bioroebe 0.10.80

data/lib/bioroebe/taxonomy/interactive.rb

@@ -0,0 +1,1933 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Taxonomy::Interactive
+#
+# This bundles together various taxonomy-related code portions.
+#
+# This file can be used interactively. It provides the central
+# point of entry for the taxonomy module.
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module Taxonomy
+
+class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy::Interactive
+
+  require 'bioroebe/taxonomy/shared.rb'
+  require 'bioroebe/taxonomy/class_methods.rb'
+  require 'bioroebe/taxonomy/info/check_available.rb'
+  require 'bioroebe/taxonomy/info/is_dna.rb'
+  require 'bioroebe/taxonomy/info/info.rb'
+  require 'bioroebe/taxonomy/help/help.rb'
+  require 'bioroebe/taxonomy/menu.rb'
+
+  begin
+    require 'readline' # Enable readline here, if available.
+  rescue LoadError; end
+
+  begin
+    require 'cliner' # Needed in this file here.
+  rescue LoadError; end
+
+  begin
+    require 'stat_file'
+  rescue LoadError; end
+
+  include Taxonomy # Add the main namespace here.
+  include Taxonomy::Shared
+  if Object.const_defined?(:Roebe) and
+     Roebe.const_defined?(:SqlParadise)
+    include ::Roebe::SqlParadise
+  end
+
+  # ========================================================================= #
+  # The SQL-relevant parts come next.
+  # ========================================================================= #
+  begin
+    require 'roebe/sql_paradise'
+    Roebe::SqlParadise::Commands.set_temp_dir ::Bioroebe.log_dir?
+  rescue LoadError; end
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === FASTA_SQL
+  # ========================================================================= #
+  FASTA_SQL = AUTOGENERATED_SQL_FILES_DIR+'fasta.sql'
+
+  # ========================================================================= #
+  # === BE_VERBOSE
+  #
+  # Constants for this class here.
+  # ========================================================================= #
+  BE_VERBOSE = true  # This can be disabled via 'silent' from the commandline.
+  
+  # ========================================================================= #
+  # === USE_COLOURS
+  #
+  # Whether to have colourized output or not.
+  # ========================================================================= #
+  USE_COLOURS = true  # This can be disabled via 'nocolours'.
+
+  # ========================================================================= #
+  # === NO_HELP
+  # ========================================================================= #
+  NO_HELP     = false # This can be disabled via 'nohelp'.
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # The first argument are the commandline arguments.
+  # ========================================================================= #
+  def initialize(
+      optional_commandline_arguments = nil,
+      run_already                    = true
+    )
+    reset
+    set_commandline_arguments(
+      optional_commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace      = NAMESPACE
+    # ======================================================================= #
+    # === @be_verbose
+    # ======================================================================= #
+    @be_verbose     = BE_VERBOSE
+    # ======================================================================= #
+    # === @use_colours
+    # ======================================================================= #
+    @use_colours    = USE_COLOURS
+    # ======================================================================= #
+    # === @no_help
+    # ======================================================================= #
+    @no_help        = false
+    # ======================================================================= #
+    # === @run_standalone
+    # ======================================================================= #
+    @run_standalone = true
+  end
+
+  # ========================================================================= #
+  # === get                                                         (get tag)
+  #
+  # Get something from the localome table with this method.
+  # ========================================================================= #
+  def get(
+      i,
+      use_this_id = nil
+    )
+    i = i.to_s
+    _ = "SELECT #{i} from fasta".dup
+    _ << " where taxid='"+use_this_id.to_s+"';" if use_this_id
+    if i.include? 'taxid' # Sort by taxid in this case.
+      _ << ' ORDER BY taxid'
+    end
+    _ << ';'
+    result = run_sql(_, :silent, :tuples)
+    return result
+  end
+
+  # ========================================================================= #
+  # === taxtree
+  #
+  # Obtain the taxtree, then display it. Input to this should be the 
+  # Taxonomy ID. We will first check the localome table, then query
+  # from the two ncbi tables.
+  #
+  # To test this method, try:
+  #
+  #   taxtree 106583
+  #   taxtree 77166
+  #
+  # ========================================================================= #
+  def taxtree(i)
+    i = i.to_s
+    e 'The lineage for Taxonomy ID '+simp(i)+' is as follows:'
+    if has? i # Ok, the localome table has this entry.
+      lineage_ids = get('lineage_ids', i).strip.split('->').map(&:strip)
+    else
+      lineage_ids = return_full_lineage_of(i)
+      lineage_ids.map! {|entry| entry[0]}
+    end
+    report_tree_lineage(lineage_ids)
+  end
+
+  # ========================================================================= #
+  # === report_tree_lineage
+  #
+  # This method expects an Array as input, which contains all the IDs
+  # that we will report in a tree (hence the name tree here).
+  # ========================================================================= #
+  def report_tree_lineage(i)
+    i.each_with_index {|entry, index|
+      padding = ' ' * (index+1)
+      e padding+entry.to_s
+    }
+  end
+
+  # ========================================================================= #
+  # === remove_taxid_from_localome_table
+  #
+  # This method will remove a TaxID from the localome table.
+  # ========================================================================= #
+  def remove_taxid_from_localome_table(i)
+    i = i.to_s
+    if has_id? i
+      # Ok we found an entry, thus we can remove it now:
+      run_sql "
+        DELETE FROM fasta
+        WHERE taxid='"+i+"';
+      "
+      if be_verbose?
+        e 'Removed entry '+simp(i)+
+          ' (Taxonomy ID) from the localome (fasta) table.'
+      end
+    else
+      e "Could not find TaxID #{simp(i)}." if be_verbose?
+    end
+  end
+
+  # ========================================================================= #
+  # === update_local_localomes
+  #
+  # Update the local collection. This will overwrite the old dataset
+  # completely, so be careful when using this.
+  # ========================================================================= #
+  def update_local_localomes
+    show_current_time
+    create_fasta_table # Get in a new, fresh table.
+    _ = get_all_info_entries_with_tax_id
+    show_current_time
+    _.each {|entry|
+      e 'Next working on '+sfile(entry)
+      create_sql_file_from_local_fasta_entry(entry)
+    }
+    report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
+    old_time = @time
+    show_time_now # Show the end time.
