
-  else
-    RUBY_SRC = "#{HOME_DIRECTORY_OF_USER_X}programming/ruby/src/"
-  end
-
-  # ========================================================================= #
-  # === RUBY_BIOROEBE
-  #
-  # This allows a user to designate another home directory.
-  # ========================================================================= #
-  if ENV['RUBY_BIOROEBE']
-    BIOROEBE = ENV['RUBY_BIOROEBE'].to_s
-  else
-    BIOROEBE = ENV['HOME']
-  end
-
-  # ========================================================================= #
-  # === BIOSHELL_SAVE_FILE
-  #
-  # Designate the default location for the save-file, a markdown file.
-  # ========================================================================= #
-  if Dir.exist? ::Bioroebe.log_dir?
-    BIOSHELL_SAVE_FILE = "#{::Bioroebe.log_dir?}shell_file.md"
-  else
-    BIOSHELL_SAVE_FILE = '/home/Temp/bioroebe/shell_file.md'
-  end
-
-  # ========================================================================= #
-  # === HOME_DIR
-  #
-  # This probably is not used a lot anymore these days.
-  # ========================================================================= #
-  if RUBY_SRC # This is valid at home.
-    HOME_DIR = "#{ENV['RSRC']}/bioroebe/lib/bioroebe/"
-  else
-    begin
-      home_dir = File.expand_path('~')
-    rescue Exception
-      home_dir = '/root/'
-    end
-    HOME_DIR = home_dir+'.gem/gems/bioroebe-'+
-               Bioroebe.version?.to_s+'/lib/bioroebe/'
-  end
-
-  require 'bioroebe/project/project.rb'
-  # ========================================================================= #
-  # === FILE_USE_SILENT_STARTUP
-  # ========================================================================= #
-  FILE_USE_SILENT_STARTUP = 
-    "#{::Bioroebe.project_base_directory?}shell/configuration/use_silent_startup.yml"
-
-  # ========================================================================= #
-  # === SHALL_WE_DEBUG
-  # ========================================================================= #
-  SHALL_WE_DEBUG = false
-
-  _ = ::Bioroebe.project_yaml_directory?+
-      'default_dna_input.yml' # cat $RUBY_BIO/YAML/default_dna_input.yml
-  # ========================================================================= #
-  # === DEFAULT_DNA_INPUT_YAML_FILE
-  # ========================================================================= #
-  DEFAULT_DNA_INPUT_YAML_FILE = YAML.load_file(_) if File.exist? _
-
-  require 'bioroebe/toplevel_methods/log_directory.rb' # ← Required for: Bioroebe.store_here?
-  # ========================================================================= #
-  # === store_here?
-  #
-  # Where to store output generated by BioRoebe. Should point to a
-  # locally existing directory.
-  # ========================================================================= #
-  def store_here?
-    ::Bioroebe.store_here?
-  end
-
-  # ========================================================================= #
-  # === show_log_dir
-  # ========================================================================= #
-  def show_log_dir
-    e ::Bioroebe.log_dir?
-  end
-
-end; end