bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/shell/gtk.rb

@@ -1,76 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file contains some GTK-related code, which allows us to load up
-# the gtk GUI section of the traditional commandline programs.
-# =========================================================================== #
-# require 'bioroebe/shell/gtk.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === load_gtk3_component_aminoacid_composition
-  # ========================================================================= #
-  def load_gtk3_component_aminoacid_composition
-    require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
-    Bioroebe::GUI::Gtk::AminoacidComposition.run(aminoacid_sequence?)
-  end
-
-  # ========================================================================= #
-  # === load_gtk
-  #
-  # Load my gtk module.
-  # ========================================================================= #
-  def load_gtk
-    begin
-      require 'gtk_paradise/require_gtk3.rb'
-    rescue LoadError; end
-  end
-
-  # ========================================================================= #
-  # === enable_gtk
-  #
-  # This enables gtk.
-  # ========================================================================= #
-  def enable_gtk
-    begin
-      if ENV['IS_ROEBE'].to_s
-        load_gtk
-        # =================================================================== #
-        # Pulling in the controller.rb file is enough to also require the
-        # other GTK-GUI components of the Bioroebe project.
-        # =================================================================== #
-        require 'bioroebe/gui/gtk3/controller/controller.rb'
-      end
-      return ::Bioroebe.controller # This will instantiate a new GTK widget.
-    rescue LoadError => error
-      e 'Failed to load GTK-related files. Showing the specific error next:'
-      pp error
-    end
-  end
-
-  # ========================================================================= #
-  # === start_gtk_controller
-  # ========================================================================= #
-  def start_gtk_controller
-    require 'bioroebe/gui/gtk3/controller/controller.rb'
-    ::Bioroebe.run_gtk_controller
-  end
-
-  # ========================================================================= #
-  # === enable_gtk_section_antisensestrand
-  # ========================================================================= #
-  def enable_gtk_section_antisensestrand
-    require 'bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb'
-    e 'Starting AntiSenseStrand ...'
-    Bioroebe::GUI::Gtk::AntiSenseStrand.start_gui_application
-  end
-
-end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::Shell.new.enable_gtk_section_antisensestrand  
-end

data/lib/bioroebe/shell/history.rb

@@ -1,132 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# Note that the word history means "user-inputted commands", in the
-# context of this file here.
-# =========================================================================== #
-# require 'bioroebe/shell/history.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === add_the_current_user_input_to_the_history
-  # ========================================================================= #
-  def add_the_current_user_input_to_the_history
-    # ======================================================================= #
-    # And add the user-input to the array that keeps track of it. This
-    # has to be done through a specific method, which can do additional
-    # checks before adding the user-input onto the history.
-    # ======================================================================= #
-    add_to_history(user_input?)
-  end
-
-  # ========================================================================= #
-  # === array_history?
-  #
-  # Access the input-history of the bioshell.
-  # ========================================================================= #
-  def array_history?
-    @internal_hash[:array_history]
-  end
-
-  # ========================================================================= #
-  # === add_to_history
-  #
-  # This method should be used consistently whenever content is added onto
-  # the history of the bioshell. Content in this context refers primarily
-  # to user-submitted input.
-  # ========================================================================= #
-  def add_to_history(i = user_input?)
-    if i.is_a? Array
-      i.each {|entry| add_to_history(entry) }
-    else
-      i = i.to_s.chomp
-      unless i.empty?
-        if array_history? and array_history?.respond_to?(:last)
-          last_history_element = array_history?.last # <- On startup there is no history, hence this check as safeguard.
-          if last_history_element
-            unless (last_history_element.strip == i.strip) # Only add if it is new input.
-              array_history? << i
-              if log_user_input?
-                what = "#{i}#{N}"
-                into = "#{bioshell_log_dir?}input_history.yml"
-                append_what_into(what, into)
-              end
-            end
-          else # This clause is valid for new entries.
-            array_history? << i
-          end
-        end
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === log_user_input?
-  #
-  # Delegate to the class method here, via this wrapper-method.
-  # ========================================================================= #
-  def log_user_input?
-    ::Bioroebe::Configuration.log_user_input?
-  end
-
-  # ========================================================================= #
-  # === verbose_save_history_to_file
-  # ========================================================================= #
-  def verbose_save_history_to_file
-    erev 'We will next save the input-history into a file.'
-    save_history_to_file
-  end
-
-  # ========================================================================= #
-  # === save_history_to_file
-  #
-  # This method will save the history to a local file.
-  # ========================================================================= #
-  def save_history_to_file(
-      dataset = array_history?[0..-2]
-    )
-    what = YAML.dump(dataset) # Save all but the last entry. Last entry will be "replay" usually.
-    into = "#{log_dir?}replay_file.yml"
-    write_what_into(what, into)
-  end
-
-  # ========================================================================= #
-  # === last_inputted_command?
-  #
-  # This method will return the last user-inputted element.
-  # ========================================================================= #
-  def last_inputted_command?
-    if array_history? and array_history?.respond_to?(:last)
-      return array_history?.last
-    end
-  end
-
-  # ========================================================================= #
-  # === show_history                                            (history tag)
-  #
-  # Method to show the history.
-  # ========================================================================= #
-  def show_history
-    print_rev
-    cliner {
-      erev "Now showing the #{sfancy('history')}#{rev} of the BioShell:"
-    }
-    array_history = array_history?
-    if array_history.empty?
-      erev 'No input-history was used yet.'
-    else
-      array_history.each_with_index {|item, index|
-        index += 1
-        _ = ' - '.dup # Need to unfreeze the string.
-        _ << ' ' if array_history.size > 9 and index.to_s.size < 2
-        _ << '('+simp((index).to_s)+rev+') '+item.to_s
-        erev _
-      }
-    end
-  end
-
-end; end