+    new_time = @time
+    difference = Time.parse(new_time) - Time.parse(old_time)
+    report_how_long_it_took_us(difference, 'localome table')
+  end
+
+  # ========================================================================= #
+  # === try_to_display_the_status
+  # ========================================================================= #
+  def try_to_display_the_status(i = nil)
+    if i # if an argument was provided
+      StatFile.new(i) if Object.const_defined?(:StatFile)
+    else
+      Taxonomy.status?
+      Info.status
+    end
+  end
+
+  # ========================================================================= #
+  # === generate                                               (generate tag)
+  #
+  # This method can be used to generate nodes or names .sql files.
+  # These .sql files will be generated in the TEMP_DIR, which
+  # at the time of writing this documentation is at
+  # /tmp/robert.
+  # ========================================================================= #
+  def generate(i)
+    i = i.to_s
+    case i # case tag
+    when 'nodes','names','nodes.sql','names.sql'
+      i.gsub!(/\.sql/,'')
+      menu(i) # Delegate towards the main menu here.
+    end
+  end; alias create generate # === create
+
+  # ========================================================================= #
+  # === show_all_eukarya
+  # ========================================================================= #
+  def show_all_eukarya(
+      optional_show_path = false
+    )
+
+    e 'We found these Eukaryota in the localomes Database:'+N+N
+    if optional_show_path.is_a? String
+      _ = select_name_and_tax_id_and_lineage_ids_and_path # 0,1,2,3
+    else
+      _ = select_name_and_tax_id_and_lineage_ids
+    end
+
+    n_entries = _.split(N).size
+    result  = []
+    counter = 0
+    _.split(N).each_with_index {|entry|
+      splitted = entry.split('|')
+      lineage = splitted[2]
+      if lineage =~ / #{Eukaryota_Taxonomy_ID} /
+        scientific_name = splitted.first.strip
+        counter += 1
+        result = simp(counter.to_s)+') '+scientific_name+
+                 ' ('+sfancy('TaxID')+': '+splitted[1].to_s.strip+')'
+        if optional_show_path.is_a? String
+          result << (' Path: '+splitted[3]).ljust(40) # Append the path.
+        end
+        e result
+        result << scientific_name
+      else # debug
+      end
+    }
+    e N+N+'Out of '+sfancy(n_entries.to_s)+' registered '\
+      'entries in total in the localomes database,'
+    e sfancy(result.size.to_s)+' belong to Eukaryota (the Taxonomy '\
+      'ID of Eukaryota is '+sfancy(Eukaryota_Taxonomy_ID.to_s)+').'
+    array = _.split(N).map {|entry| entry.split('|')[1].strip}
+    report_total_amount_of_proteomes(array)
+  end
+
+  # ========================================================================= #
+  # === query_from_localome_table
+  #
+  # This will display the result as well.
+  # ========================================================================= #
+  def query_from_localome_table(i)
+    e get(i)
+  end
+
+  # ========================================================================= #
+  # === disable_colours
+  # ========================================================================= #
+  def disable_colours
+    @use_colours = false
+  end
+
+  # ========================================================================= #
+  # === try_to_show_when_the_last_update_has_happened
+  # ========================================================================= #
+  def try_to_show_when_the_last_update_has_happened
+    e cat(SAVE_FILE) if File.exist? SAVE_FILE
+  end
+
+  # ========================================================================= #
+  # === query_whether_we_have_this_id(i)
+  #
+  # We query whether we have a specific ID or whether we don't.
+  # ========================================================================= #
+  def query_whether_we_have_this_id(i)
+    if has_id? i
+      e 'We do have the id '+simp(i.to_s)+'.'
+    else
+      e 'We do not have the id '+simp(i.to_s)+'.'
+    end
+  end
+
+  # ========================================================================= #
+  # === report_lineage_ids_and_lineage_scientific_name
+  # ========================================================================= #
+  def report_lineage_ids_and_lineage_scientific_name(i)
+    e 'The lineage of all parent ids for Tax ID '+sfancy(i)+' is: '+
+    @lineage_ids+', and in long form '+@lineage_scientific_name
+  end
+
+  # ========================================================================= #
+  # === drop_nodes_table
+  # ========================================================================= #
+  def drop_nodes_table(be_verbose = true)
+    run_sql POSTGRE_DROP_NODES_COMMAND, be_verbose
+  end
+
+  # ========================================================================= #
+  # === drop_names_table
+  # ========================================================================= #
+  def drop_names_table(be_verbose = true)
+    run_sql POSTGRE_DROP_NAMES_COMMAND, be_verbose
+  end
+
+  # ========================================================================= #
+  # === show_scientific_name_of
+  # ========================================================================= #
+  def show_scientific_name_of(i)
+    result = get_scientific_name_of(i).to_s
+    if result.empty?
+      e 'We tried to find a Tax ID but we got no result.'
+      e 'Are you able to connect to the postgresql-database?'
+      e 'Perhaps this Tax ID does not exist.'
+    else
+      e 'The scientific name of Tax ID '+lightblue(i.to_s)+
+        ' is: '+simp(result)
+    end
+  end
+
+  # ========================================================================= #
+  # === lupdate                                                  (update tag)
+  #
+  # This is the general way to update something. "update everything' is
+  # the most important component - it will update everything, including
+  # the localomes entry.
+  # ========================================================================= #
+  def lupdate(i = :ncbi)
+    i = i.to_s
+    case i
+    when 'all','everything','both'
+      update_ncbi_database
+      update_local_localomes
+      update_lineage
+    # ======================================================================= #
+    # === ncbi_database
+    # ======================================================================= #
+    when /^ncbi(-|_| )?database$/, 'ncbi','1',
+         'update_ncbi'
+      update_ncbi_database
+    # ======================================================================= #
+    # === localomes
+    # ======================================================================= #
+    when 'localomes','local','loc','localome','2',
+         'fasta','database','databases'
+      update_local_localomes # This will overwrite the old dataset completely, be careful.
+    # ======================================================================= #
+    # === lineage
+    # ======================================================================= #
+    when 'lineage','lin','li'
+      update_lineage
+    else
+      e 'Not sure what to update - the input was '+sfancy(i.to_s)
+    end
+  end
+
+  # ========================================================================= #
+  # === disable                                                 (disable tag)
+  # ========================================================================= #
+  def disable(i)
+    case i.to_sym
+    when :colours
+      disable_colours
+    end
+  end
+
+  # ========================================================================= #
+  # === query_localome_including_path
+  #
+  # We also show the path here.
