bioroebe 0.10.80

data/lib/bioroebe/shell/chop_and_cut.rb

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+#!/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/colours/colours.rb

@@ -0,0 +1,235 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Shell
+#
+# Colour-related code relevant for the Bioroebe::Shell component will
+# be gathered in this file. 
+# =========================================================================== #
+# require 'bioroebe/shell/colours/colours.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class Shell < ::Bioroebe::CommandlineApplication # === Bioroebe::Shell
+
+  require 'bioroebe/colours/colours.rb'
+
+  # ========================================================================= #
+  # === @default_colour
+  # ========================================================================= #
+  @default_colour = :steelblue
+
+  # ========================================================================= #
+  # === Bioroebe::Shell.set_colour
+  #
+  # Set the default colour here.
+  # ========================================================================= #
+  def self.set_colour(i)
+    @default_colour = i
+  end
+
+  # ========================================================================= #
+  # === use_colours?
+  #
+  # This method will tell us whether we will use colours or whether we
+  # will not. If we use colours, then the colours from the module called
+  # Colours will be used.
+  #
+  # In the past the code allowed for konsole-colours support (KDE konsole)
+  # and simpler terminals without RGB colour support.
+  #
+  # When the bioroebe project was rewritten in April 2020, this was 
+  # dropped. The project now depends on the Colours module, and it
+  # will try to use that project to its full possibilities, including
+  # KDE konsole colours (RGB colours) by default. This will also include
+  # so called "HTML colours", such as :slateblue or :steelblue.
+  # ========================================================================= #
+  def use_colours?
+    @use_colours
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Shell.colour?
+  # ========================================================================= #
+  def self.colour?
+    @default_colour
+  end
+
+  # ========================================================================= #
+  # === remove_trailing_escape_code
+  # ========================================================================= #
+  def remove_trailing_escape_code(i)
+    return i unless use_colours?
+    Colours.remove_trailing_escape_code(i)
+  end
+
+  # ========================================================================= #
+  # === swarn
+  # ========================================================================= #
+  def swarn(i = '')
+    return i unless use_colours?
+    return Colours.swarn(i)
+  end
+
+  # ========================================================================= #
+  # === sfile
+  # ========================================================================= #
+  def sfile(i = '')
+    return i unless use_colours?
+    return Colours.sfile(i)
+  end
+
+  # ========================================================================= #
+  # === sfancy
+  # ========================================================================= #
+  def sfancy(i = '')
+    return i unless use_colours?
+    return Colours.sfancy(i)
+  end
+
+  # ========================================================================= #
+  # === simp
+  # ========================================================================= #
+  def simp(i = '')
+    return i unless use_colours?
+    return Colours.simp(i)
+  end
+
+  # ========================================================================= #
+  # === enable_colours                                           (enable tag)
+  #
+  # We bundle all colour stuff here. Right now we use only the
+  # colour yellow.
+  # ========================================================================= #
+  def enable_colours(
+      be_verbose = true
+    )
+    case be_verbose
+    when :be_quiet, :be_silent
+      be_verbose = false
+    end
+    e 'Enabling colours.' if be_verbose
+    ::Bioroebe.enable_colours
+    @use_colours = true
+    set_default_highlight_colour
+  end
+
+  # ========================================================================= #
+  # === disable_colours                                         (disable tag)
+  # ========================================================================= #
+  def disable_colours
+    ::Bioroebe.disable_colours
+    @use_colours = false
+    @highlight_colour = '' # Use this colour to highlight important sequences.
+    set_prompt
+  end
+
+  # ========================================================================= #
+  # === set_highlight_colour
+  #
+  # You can use this method to highlight different substrings.
+  # ========================================================================= #
+  def set_highlight_colour(
+      i          = :violet,
+      be_verbose = false
+    )
+    if be_verbose == :be_verbose
+      be_verbose = true
+    end
+    i = i.to_s unless i.is_a? String
+    case i
+    when 'random'
+      i = ::Colours.random_html_colour
+    end
+    if i
+      if be_verbose
+        erev "We will use the colour #{sfancy(i.to_s)}#{rev}"\
+             " for highlighting important subsequences."
+      end
+      if ::Colours.respond_to? i
+        i = ::Colours.send(i) # Assume that the user wants to use a KDE Konsole colour.
+      else # else Konsole does not respond to this particular colour.
+        erev "You are trying to use the colour #{i}"
+        erev 'This is not part of the Colours namespace, though. '\
+             'If you are trying to use a'
+        erev 'colour, you may want to pick another colour.'
+      end
+    end
+    @highlight_colour = i
+  end
+
+  # ========================================================================= #
+  # === set_default_highlight_colour
+  # ========================================================================= #
+  def set_default_highlight_colour
+    @highlight_colour = Colours::YELLOW # So to avoid a warning if we were to use the method.
+  end
+
+  # ========================================================================= #
+  # === set_highlight_colour_or_search_for_this_sequence
+  # ========================================================================= #
+  def set_highlight_colour_or_search_for_this_sequence(
+      i, be_verbose = false
+    )
+    # ======================================================================= #
+    # First check if the input consists of only upcased characters.
+    # ======================================================================= #
+    if (i == i.upcase)
+      report_main_sequence(i)
+    else
+      set_highlight_colour(i, be_verbose)
+    end
+  end
+
+  # ========================================================================= #
+  # === colour_scheme_for_aminoacids
+  #
+  # Invocation example:
+  #   caa TTTHGHGHGIHIHRGGGGAATTTTHGHGHGIHIHRGGGGAATTHGHGHGIHIHRGGGGAAATTT
+  # ========================================================================= #
+  def colour_scheme_for_aminoacids(
+      i = aminoacid_sequence?
+    )
+    i = aminoacid_sequence? if i.nil?
+    hash = ::Bioroebe::ColourScheme::Taylor.colours?
+    tokens = i
+    if tokens.is_a? String
+      tokens = tokens.chars
+      tokens = tokens.each_slice(80).to_a
+    end
+    # ======================================================================= #
+    # Get it in chunks of 30.
+    # ======================================================================= #
+    n_chunks = 30
+    chunks = tokens.each_slice(n_chunks).to_a
+    e; chunks.each {|array|
+      array.each {|entry|
+        chars = entry.chars
+        chars.each {|aminoacid|
+          if hash.has_key? aminoacid
+            value = hash[aminoacid]
+            array = HexToRGB[value] # Obtain the R,G,B Array from here.
+            ::Colours.rgb_print(array, aminoacid)
+          else
+            erev "The hash does not include the key #{simp(aminoacid)}#{rev}."
+          end
+        }
+      }
+      e
+    }; e
+  end
+
+  # ========================================================================= #
+  # === highlight_colour?
+  #
+  # The highlight colour is primarily the colour that we will use on
+  # the commandline, for instance, to denote pretty colours.
+  # ========================================================================= #
+  def highlight_colour?
+    @highlight_colour
+  end; alias yellow highlight_colour? # === yellow
+
+end; end

data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml

@@ -0,0 +1 @@
+false

data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml

@@ -0,0 +1 @@
+true

data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml

@@ -0,0 +1 @@
+true

data/lib/bioroebe/shell/configuration/use_silent_startup.yml

@@ -0,0 +1 @@
+use_silent_startup: false

data/lib/bioroebe/shell/constants.rb

@@ -0,0 +1,166 @@
+#!/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