bioroebe 0.10.80

data/lib/bioroebe/shell/gtk.rb

@@ -0,0 +1,76 @@
+#!/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/help/class.rb

@@ -0,0 +1,443 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Shell::Help
+#
+# This class will show the help options for the Bioroebe project.
+# =========================================================================== #
+require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
+class Shell
+
+class Help < Base
+
+  # ========================================================================= #
+  # === N_LEFT_PADDING
+  #
+  # How many space characters to pad to the left. Currently 4 ' ' space
+  # tokens.
+  # ========================================================================= #
+  N_LEFT_PADDING = 4
+
+  # ========================================================================= #
+  # === DEFAULT_MIDDLE_PADDING
+  # ========================================================================= #
+  DEFAULT_MIDDLE_PADDING = 25
+
+  # ========================================================================= #
+  # === TITLE
+  #
+  # This constant specifies the title that we will use for the
+  # bioshell help options.
+  # ========================================================================= #
+  TITLE = "#{::Bioroebe.rev}BioShell Help Options:"
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # The first argument determines whether we will use colours or not.
+  #
+  # We can either use KDE Konsole colours, or the regular colours.
+  # ========================================================================= #
+  def initialize(
+      use_colours = true,
+      run_already = true
+    )
+    reset
+    @use_colours = use_colours
+    # ======================================================================= #
+    # The user may pass in a block, which usually means that the user
+    # wants to display only some subcommands.
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      if yielded
+        unless yielded.empty?
+          # ================================================================= #
+          # @what_to_show can limit to show only some help-options.
+          # ================================================================= #
+          @what_to_show = yielded
+          @what_to_show = @what_to_show.first if @what_to_show.is_a? Array
+          if @what_to_show == '?'
+            _  = "#{rev}You can provide an argument such as \"a\" "\
+                 "or \"b\" and we will#{N}".dup
+            _ << 'feedback all help options that start with '\
+                 'this letter.'+N+N
+            _ << 'Example:'+N+N
+            _ << '  help a'+N+N
+            show_help(_)
+            return
+          end
+        end
+      end
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    # ======================================================================= #
+    # === @_
+    # ======================================================================= #
+    @_ = ''.dup # This is the output/result string.
+    # ======================================================================= #
+    # === @middle_padding
+    # ======================================================================= #
+    @middle_padding = DEFAULT_MIDDLE_PADDING # Must be a number.
+    # ======================================================================= #
+    # === @left_padding
+    # ======================================================================= #
+    @left_padding = ' ' * N_LEFT_PADDING # This one will be prepended to the displayed input.
+    # ======================================================================= #
+    # === @what_to_show
+    # ======================================================================= #
+    @what_to_show = :everything
+  end
+
+  # ========================================================================= #
+  # === middle_padding?
+  #
+  # How much to pad in the middle.
+  # ========================================================================= #
+  def middle_padding?
+    @middle_padding
+  end
+
+  # ========================================================================= #
+  # === expanded_middle_padding?
+  #
+  # As middle_padding but returns a String with the properly padded format.
+  #
+  # ========================================================================= #
+  def expanded_middle_padding?
+    ' ' * middle_padding?
+  end
+
+  # ========================================================================= #
+  # === left_padding?
+  # ========================================================================= #
+  def left_padding?
+    @left_padding
+  end
+
+  # ========================================================================= #
+  # === use_konsole?
+  # ========================================================================= #
+  def use_konsole?
+    true
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Shell::Help[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === build_help_string
+  #
+  # Called from within the run() method.