+  # ========================================================================= #
+  def query_localome_including_path
+    e 'These organisms are available locally:'
+    result = run_query(
+      'select name,taxid,path from fasta ORDER BY taxid;',
+      false, :tuples)
+    splitted = result.split(N)
+    splitted.each_with_index {|entry, index|
+      index += 1
+      inner_splitted = entry.split('|')
+      name = inner_splitted[0].strip.ljust(40)
+      path = 'the local path is at '+N+'       '+sfancy(inner_splitted[2])
+      e ' ('+index.to_s+') '+name+' -> TaxID: '+
+        simp(inner_splitted[1].strip)+', '+path
+    }
+    report_n_registered_organisms_in_localome(splitted.size)
+  end; alias localome? query_localome_including_path # === localome?
+
+  # ========================================================================= #
+  # === report_n_registered_organisms_in_localome
+  # ========================================================================= #
+  def report_n_registered_organisms_in_localome(i)
+    e 'We have a total of '+sfancy(i.to_s)+' organisms '+
+      'registered in the localome (== fasta) table.'
+  end
+
+  # ========================================================================= #
+  # === drop_nodes_and_names_database_tables
+  # ========================================================================= #
+  def drop_nodes_and_names_database_tables(be_verbose = true)
+    drop_nodes_table(be_verbose)
+    drop_names_table(be_verbose)
+  end
+
+  # ========================================================================= #
+  # === query_localome
+  #
+  # Query the localome table.
+  # ========================================================================= #
+  def query_localome
+    e 'These organisms are available locally:'
+    result = run_query(
+      'select name,taxid from fasta ORDER BY taxid;',
+    false, :tuples)
+    splitted = result.split(N)
+    splitted.each_with_index {|entry, index|
+      index += 1
+      inner_splitted = entry.split('|')
+      name = inner_splitted[0].strip.ljust(30)
+      e ' ('+index.to_s+') '+name+' -> TaxID: '+
+        simp(inner_splitted[1].strip)
+    }
+    report_n_registered_organisms_in_localome(splitted.size)
+  end
+
+  # ========================================================================= #
+  # === update_ncbi_database
+  # 
+  # We will update the NCBI Taxonomy database with this method. This
+  # includes a download, extracting it, generating the .sql files,
+  # and then populating the postgresql database.
+  # ========================================================================= #
+  def update_ncbi_database
+    # show_time_now # Show the start time. No longer needed as the next call does that.
+    download :ncbi # Defined in this file here.
+    if be_verbose?
+      e 'We will update the local postgre NCBI Table '\
+        'now (this may take about one hour in total):'
+    end
+    # This will generate names.sql and nodes.sql.
+    menu 'names'
+    menu 'nodes'
+    # Next, connect to the postgre database and read in the auto-generated dumps:
+    if be_verbose?
+      e 'We will next load this dataset into the Database.'
+      e 'First, dropping the old table entries in the Postgresql database '
+      e 'via the DROP TABLE command:'
+    end
+    drop_nodes_and_names_database_tables
+    nodes_size = File.size(NODES_SQL).to_s
+    names_size = File.size(NAMES_SQL).to_s
+    e 'Next we will populate the two tables with '+sfancy('names.sql')+
+      ' (Filesize: '+names_size+') and '+sfancy('nodes.sql')+
+      ' (Filesize: '+nodes_size+') file.'
+    e 'This may take a while, possibly about an hour, so '\
+      'please remain patient.'
+    read_in_names_and_nodes_sql_files
+    e 'Nota bene: the above commands can only work if psql '\
+      'is in your $PATH.'
+    e 'If it did not work, please check and see first '\
+      'whether your $PATH variable is proper.'
+    e N+'We will display the content of the $PATH variable '\
+      'now: '+sfancy(ENV['PATH'])
+    old_time = @time
+    show_time_now # Show the end time.
+    new_time = @time
+    difference = Time.parse(new_time) - Time.parse(old_time)
+    report_how_long_it_took_us(difference)
+  end; alias update_database update_ncbi_database
+
+  # ========================================================================= #
+  # === report_lineage_of
+  # ========================================================================= #
+  def report_lineage_of(f)
+    obtain_full_lineage_for(f)
+    report_lineage_ids_and_lineage_scientific_name(f)
+    e
+    generate_html_links_for( @lineage_ids.split(' -> ') )
+  end
+
+  # ========================================================================= #
+  # === report_how_long_it_took_us
+  #
+  # The input to this method should be the number of seconds, i.e.
+  # 60 seconds.
+  # ========================================================================= #
+  def report_how_long_it_took_us(
+      i = 0,
+      title_of_table = 'NCBI-based taxonomy table'
+    )
+    n_minutes = (i.to_f / 60.0).to_s
+    if n_minutes.size > 4
+      n_minutes = n_minutes[0,4]
+    end
+    e 'Updating the '+title_of_table+' took us '+
+      sfancy(i.to_s)+' seconds (= '+n_minutes.to_s+' minutes).'
+  end
+
+  # ========================================================================= #
+  # === read_sql
+  #
+  # Read in sql into the Postgre Database.
+  # ========================================================================= #
+  def read_sql(i = :fasta)
+    set_pgpassword
+    case i
+    # ======================================================================= #
+    # === :fasta
+    # ======================================================================= #
+    when :fasta
+      if at_home? # On my home system.
+        cmd = POSTGRE_LOGIN_COMMAND_HOME
+      else
+        cmd = POSTGRE_LOGIN_COMMAND
+      end
+      cmd << ' -f '+FASTA_SQL
+      e 'Next, we will read in from '+FASTA_SQL if be_verbose?
+      esystem cmd
+      e 'Done reading in the dataset!' if be_verbose?
+    end
+  end
+
+  # ========================================================================= #
+  # === search_in_localomes
+  #
+  # This will search in localomes.
+  # ========================================================================= #
+  def search_in_localomes(i = 'Blastocystis hominis')
+    if be_verbose?
+      e 'We will now try to search the fasta table for `'+sfancy(i)+'`.'
+    end
+    _ = "select name,modification_time FROM fasta WHERE name LIKE '%"+i+"%' LIMIT 3;"
+    result = run_sql_query(_, true)
+    return result
+  end
+
+  # ========================================================================= #
+  # === open_project_files                                         (open tag)
+  #
+  # This method will open the various project files in the editor.