data/lib/bioroebe/shell/initialize.rb

@@ -1,217 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/initialize.rb'
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/toplevel_methods/statistics.rb'
-  require 'bioroebe/shell/startup.rb'
-  require 'bioroebe/shell/readline/readline.rb' # ← Needed in this file here.
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      i = ARGV
-    )
-    reset
-    set_commandline_arguments(i)
-    # ======================================================================= #
-    # Intercept some important commandline arguments next.
-    # ======================================================================= #
-    case first?
-    # ======================================================================= #
-    # === bioshell --controller
-    # ======================================================================= #
-    when /^-?-?controller$/i
-      require 'bioroebe/gui/gtk3/controller/controller.rb'
-      ::Bioroebe.run_gtk_controller
-      exit_program
-    # ======================================================================= #
-    # === bioshell --do-not-create-directories-on-startup
-    # === bioshell --do-not-create-directories
-    #
-    # Do not create directories on startup.
-    #
-    # Invocation example:
-    #
-    #   bioshell --do-not-create-directories-on-startup
-    #
-    # ======================================================================= #
-    when /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories(-|_| )?on(-|_| )?startup$/i,
-         /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories$/i
-      @internal_hash[:create_directories_on_startup_of_the_shell] = false
-    # ======================================================================= #
-    # === bioroebe --protein-to-dna
-    #
-    # This entry point will try to start the ruby-gtk3 protein-to-DNA
-    # converting widget.
-    # ======================================================================= #
-    when /^-?-?protein(-|_| )?to(-|_| )?dna$/i
-      require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
-      ::Bioroebe::GUI::Gtk::ProteinToDNA.run_gtk3_widget
-      exit
-    # ======================================================================= #
-    # === bioroebe --help
-    #
-    # This entry-point will quickly show which options are available for
-    # the bioshell.
-    # ======================================================================= #
-    when /^-?-?help$/
-      show_commandline_options
-    # ======================================================================= #
-    # === bioshell --permanently-disable-startup-intro
-    # === bioshell --permanently-disable-startup-notice
-    # === bioshell --permanently-no-startup-intro
-    # === bioshell --permanently-no-startup-info
-    # ======================================================================= #
-    when /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?intro$/,
-         /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?notice$/,
-         /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?intro$/,
-         /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?info$/
-      permanently_disable_startup_intro
-    # ======================================================================= #
-    # === :no_commandline_arguments
-    # ======================================================================= #
-    when :no_commandline_arguments
-      # ===================================================================== #
-      # Simply pass through in this case.
-      # ===================================================================== #
-    # ======================================================================= #
-    # === :exit_gracefully
-    # ======================================================================= #
-    when :exit_gracefully
-      set_exit_gracefully
-    # ======================================================================= #
-    # === bioroebe --silent-startup
-    # ======================================================================= #
-    when /^-?-?silent(-|_)?startup$/,
-         /^-?-?silent$/
-      do_a_silent_startup
-    # ======================================================================= #
-    # === bioroebe --random-aminoacids=33
-    # === bioroebe --n-aminoacids=33
-    # ======================================================================= #
-    when /^-?-?random(-|_)?aminoacids=(.+)$/i,
-         /^-?-?n(-|_)?aminoacids=(.+)$/i
-      n_aminoacids = $2.to_s.dup
-      ::Bioroebe.create_random_aminoacids(n_aminoacids) { :do_report }
-      exit
-    # ======================================================================= #
-    # === bioroebe --rnafold=cdna.MT.fa
-    # ======================================================================= #
-    when /^-?-?rnafold=(.+)$/
-      try_to_run_rnalfold_on_this_file($1.to_s.dup)
-      exit
-    # ======================================================================= #
-    # === bioroebe --fasta=/Depot/Bioroebe/Arabidopsis_thaliana_chromosome_5_sequence.fasta
-    # ======================================================================= #
-    when /^-?-?fasta=(.+)$/
-      this_fasta_file = $1.to_s.dup
-      if File.exist?
-        handle_fasta(this_fasta_file)
-      else
-        e 'No file could be found at `'+sfile(this_fasta_file)+'`.'
-      end
-    # ======================================================================= #
-    # === bioroebe --n-fasta-entries
-    #
-    # Usage example:
-    #
-    #   cd /root/Bioroebe/Downloads/; bioroebe --n-fasta-entries
-    #
-    # ======================================================================= #
-    when /^-?-?n(-|_)?fasta(-|_)?entries$/
-      require 'bioroebe/fasta/display_how_many_fasta_entries_are_in_this_directory.rb'
-      ::Bioroebe::DisplayHowManyFastaEntriesAreInThisDirectory.new
-      exit
-    # ======================================================================= #
-    # === bioroebe --split-this-fasta-file-into-chromosomes=Mus_musculus.GRCm38.ncrna.fa
-    # ======================================================================= #
-    when /^-?-?split(-|_)?this(-|_)?fasta(-|_)?file(-|_)?into(-|_)?chromosomes=(.+)$/i # $6
-      _ = $6.to_s.dup
-      require 'bioroebe/fasta/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb'
-      ::Bioroebe::SplitThisFastaFileIntoChromosomes.new(_)
-      exit
-    # ======================================================================= #
-    # === bioroebe --stats
-    #
-    # This entry-point will show some simple fasta-statistics, from
-    # the current directory.
-    #
-    # Usage example:
-    #
-    #   cd /root/Bioroebe/Downloads/; bioroebe --stats
-    #
-    # ======================================================================= #
-    when /^-?-?stats$/i,
-         /^-?-?statistics$/i,
-         /^-?-?fasta(-|_)?stats$/i
-      require 'bioroebe/fasta/show_fasta_statistics.rb'
-      ::Bioroebe.show_fasta_statistics(Dir['*'])
-      exit
-    # ======================================================================= #
-    # === bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
-    #
-    # This entry point allows us to download a remote program.
-    #
-    # Invocation example:
-    #
-    #   bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
-    #   bioroebe --download ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
-    #
-    # Note that the second variant currently (April 2020) does not work -
-    # let's see if we need it again in the future.
-    # ======================================================================= #
-    when /^-?-?download=(.+)/
-      ::Bioroebe.download($1.to_s.dup)
-    # ======================================================================= #
-    # === bioroebe --sequence=150
-    #
-    # This entry point allows us to use any sequence, on startup.
-    #
-    # Invocation example:
-    #
-    #   bioroebe --sequence=1505
-    #
-    # ======================================================================= #
-    when /^-?-?sequence (.+)/,
-         /^-?-?sequence=(.+)/
-      set_dna($1.to_s.dup, :be_quiet) # Be quiet here when doing the assignment.
-    # ======================================================================= #
-    # === bioroebe --show-exon-statistics-for=/tmp/praktikum/Mouse/chromosome_8/parsed/cdna.8.L100.global.gtf
-    # ======================================================================= #
-    when /^-?-?show(-|_)?exon(-|_)?statistics(-|_)?for=(.+)$/ # === $4
-      ::Bioroebe.show_exon_statistics($4.to_s.dup)
-      exit
-    # ======================================================================= #
-    # === bioroebe --sinatra
-    # ======================================================================= #
-    when /^-?-?sinatra$/i
-      do_start_the_sinatra_interface
-      return
-    end
-    run
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    setup_readline if use_readline?
-    perform_startup_actions # Should come before we show the welcome message.
-    show_welcome_message
-    menu(
-      commandline_arguments?,
-      :be_quiet_if_the_input_was_not_found
-    )
-    enter_main_loop # Enter the main user-input loop here.
-  end
-
-end; end