+  # ========================================================================= #
+  def build_help_string
+    # ======================================================================= #
+    # Add the title first
+    # ======================================================================= #
+    add TITLE+N # Add a newline to start with.
+    # ======================================================================= #
+    # a tag
+    # ======================================================================= #
+    add '(aasequence?) to show the amino acid sequence assigned'
+    add '(align) to align two difference sequences to one another, '\
+        'such as in "align 1 3"'
+    add '(align_ORFS) to align all ORFs in the given main DNA sequence'
+    add '(analyze_sequence) to analyze the main sequence for '\
+        'special sequences'
+    add '(aminoacid?) to show the long name of an aminoacid. '\
+        'Usage: aminoacid? K'
+    add '(ana)lyze to analyze a given aminoacid string. Will '\
+        'show percentage of DNA used (if you use dna_analyze).'
+    add '(aminoacids?) to show information about the aminoacids'
+    add
+    # ======================================================================= #
+    # === b tag
+    # ======================================================================= #
+    add '(b)losum ','show blosum matrix (use e. g. "blosum62" to '\
+        'show the values for this blosum)'
+    add '(backtrack) translate into the most likely '\
+        'DNA sequence, from the given aminoacid sequence'
+    add '(bparse) to show all available genomes in the bio_lang file'
+    add
+    # ======================================================================= #
+    # === c tag
+    # ======================================================================= #
+    add '(cat) to display the content of a file'
+    add '(chop) to chop off some nucleotides from the end'
+    add '(CpG?) to show which CpG islands may exist'
+    add '(codon) to translate a RNA Codon into the proper Aminoacids'
+    add '(codon?) similar to the above ^^^ but limited to only one '\
+        'input-codon at a time'
+    add '(codon_usage) to show the codon usage of your '\
+        'DNA string'
+    add '(codontable) to show the codon table'
+    add '(codontables) to show all registered codon tables'
+    add '(cola) to colourize a given aminoacid'
+    add '(compact) to compact a FASTA (.fa / .fasta) file, '\
+        'into a single line in the file'
+    add '(complement) to find the complementary sequence of a '\
+        'DNA strand'
+    add '(cscheme) to colourize the nucleotides in the main '\
+        'nucleotide colour scheme'
+    add
+    # ======================================================================= #
+    # === d tag
+    # ======================================================================= #
+    add '(discover_all_palindromes) to discover all palindromes (min: 4, max: 10)'
+    add
+    # ======================================================================= #
+    # === f tag
+    # ======================================================================= #
+    add '(files?) to get an overview where some various '\
+        'important files are kept locally'
+    add '(fasta) to parse some ', 'FASTA data'
+    add '(find) to find a subsequence. Example: find ATG'
+    add '(fr)ameshift to ', 'perform a frameshift (add '\
+        'argument like 1, 2, 3)'
+    add '(first) change the first nucleotide to another one'
+    add '(find_gene) to find a gene in the given sequence'
+    add
+    # ======================================================================= #
+    # === g tag
+    # ======================================================================= #
+    add '(gc_content) to calculate the GC content of a sequence '\
+        'sequence (They will cut at that sequence. "rest?" '\
+        'is an alias.)'
+    add '(gff3?) to read and handle .gff or .gff3 files, through the '\
+        'parser Bioroebe::Parser::GFF'
+    add
+    # ======================================================================= #
+    # === h tag
+    # ======================================================================= #
+    add '(h)istory to show the ', 'input history'
+    add
+    # ======================================================================= #
+    # === l tag
+    # ======================================================================= #
+    add '(load) to load the main string from a file'
+    add '(list) age to list the age of different organisms'
+    add '(ll) to get a listing of local files and directories'
+    add
+    # ======================================================================= #
+    # === m tag
+    # ======================================================================= #
+    add '(ma)ss_weight to calculate weight of a Protein (Input must '+
+        'be Aminoacids)'
+    add '(mmasse) to display the molecular mass of an Aminoacid'
+    add '(mt) ', 'to calculate the melting temperature'
+    add '(multi_line) ',
+        'to assign a FASTA file with several lines'
+    add