+  # ========================================================================= #
+  def open_project_files
+    ARRAY_PROJECT_FILES.each {|entry|
+      _ = (editor?+' '+PROJECT_BASE_DIR+'lib/taxonomy/'+entry.to_s).squeeze '/'
+      esystem _
+    }
+  end
+
+  # ========================================================================= #
+  # === do_run_connected
+  # ========================================================================= #
+  def do_run_connected
+    @run_standalone = false
+  end; alias run_connected do_run_connected # === run_connected
+
+  # ========================================================================= #
+  # === use_colours?
+  # ========================================================================= #
+  def use_colours?
+    @use_colours
+  end
+
+  # ========================================================================= #
+  # === create_default_directories
+  # ========================================================================= #
+  def create_default_directories
+    e 'Creating some directories now.'
+    array_create_these_directores = %w(
+      /data/ncbi/taxonomy/
+      /tmp/robert/autogenerated_sql_files/
+      /data/curated/sequences/localome/
+      /data/curated/sequences/aa/
+      /data/curated/sequences/nt/
+      /data/curated/sequences/INFO/
+      /data/curated/sequences/localome/incoming/
+    ); pp array_create_these_directores
+    mkdir(array)
+  end
+
+  # ========================================================================= #
+  # === user_input?
+  # ========================================================================= #
+  def user_input?
+    @user_input
+  end
+
+  # ========================================================================= #
+  # === create_dirs
+  # ========================================================================= #
+  def create_dirs(be_verbose = false)
+    case be_verbose
+    when :be_verbose
+      be_verbose = true
+    end
+    if be_verbose
+      opnn; e 'We will create the temp directory and the download directory next.'
+    end
+    ensure_that_temp_dir_exists
+    ensure_that_download_dir_exists
+  end
+
+  # ========================================================================= #
+  # === try_to_show_dependencies
+  #
+  # Show the dependencies of the Taxonomy Module. This will tell us which
+  # dependencies we have to satisfy.
+  # ========================================================================= #
+  def try_to_show_dependencies
+    _ = return_dependencies
+    if File.exist? _
+      e 'The Taxonomy Module depends on these Ruby Gems:'+N+N
+      cat _
+    else
+      e 'We could not find a file at position `'+sfile(_)+'`.'
+    end
+  end
+
+  # ========================================================================= #
+  # === show_login_information
+  # ========================================================================= #
+  def show_login_information
+    e 'The login information is stored in the file '
+    e
+    e '  '+sfile(PROJECT_BASE_DIR2+'databases/postgresql_login_command.rb')
+    e
+    show_port # Show the port as well here.
+  end
+
+  # ========================================================================= #
+  # === return_shared_code
+  # ========================================================================= #
+  def return_shared_code
+    return PROJECT_BASE_DIR2+'shared/shared'
+  end
+
+  # ========================================================================= #
+  # === return_gemspec_file
+  #
+  # We return the main taxonomy.gemspec file here.
+  # ========================================================================= #
+  def return_gemspec_file
+    return PROJECT_BASE_DIR+'taxonomy.gemspec'
+  end
+
+  # ========================================================================= #
+  # === return_login_file
+  # ========================================================================= #
+  def return_login_file
+    return PROJECT_BASE_DIR2+'postgresql_login_command.rb'
+  end
+
+  # ========================================================================= #
+  # === show_nodes_table
+  # ========================================================================= #
+  def show_nodes_table
+    e 'We use these values for the nodes table:'
+    e
+    efancy '  taxid'
+    efancy '  parent_taxid'
+    efancy '  rank'
+    e
+    e 'We will also try to show a random selection of 10 entries from '\
+      'there now:'
+    run_sql 'SELECT taxid,parent_taxid,rank FROM nodes
+      ORDER BY RANDOM(), taxid LIMIT 10'
+  end
+
+
+  # ========================================================================= #
+  # === show_port
+  #
+  # Use this method to show the port.
+  # ========================================================================= #
+  def show_port
+    e "The port we will use is: #{simp('UNKNOWN')}"
+  end
+
+  # ========================================================================= #
+  # === update_lineage
+  #
+  # This will update only the lineage part of the localome database, which
+  # means the lineageIDs and the lineage scientific names.
+  # In order for this to work, we need to obtain the TaxID of the
+  # specific organism.
+  # ========================================================================= #
+  def update_lineage
+    e 'We will now obtain all TaxIDs in the localome table.' if be_verbose?
+    obtain_taxids = run_sql('select taxid from fasta;', false, :tuples).split(N).
+      map(&:strip).map(&:to_i).sort
+    # Ignore all entries that are 0.
+    obtain_taxids.reject! {|entry|
+      entry.to_i == 0
+    }
+    # We will have to update the following taxids, which is the collection
+    # of all TaxIDs available in the table:
+    obtain_taxids.each {|taxid|
+      e 'Now updating entry with the TaxID: '+sfancy(taxid.to_s)
+      get_lineage_ids_and_lineage_scientific_name(taxid)
+      report_lineage_ids_and_lineage_scientific_name(taxid)
+      if has_id?(taxid)
+        # We pad the two entries with proper quotes.
+        lineage_id              = pad_with_single_quotes(@lineage_ids)
+        lineage_scientific_name = pad_with_single_quotes(@lineage_scientific_name)
+        _ = "UPDATE fasta SET lineage_ids="+lineage_id+", lineage_scientific_name="+lineage_scientific_name+" WHERE taxid='"+taxid.to_s+"'"
+        run_sql_query(_)
+        e 'Updated entry.' if be_verbose?
+      else
+        e 'We did not find the TaxID: '+simp(taxid.to_s)
+      end
+    }
+    e 'Finished updating lineage.' if be_verbose?
+  end
+
+  # ========================================================================= #
+  # === make_taxonomy_gem
+  #
+  # This is the code that creates the taxonomy .gem.
+  # ========================================================================= #
+  def make_taxonomy_gem
+    unless Dir[TAXONOMY_HOME_DIR+'*.gemspec'].empty? # Do we have a .gemspec file there?
+      cd TAXONOMY_HOME_DIR
+    end
+    e
+    e 'We will now attempt to build the taxonomy .gem (from '+
+      'directory '+(Dir.pwd+'/').squeeze('/')+')'
+    e
+    if File.exist? 'taxonomy.gemspec'
+      esystem 'gem build taxonomy.gemspec', :use_colours
+      e
+      e 'Done. There should now be a .gem file here.'
+      location = Dir['*.gem']
+      if location
+        e 'We assume the full file path to be at:'
+        e '  '+sfile(location.first)
+        cp(location.first, TEMP_DIR)
+        e 'All done - the .gem should be ready now.'
+      end
+    else
+      e 'Could not find a file called taxonomy.gemspec, thus aborting now.'
