bioroebe 0.10.80 → 0.11.12

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

data/lib/bioroebe/shell/scan_and_parse.rb

@@ -1,135 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/scan_and_parse.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === parse                                                     (parse tag)
-  # ========================================================================= #
-  def parse(i)
-    if i.is_a? Array
-      i = i.join(' ').strip
-    end
-    i = i.dup if i.frozen?
-    i.chop! if i.end_with?('.')
-    # ======================================================================= #
-    # We will parse here based on the file-suffix.
-    # ======================================================================= #
-    case i
-    # ======================================================================= #
-    # === fasta file
-    # ======================================================================= #
-    when /\.fasta$/i,
-         /\.fa$/i
-      parse_fasta_format(i)
-      unless array_fasta?.empty?
-        # =================================================================== #
-        # Assign this dataset next to become the new main sequence.
-        # =================================================================== #
-        opnn; erev "We will now assign this data to #{sfancy('@_')}#{rev}."
-        set_mode :protein if array_fasta?.last.is_protein?
-        assign(array_fasta?.last.sequence)
-      end
-    # ======================================================================= #
-    # === pdb file
-    # ======================================================================= #
-    when /\.pdb$/i
-      parse_this_pdb_file(i)
-    else
-      erev "Not yet handled: #{steelblue(i)}"
-    end
-  end
-
-  # ========================================================================= #
-  # === scan_for_leucine_zippers
-  #
-  # What is a leucine zipper?
-  #
-  #   https://en.wikipedia.org/wiki/Leucine_zipper
-  #
-  # ========================================================================= #
-  def scan_for_leucine_zippers(
-      i = amino_acid_sequence?
-    )
-    if i.nil?
-      i = amino_acid_sequence?
-    end
-    chars = i.chars
-    # ======================================================================= #
-    # We start to count at the first leucine zipper.
-    # ======================================================================= #
-    index = chars.index('L')
-    erev 'The string '+simp(i)+rev+' has these at every 7th step.'
-    print '  ' # Leading indent.
-    (index..chars.size).step(7) {|token|
-      print simp(chars[token]),' '
-    }; e # And a final newline.
-  end
-
-  # ========================================================================= #
-  # === parse_this_gff_file
-  #
-  # Use this method if you wish to parse a .gff or .gff3 file.
-  # ========================================================================= #
-  def parse_this_gff_file(i)
-    if i.is_a? Array
-      i.each {|entry| parse_this_gff_file(entry) }
-    else
-      ::Bioroebe::Parser::GFF.new(i)
-    end
-  end
-
-  # ========================================================================= #
-  # === scan_for_gff_files
-  # ========================================================================= #
-  def scan_for_gff_files
-    results_for_gff_files  = Dir['*.gff']
-    results_for_gff3_files = Dir['*.gff3']
-    unless results_for_gff_files.empty?
-      erev 'There are '+sfancy(results_for_gff_files.size.to_s)+rev+
-           ' .gff files in the current directory.'
-    end
-    unless results_for_gff3_files.empty?
-      erev 'There are '+sfancy(results_for_gff3_files.size.to_s)+
-           ' .gff3 files in the current directory.'
-      erev 'We will simply pass the first entry there into '\
-           'class Bioroebe::Parser::GFF.'
-      parse_this_gff_file(results_for_gff3_files.first)
-    end
-  end
-
-  # ========================================================================= #
-  # === scan_or_parse_for_this_gff_file_or_any_gff_file
-  # ========================================================================= #
-  def scan_or_parse_for_this_gff_file_or_any_gff_file(i)
-    if i.is_a? Array
-      i.each {|entry|
-        if entry.nil?
-          scan_for_gff_files
-        else
-          scan_or_parse_for_this_gff_file_or_any_gff_file(entry)
-        end
-      }
-    else
-      if File.exist? i.to_s
-        parse_this_gff_file(i)
-      else # else scan for any .gff or .gff3 file.
-        scan_for_gff_files
-      end
-    end
-  end
-
-  require 'bioroebe/pdb/parse_pdb_file.rb'
-  # ========================================================================= #
-  # === parse_this_pdb_file
-  # ========================================================================= #
-  def parse_this_pdb_file(i)
-    ParsePdbFile.new(i)
-  end
-
-end; end