+    # ======================================================================= #
+    # === n tag
+    # ======================================================================= #
+    add '(nucleotides_table?) to show the molecular mass of '\
+        'the Nucleotides'
+    add
+    # ======================================================================= #
+    # === o tag
+    # ======================================================================= #
+    add '(orf?) ','to seek for ORFs in our target sequence'
+    if ::Bioroebe.is_on_roebe? # Only relevant for my home system.
+      add '(open) to open all my relevant files in an editor'
+    end
+    add
+    # ======================================================================= #
+    # === p tag
+    # ======================================================================= #
+    add '(palindrome) to generate a Palindrome. Input the length of the '\
+        'palindrome which should be an even number such as "6" or "12".'
+    add '(parse_fasta) to parse a fasta file. pfasta is an '\
+        'alias. If input is omitted, we try to '\
+        'find a fasta file in the working directory.'
+    add '(pathways) to show metabolic pathways'
+    add '(phosphorylation_sites?) to find phosphorylation sites '\
+        'in the aminoacid sequence'
+    add '(pitch) to show how long an alpha helix is (optionally '\
+        'pass the amount of aminoacids into it)'
+    add '(print_table) to print a useful mnemo-table'
+    add '(pun)net ', 'show a punnet square'
+    add '(pub)med to ', 'visit pubmed'
+    add
+    # ======================================================================= #
+    # === q tag
+    # ======================================================================= #
+    add '(q) to exit/quit' # should always be last.
+    e
+    # ======================================================================= #
+    # === r tag
+    # ======================================================================= #
+    add '(ra)ndom to generate random DNA or random '\
+        'Aminoacids (the latter when given two arguments)'
+    add '(rest)riction sites to show some restriction sites'
+    add '(rest) <sequence> to find restriction sites within a given'
+    add '(replay) to replay (or save) input-history' 
+    add '(reverse) to simply display the reversed main DNA sequence '\
+        'presently in use'
+    add '(reverse!) to not only display the reversed main DNA sequence '\
+        'presently in use, but to also assign it as the new DNA sequence'
+    # ======================================================================= #
+    # === s tag
+    # ======================================================================= #
+    add '(save) to save the main string to a file'
+    add '(seq)uence to assign a DNA sequence to use '
+    add '(sscompare) to ', 'compare two different strings, '\
+        'with + and . characters - or | rather than +'
+    add '(shuffle) to re-arrange the nucleotide string'
+    add '(shine) to search for a ', colourize: 'Shine-Dalgarno Sequence'
+    add '(sub)string to find the longest common substring of two strings'
+    add '(shorten_aminoacid) to shorten a 3 letter Aminoacid to '\
+        '1 letter'
+    add '(showorf) will show all ORFs in the given DNA sequence'
+    add '(split) to split the sequence into chunks of n size, such as: split 3'
+    add '(stop?) will show all STOP codons in the given '\
+        'sequence'
+    add
+    # ======================================================================= #
+    # === t tag
+    # ======================================================================= #
+    add '(tata?, TATA?) to find a TATA consensus sequence'
+    add '(dna_translate) to give out the complementary '\
+        'DNA sequence. Example: dna_translate GCATCTGCATTCGA' # This line belongs to dna_translate
+    add '(to_protein) convert a DNA sequence to an Amino Acid Sequence.'
+    add '(taxonomy) to list some taxonomy thingies'
+    add '(to_rna) convert', 'DNA to RNA'
+    add '(to_dna) convert', 'RNA to DNA'
+    add '(t)ranslate to translate aminoacids into their long '\
+        'form (i.e. A -> Alanin)'
+    add
+    # ======================================================================= #
+    # === u tag
+    # ======================================================================= #
+    add '(upcase) to upcase the main sequence'
+    add '(uncola) to uncolourize an amino acid again'
+    add
+    add 'Note that you can also simply input the name of an amino acid '\
+        'and we will'
+    add 'feedback its -R group.'
+    add
+    # ======================================================================= #
+    # === Special instructions
+    # ======================================================================= #
+    add 'You can add and remove nucleotides in a simple manner, via +3 '\
+        'or -3, too.'
+  end
+
+  # ========================================================================= #
+  # === add                                                         (add tag)