+    end
+  end
+
+  # ========================================================================= #
+  # === silently_update_ncbi_database
+  #
+  # This method is the one that can be used to silently update the NCBI table
+  # via a cron job.
+  # ========================================================================= #
+  def silently_update_ncbi_database
+    download :ncbi, :be_silent
+    menu 'names'
+    menu 'nodes'
+    drop_nodes_and_names_database_tables(:be_silent)
+    read_in_names_and_nodes_sql_files(:be_silent)
+  end
+
+  # ========================================================================= #
+  # === select_name_and_lineage_ids
+  # ========================================================================= #
+  def select_name_and_lineage_ids
+    run_query('select name,lineage_ids from fasta;', false, :tuples)
+  end
+
+  # ========================================================================= #
+  # === select_name_and_tax_id_and_lineage_ids
+  # ========================================================================= #
+  def select_name_and_tax_id_and_lineage_ids
+    run_query('select name,taxid,lineage_ids from fasta;', false, :tuples)
+  end
+
+  # ========================================================================= #
+  # === select_name_and_tax_id_and_lineage_ids_and_path
+  # ========================================================================= #
+  def select_name_and_tax_id_and_lineage_ids_and_path
+    run_query('select name,taxid,lineage_ids,path from fasta;', false, :tuples)
+  end
+
+  # ========================================================================= #
+  # === report_total_amount_of_proteomes
+  #
+  # The input should be an array of Taxonomy IDs.
+  # ========================================================================= #
+  def report_total_amount_of_proteomes(i)
+    if i.is_a? Array
+      n_entries = 0
+      i.each {|entry|
+        n_entries += run_query("select n_accession_numbers from fasta WHERE taxid='"+entry+"';",
+            false,
+            :tuples).strip.to_i
+      }
+      e 'We have found a total of '+sfancy(n_entries.to_s)+' accession '+
+        'numbers from the above dataset.'
+    end
+  end
+
+  # ========================================================================= #
+  # === search_in_database_for_name
+  #
+  # Use this method to search in a database for a name.
+  #
+  # This is something such as the following SQL query:
+  #   select taxid FROM names WHERE name_txt LIKE '%Zygosaccharomyces rouxii%' limit 30;
+  #
+  # It will return the TaxID of the organism.
+  # ========================================================================= #
+  def search_in_database_for_name(i = 'Zygosaccharomyces rouxii')
+    e 'We will now try to search the names table for '+sfancy(i)+'.'
+    _ = "select taxid,name_txt FROM names WHERE name_txt LIKE '%"+i+"%' LIMIT 3;"
+    result = run_sql_query(_, false, :tuples)
+    return result
+  end
+
+  # ========================================================================= #
+  # === set_path
+  #
+  # Use this method to update the path to a local fasta entry, inside the
+  # localome entry. In order for this to work, the ID must exist.
+  #
+  # Complete usage example:
+  #
+  #   spath 1257118 /resources/seqdata/curated/sequences/localome/proteomes/Acanthamoeba_castellanii_Neff_pep.fa
+  #
+  # ========================================================================= #
+  def set_path(i)
+    if i.include? ' '
+      splitted = i.split(' ')
+      taxid_to_update = splitted[0].to_s
+      new_path        = splitted[1].to_s
+      if has_id? taxid_to_update # If localomes has this ID, we continue here:
+        e 'Now updating path for TaxID '+sfancy(taxid_to_update)+'.'
+        run_sql "UPDATE fasta SET path='"+new_path+"' WHERE taxid='"+taxid_to_update+"'"
+      else
+        e 'We could not find a TaxID '+sfancy(taxid_to_update)+
+          ' in the localome table. Thus can not update the path.'
+      end
+    else
+      if File.exist? i
+        data = File.readlines(i).map(&:chomp).reject {|entry| entry.empty? }
+        data.each {|entry|
+          entry = entry.strip
+          if entry.include? '|'
+            splitted = entry.split('|')
+          else # else assume \t
+            splitted = entry.split("\t")
+          end
+          set_path(splitted.first+' '+splitted[1])
+        }
+        e 'Note: if you wish to see the modified dataset, input: taxid,path'
+      else
+        e 'Format was not correct. Please either provide a file as argument,'
+        e 'or use input such as this here:'
+        e
+        e '   spath 1257118 /resources/seqdata/curated/sequences/localome/proteomes/Acanthamoeba_castellanii_Neff_pep.fa'
+        e
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === nohelp
+  # ========================================================================= #
+  def nohelp
+    @no_help = true
+  end
+
+  # ========================================================================= #
+  # === show_short_help
+  # ========================================================================= #
+  def show_short_help
+    e '(Type "help" or "?" for help, or "nohelp" to disable '\
+      'this notification here).' unless @no_help
+  end
+
+  # ========================================================================= #
+  # === show_postgres_size
+  #
+  # This method will show the size of the postgres database.
+  # ========================================================================= #
+  def show_postgres_size
+    e 'Next querying the size of the postgresql table:'
+    sql_query POSTGRESQL_QUERY_SIZE, true
+    # relpages are not too useful to look at, so we commented it out again.
+    # sql_query 'SELECT relname, relpages FROM pg_class ORDER BY relpages DESC LIMIT 5;'
+    e 'The total disk size for the robert_db is:'
+    sql_query "SELECT pg_size_pretty(pg_database_size('robert_db'));",true
+    e 'Size of '+sfancy(:names)+' is: '+
+      sql_query(
+        "SELECT pg_size_pretty(pg_total_relation_size('names'));",false, :tuples)
+    e 'Size of '+sfancy(:nodes)+' is:  '+
+      sql_query(
+        "SELECT pg_size_pretty(pg_total_relation_size('nodes'));",false, :tuples)
+    e 'Size of '+sfancy(:fasta)+' is:  '+
+      sql_query(
+        "SELECT pg_size_pretty(pg_total_relation_size('fasta'));",false, :tuples)
+  end
+
+  # ========================================================================= #
+  # === obtain_full_lineage_for
+  #
+  # The input to this method should be an existing TaxID.
+  # ========================================================================= #
+  def obtain_full_lineage_for(f)
+    result = return_full_lineage_of(f) # in taxonomy.rb
+    if result
+      @lineage_ids = ''.dup
+      @lineage_scientific_name = ''.dup
+      hash = Hash[result]
+      hash.each {|taxid, scientific_name|
+        @lineage_ids << taxid.to_s+' -> '
+        @lineage_scientific_name << scientific_name.chomp+' (Tax id: '+taxid.to_s+'), '
+      }
+      @lineage_scientific_name = @lineage_scientific_name.strip
+      # Next, get rid of trailing , characters.