data/lib/bioroebe/shell/loop.rb

@@ -1,74 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/loop.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === enter_main_loop                                            (loop tag)
-  #
-  # This is the main-loop of the shell.
-  # ========================================================================= #
-  def enter_main_loop
-    exit_from_the_main_loop = false
-    loop {
-      begin
-        read_user_input
-        add_the_current_user_input_to_the_history
-        if @internal_hash[:user_input]
-          unless @internal_hash[:user_input].empty?
-            # =============================================================== #
-            # Pass the user input into the menu next. We will use an
-            # Array for this, as user input such as "ls; random 20" should
-            # also be valid.
-            # =============================================================== #
-            user_input = [ @internal_hash[:user_input] ].flatten
-            user_input.each {|use_this_as_user_input|
-              result_from_the_menu = menu(
-                use_this_as_user_input
-              )
-              case result_from_the_menu
-              when :exit_gracefully
-                say_goodbye
-                exit_from_the_main_loop = true
-              # =============================================================== #
-              # === :break
-              # =============================================================== #
-              when :break
-                case exit_the_shell_how?
-                # ============================================================= #
-                # === :exit_gracefully
-                # ============================================================= #
-                when :exit_gracefully # User wants to exit here.
-                  say_goodbye
-                  exit_from_the_main_loop = true
-                # ============================================================= #
-                # === :instantly
-                # ============================================================= #
-                when :instantly
-                  exit_from_the_main_loop = true
-                end
-                exit_from_the_main_loop = true
-              else
-              end
-            }
-            @internal_hash[:user_input] = nil # And clear it here again.
-          end
-        end
-      # ===================================================================== #
-      # Rescue sigints (aka ctrl-c) and SystemExit.
-      # ===================================================================== #
-      rescue Interrupt, SystemExit
-        e
-      end
-      if exit_from_the_main_loop == true
-        break
-      end
-    }
-  end; alias loop_get_user_input enter_main_loop # Legacy name.
-
-end; end

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