+  # ========================================================================= #
+  def add(
+      i           = '',
+      append_this = nil
+    )
+    original_append_this = nil
+    original_append_this = append_this.dup if append_this
+    # ======================================================================= #
+    # Handle subcommands next.
+    # ======================================================================= #
+    unless @what_to_show == :everything
+      # ===================================================================== #
+      # Note that @what_to_show can be 'a' but also 'a-d', so
+      # we must check whether it has a '-' token.
+      # ===================================================================== #
+      _ = @what_to_show # Keep track of what to show here.
+      if _.include? '-' # Check for a "range"-like input here.
+        splitted       = _.split('-')
+        start_position = splitted.first
+        end_position   = splitted.last
+        range = (start_position .. end_position).to_a
+        unless range.any? {|entry| i.delete('(').strip.start_with? entry }
+          return
+        end
+      else
+        unless i.delete('(').strip.start_with? _
+          return # ^^^ We exclude all entries that do NOT start with this character.
+        end
+      end
+    end unless i.include? TITLE
+    # ======================================================================= #
+    # === Handle input that includes ()
+    # ======================================================================= #
+    if i.include? '(' # Assume that we must parse it.
+      # ===================================================================== #
+      # First pad it.
+      # ===================================================================== #
+      regex_to_use = /^(\(.+?\)\w*)/ # See: http://rubular.com/r/AbZ0fGRTvd
+      splitted = i.split(regex_to_use).reject(&:empty?)
+      splitted[0] = splitted[0].ljust(middle_padding?)
+      # ===================================================================== #
+      # If the second half is too long, we will insert a newline
+      # ===================================================================== #
+      if splitted[1].size > 75
+        splitted[1] = splitted[1].gsub(/(.{1,75})(\s+|$)/,
+                                       "\\1\n#{left_padding?} #{expanded_middle_padding?}").rstrip
+      end
+      i = splitted.join
+      if use_colours?
+        i.gsub!(regex_to_use, burlywood('\\1')+rev)
+      end
+      i.prepend(@left_padding)
+    end
+    # ======================================================================= #
+    # Next, colourize the input if the user requested it so.
+    # ======================================================================= #
+    if append_this
+      if append_this.is_a?(Hash)
+        if append_this.has_key? :colourize
+          # ================================================================= #
+          # Use Konsole colours next.
+          # ================================================================= #
+          append_this = append_this.delete(:colourize)
+          append_this = slateblue(append_this) if @use_colours
+          i << append_this
+        end
+      end
+      unless i.end_with? ' '
+        append_this = append_this.dup if append_this.frozen?
+        append_this.prepend(' ')
+      end
+      if use_colours?
+        i << sfancy(append_this)
+      else
+        i << append_this
+      end unless original_append_this.is_a? Hash
+    end
+    @_ << i+N # This is mostly just an append-action. We will add a newline too.
+  end
+
+  # ========================================================================= #
+  # === show_help
+  #
+  # This method will show the help subsection for the BioShell.
+  # ========================================================================= #
+  def show_help(display_this = @_)
+    e "#{display_this}#{N}"
+  end; alias display_result show_help # === display_result
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    build_help_string
+    show_help
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::Shell::Help.new { ARGV }
+end

data/lib/bioroebe/shell/help/help.rb

@@ -0,0 +1,25 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/shell/help/help.rb'
+# =========================================================================== #
+require 'bioroebe/shell/help/class.rb'
+
+module Bioroebe
+
+class Shell < ::Bioroebe::CommandlineApplication
+
+  # ========================================================================= #
+  # === show_help                                          (help tag, he tag)
+  #
+  # This is a wrapper over the class Help. For more documentation, please
+  # look at the class Bioroebe::BioShell::Help.
+  # ========================================================================= #
+  def show_help(
+      optional_arguments = nil
+    )
+    ::Bioroebe::Shell::Help.new(use_colours?) { optional_arguments }
+  end
+
+end; end

data/lib/bioroebe/shell/history.rb

@@ -0,0 +1,132 @@
+#!/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