+      @lineage_scientific_name.chop! if @lineage_scientific_name.end_with? ','
+      @lineage_ids.strip!
+      if @lineage_ids.end_with? '->'
+        @lineage_ids[-2,2] = ''.dup
+        @lineage_ids.strip!
+      end
+      @lineage_scientific_name.chomp!
+    end
+    return result
+  end; alias get_lineage_ids_and_lineage_scientific_name obtain_full_lineage_for
+
+  # ========================================================================= #
+  # === drop_table                                                 (drop tag)
+  #
+  # Use this method when you wish to drop a table.
+  # ========================================================================= #
+  def drop_table(i = DROP_FASTA_TABLE)
+    case i.to_s
+    when 'nodes'
+    when 'fasta',
+         'localomes',
+         'localome'
+      i = DROP_FASTA_TABLE
+    end
+    ::Bioroebe.run_sql_query(i)
+  end
+
+  # ========================================================================= #
+  # === query_localomes_by_modtime
+  # ========================================================================= #
+  def query_localomes_by_modtime
+    _ = 'SELECT name,modification_time FROM fasta ORDER BY modification_time;'
+    run_sql_query _
+  end
+
+  # ========================================================================= #
+  # === query
+  #
+  # Formulate a query against the database.
+  # ========================================================================= #
+  def query(i)
+    case i.to_s
+    when 'localome','extended','main'
+      query_localome_including_path
+    when 'modtime'
+      query_localomes_by_modtime
+    when 'ncbi'
+      e 'https://www.ncbi.nlm.nih.gov/taxonomy'
+    end
+  end
+
+  # ========================================================================= #
+  # === get_all_info_entries_with_tax_id
+  # ========================================================================= #
+  def get_all_info_entries_with_tax_id
+    result = []
+    if be_verbose?
+      e 'We will now attempt to find all .INFO files that do have a'
+      e 'proper Taxonomy ID entry.'
+    end
+    Dir[INFO_DIR+'*.INFO'].each {|file|
+      _ = Info.new(file, :be_verbose => false)
+      if _.has_taxonomy_id?
+        e sfile(file)+' has a Taxonomy ID.' if be_verbose?
+        result << file
+      end
+    }
+    return result
+  end
+
+  # ========================================================================= #
+  # === read_in_names_and_nodes_sql_files
+  #
+  # We use two commands for populating names.sql and nodes.sql tables.
+  # ========================================================================= #
+  def read_in_names_and_nodes_sql_files(be_verbose = true)
+    be_verbose = false if be_verbose == :be_silent
+
+    if at_home? # We use another command at home.
+      cmd = POSTGRE_LOGIN_COMMAND_HOME
+    else
+      cmd = POSTGRE_LOGIN_COMMAND
+    end
+
+    if be_verbose
+      esystem cmd+' -f '+SHARED_HOME+'names.sql'
+      esystem cmd+' -f '+SHARED_HOME+'nodes.sql'
+    else # Else just use system.
+      system cmd+' -f '+SHARED_HOME+'names.sql'
+      system cmd+' -f '+SHARED_HOME+'nodes.sql'
+    end
+  end
+
+  # ========================================================================= #
+  # === be_silent
+  # ========================================================================= #
+  def be_silent
+    if @be_verbose == false
+      e 'We are already silent.'
+    else
+      @be_verbose = false
+      e 'We will now be silent.'
+    end
+  end
+
+  # ========================================================================= #
+  # === record_last_command
+  #
+  # Use this method to record the last command issued.
+  #
+  # The constant LAST_INTERACTIVE_COMMAND determines where we store this.
+  # ========================================================================= #
+  def record_last_command(
+      consider_storing_this = '',
+      optional              = ''
+    )
+    what = consider_storing_this.to_s.dup # Work on a copy from this point onwards.
+    what << '|'+optional.to_s unless optional.to_s.empty?
+    unless what.empty?
+      # ===================================================================== #
+      # Before we can store into the file, we need to ensure that the
+      # TEMP_DIR exists. We ensure this with the next check - if it
+      # does not exist then we will create it.
+      # ===================================================================== #
+      unless Dir.exist? TEMP_DIR
+        e 'We will now create the directory '+sdir(TEMP_DIR)+'.'
+        ensure_that_temp_dir_exists
+      end
+      begin
+        write_what_into(what, LAST_INTERACTIVE_COMMAND)
+      rescue Exception => error
+        e "A small error has happened in the method: "\
+          "#{__method__}()"
+        p error
+        e "Could not write into `#{sfile(into)}`."
+      end
+    end unless what.include? 'last?' # Exception for "last?".
+  end
+
+  # ========================================================================= #
+  # === be_verbose?
+  # ========================================================================= #
+  def be_verbose?
+    @be_verbose
+  end
+
+  # ========================================================================= #
+  # === repeat_last_command
+  # ========================================================================= #
+  def repeat_last_command
+    if File.exist? LAST_INTERACTIVE_COMMAND
+      show_last_command
+    else
+      e 'No file at '+sfile(LAST_INTERACTIVE_COMMAND)+' could be found.'
+    end
+  end
+
+  # ========================================================================= #
+  # === be
+  # ========================================================================= #
+  def be(i)
+    case i.to_sym
+    when :verbose
+      be_verbose
+    when :silent
+      be_silent
+    end
+  end
+
+  # ========================================================================= #
+  # === show_table_names
+  # ========================================================================= #
+  def show_table_names
+    e N+'The SQL table structure is as follows:'+N+N
+    efancy 'names.sql'
+    e '  (1) '+NAMES_ENTRIES+N+N
+    efancy 'nodes.sql'
+    e '  (2) '+NODES_ENTRIES+N+N
+    efancy 'fasta.sql'
+    e '  (3) '+FASTA_ENTRIES+N+N
+  end
+
+  # ========================================================================= #
+  # === be_verbose
+  # ========================================================================= #
+  def be_verbose
+    if @be_verbose == true
+      e 'We are already verbose.'
+    else
+      @be_verbose = true
+      e 'We will now be verbose.'
+    end
+  end
+
+  # ========================================================================= #
+  # === finished
+  #
+  # Here we simply report to the user that we have finished.
+  # ========================================================================= #
+  def finished(optional_extra_message = '')
+    unless optional_extra_message.empty?
+      optional_extra_message << '.' unless optional_extra_message.end_with? '.'
+    end
+    e 'Done! '+optional_extra_message
+  end
+
+  # ========================================================================= #
+  # === has_id?
+  #
+  # We ask the localome if an ID is registered.
+  # run_sql is defined in the file shared.rb
+  # ========================================================================= #
+  def has_id?(i)
+    i = i.to_s
+    _ = "SELECT taxid from fasta where taxid='"+i+"'"
+    if run_sql(_, false, :tuples).strip.empty?
+      return false
+    else
+      return true
+    end
+  end; alias has? has_id? # === has?
+
+  # ========================================================================= #
+  # === show_shared_code_location
+  #
+  # To invoke this method, do:
+  #   shared_code?
+  # ========================================================================= #
+  def show_shared_code_location
+    e 'You can find the file shared.rb here:'
+    _ = base_dir?
+    e '  '+sfile(_+'/shared.rb')
+  end
+
+  # ========================================================================= #
+  # === show_important_directories
+  #
+  # Delegate towards Taxonomy.status? from here.
+  # ========================================================================= #
+  def show_important_directories
+    Taxonomy.status?
+  end
+
+  # ========================================================================= #
+  # === first_argument?
+  # ========================================================================= #
+  def first_argument?
+    @first_argument
+  end; alias f? first_argument? # === f?
+       alias f  first_argument?
+
+  # ========================================================================= #
+  # === show_lineage_from_localome_table
+  #
+  # The TaxID must exist before we can use this.
+  #
+  # Usage examples:
+  #
+  #   show_lineage_from_localome_table 2762
+  #   slocalome 2762
+  #
+  # ========================================================================= #
+  def show_lineage_from_localome_table(i)
+    result = run_sql(
+      "select lineage_ids from fasta WHERE taxid='"+i.to_s+"';", false, :tuples
+    ).chomp.strip
+    if result.empty?
+      e 'This TaxID was not found in the localome table.'
+      e 'To find out which entries exist in the localome table, do "localome?".'
+    else
+      e result
+    end
+  end
+
+  # ========================================================================= #
+  # === report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
+  #
+  # This will check on at least one directory.
+  # ========================================================================= #
+  def report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
+    _ = get_all_info_entries_with_tax_id
+    e 'We will try to assess the various .INFO files from the '+
+      sdir(info_dir?)+'.'
+    n_info_files = Dir[INFO_DIR+'*.INFO'].size
+    if n_info_files > 0
+      e 'We did find '+sfancy(_.size)+' .INFO files with Taxonomy ID. '+
+        'That means that '+sfancy( Dir[INFO_DIR+'*.INFO'].size - _.size )+
+        ' .INFO files do not have '
+      e 'a Taxonomy ID. In total there are '+sfancy(n_info_files.to_s)+
+        ' .INFO files there.'
+      info_files_in_incoming_dir = Dir[INCOMING_DIR+'*.INFO']
+      if info_files_in_incoming_dir.size > 0
+        e 'We also found at least one .INFO file in '+sdir(INCOMING_DIR)+'.'
+        e 'We will display them now:'
+        pp info_files_in_incoming_dir
+      end
+    else
+      e 'We found no .INFO file there.'
+    end
+  end
+
+  # ========================================================================= #
+  # === load_from_info
+  #
+  # This method shall attempt to load from an .NFO file, right into the
+  # localome/ directory at /data/curated/sequences/localome/incoming/.
+  # ========================================================================= #
+  def load_from_info(i)
+    e 'We will now attempt to load an .INFO file.'
+    info = Info.new(i)
+    info.report_id
+    taxid = info.taxid?
+    e 'We will try to load a fasta file, if it is nearby.'
+    _ = info.fasta?
+    e _
+    ParseFasta.new(_).report
+    if has_id? taxid # If we already have an entry like that, we refuse.
+      e 'We already have an entry with the Taxonomic ID taxid '+taxid+'.'
+      e 'You would have to remove it first before you can load a new one.'
+      e '(Removing is as simple as: remove_id TAXONOMIC_ID_GOES_HERE)'
+    else
+      e 'No entry was yet found in the localome table, thus we will '+
+        'attempt to add this dataset now.'
+      create_sql_file_from_local_fasta_entry(i)
+      e 'You can update the path in the Postgresql database via:'
+      e '  set_path TAXONOMY_ID path_goes_here'
+    end
+  end
+
+  # ========================================================================= #
+  # === show_type_of_all_info_files
+  #
+  # We will get all .INFO files and display the type.
+  # ========================================================================= #
+  def show_type_of_all_info_files(i = nil)
+    if i
+      info = Info.new(i, :silent)
+      info.find_fasta
+      if info.fasta?
+        fasta = ParseFasta.new(info.corresponding_datafile)
+        e sfile(i)+' is DNA or Protein? '+fasta.type.to_s
+      else
+        e 'We could not locate a local fasta entry for '+sfile(i)
+      end
+    else # else input was nil.
+      Dir[INFO_DIR+'*'].each {|entry|
+        show_type_of_all_info_files(entry)
+      }
+    end
+  end
+
+  # ========================================================================= #
+  # === show_all_prokarya                                      (prokarya tag)
+  #
+  # This method will show all entries in the database that are from
+  # Prokaryotes.
+  # ========================================================================= #
+  def show_all_prokarya
+    _ = select_name_and_tax_id_and_lineage_ids
+    n_entries = _.split(N).size
+    result = []
+    counter = 0
+    _.split(N).each_with_index {|entry|
+      splitted = entry.split('|')
+      lineage = splitted[2]
+      if lineage =~ / #{Bacteria_Taxonomy_ID} /
+        scientific_name = splitted.first.strip
+        counter += 1
+        e simp(counter.to_s)+') '+scientific_name+' ('+
+          sfancy('TaxID')+': '+splitted[1].to_s.strip+')'
+        result << scientific_name
+      end
+    }
+    e N+N+'Out of '+sfancy(n_entries.to_s)+' registered entries in '+
+      'total in the localomes database,'
+    e sfancy(result.size.to_s)+' belong to Prokarya (the Taxonomy ID of '+
+      'Prokarya is '+sfancy(Bacteria_Taxonomy_ID.to_s)+').'
+  end
+
+  # ========================================================================= #
+  # === Interactive.run
+  # ========================================================================= #
+  def self.run(i = nil)
+    Taxonomy::Interactive.new(i)
+  end
+
+  # ========================================================================= #
+  # === Taxonomy.run_interactive
+  # ========================================================================= #
+  def self.run_interactive(i = nil)
+    Interactive.run(i) # An alias to the above.
+  end
+
+  # ========================================================================= #
+  # === get_user_input
+  #
+  # Get user input via this method. We prefer to use Readline if it is
+  # available, otherwise we will simply use a $stdin.gets() call.
+  # ========================================================================= #
+  def get_user_input
+    if Object.const_defined? :Readline
+      _ = Readline.readline('', true)
+      Readline::HISTORY.pop if _ =~ /^\s*$/
+      @user_input = _
+    else
+      @user_input = $stdin.gets.chomp
+    end
+    sanitize_user_input
+    process_user_input
+    return @user_input
+  end; alias obtain_user_input get_user_input
+
+  # ========================================================================= #
+  # === sanitize_user_input
+  # ========================================================================= #
+  def sanitize_user_input
+    splitted = @user_input.split(' ')
+    @cmd = splitted.first
+    if @user_input.empty?
+      @first_argument = nil
+    else
+      @first_argument = splitted[1..-1].join(' ') # This is equal to all remaining arguments for now, actually.
+    end
+  end
+
+  # ========================================================================= #
+  # === process_user_input
+  # ========================================================================= #
+  def process_user_input(i = @user_input)
+    if i.is_a? Array
+      i.each {|entry| process_user_input(entry) }
+    else # We assume it is a String here.
+      if i.include? ';'
+        process_user_input(i.split(';'))
+      else
+        check_against_menu(@cmd, @first_argument)
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === try_to_show_instructions
+  #
+  # This method will try to show the instructions to the user, based
+  # on what the method return_instructions() will give us.
+  # ========================================================================= #
+  def try_to_show_instructions
+    _ = return_instructions
+    if File.exist? _
+      e 'Now reading in from file `'+sfile(_)+'`.'
+      cat _
+    else
+      e 'We could not find a file at position '+_
+    end
+  end
+
+  # ========================================================================= #
+  # We return the bin/taxonomy file here.
+  # ========================================================================= #
+  def return_taxonomy_file
+    return PROJECT_BASE_DIR+'bin/taxonomy'
+  end
+
+  # ========================================================================= #
+  # === show_changelog
+  # ========================================================================= #
+  def show_changelog
+    cat PROJECT_DOC_DIR+'CHANGELOG_FROM_0.0.14_TO_0.0.15'
+  end
+
+  # ========================================================================= #
+  # === return_dependencies
+  #
+  # We return the dependencies file here.
+  # ========================================================================= #
+  def return_dependencies
+    PROJECT_DOC_DIR+'DEPENDENCIES'
+  end
+
+  # ========================================================================= #
+  # === return_instructions
+  # ========================================================================= #
+  def return_instructions
+    PROJECT_DOC_DIR+'INSTRUCTIONS'
+  end
+
+  # ========================================================================= #
+  # === show_last_command
+  # ========================================================================= #
+  def show_last_command
+    last_command = File.read(LAST_INTERACTIVE_COMMAND)
+    e 'The last command was: '+simp(last_command.to_s)
+    e 'This was read in from the file '+sfile(LAST_INTERACTIVE_COMMAND)
+  end
+
+  # ========================================================================= #
+  # === create_sql_file_from_local_fasta_entry
+  #
+  # This method will create a .sql file, based on the information
+  # obtained from the local fasta entries.
+  #
+  # The first argument to it should be an .INFO file, not a fasta file!
+  # ========================================================================= #
+  def create_sql_file_from_local_fasta_entry(i)
+    ensure_that_temp_dir_exists
+    info = Info.new(i, :be_verbose => false)
+    info.try_to_find_likely_fasta_file # Need to run it once so we can try to find the fasta file.
+    if info.taxid
+      obtain_full_lineage_for(info.taxid) # This will set @lineage_id
+    else
+      if be_verbose?
+        e 'We did not find a Tax ID for `'+sfile(i)+'`.'
+        e 'This is considered a fatal error for now - we will thus exit.'
+      end
+      exit
+    end
+    mkdir(AUTOGENERATED_SQL_FILES_DIR) unless Dir.exist?(AUTOGENERATED_SQL_FILES_DIR)
+    sql_filename = AUTOGENERATED_SQL_FILES_DIR+
+       File.basename(i).gsub(/#{File.extname(i)}/,'')+'.sql'        
+    remove(sql_filename) if File.exist? sql_filename # Get rido f the old one first.
+    # ======================================================================= #
+    # Next, we will build up our SQL string:
+    # ======================================================================= #
+    string = ''.dup # This is the string that will be stored.
+    # ======================================================================= #
+    # (1) - the scientific name comes first
+    # ======================================================================= #
+    scientific_name = get_scientific_name(info.taxid).strip
+    if scientific_name.empty? # Exit if we can not find it.
+      if be_verbose?
+        ewarn 'The scientific name for '+simp(info.taxid.to_s)+' was empty.'
+        ewarn 'This we consider to be a runtime error for now, thus '+
+              'we will exit.'
+      end
+      exit
+    end
+    string << pad_with_single_quotes(
+      scientific_name
+    )+', '
+    fasta = ParseFasta.new(info.corresponding_datafile)
+    # ======================================================================= #
+    # (2) Next we need the Taxonomic ID, which is an integer.
+    # ======================================================================= #
+    string << info.taxid.to_s+', '
+    # ======================================================================= #
+    # (3) We now need to find out whether we have DNA or Protein.
+    # ======================================================================= #
+    type = fasta.type? # DNA or Protein.
+    if type    == 'DNA'
+      type = 0
+    elsif type == 'Protein'
+      type = 1
+    end
+    string << type.to_s+', '
+    # ======================================================================= #
+    # (4) Now comes the lineage_ids, of varchar(100)
+    # ======================================================================= #
+    string << pad_with_single_quotes(@lineage_ids)+', '
+    # ======================================================================= #
+    # (5) And the lineage_scientific_name
+    # ======================================================================= #
+    string << pad_with_single_quotes(@lineage_scientific_name)+', '
+    # ======================================================================= #
+    # Here be the accession_number varchar(200000)
+    # Disabled as of Friday, needs more testing first. But is not even needed.
+    # string << pad_with_single_quotes(
+    #   fasta.all_accession_entries.join("\t|")
+    # )+', '
+    # string << pad_with_single_quotes(0)+', '
+    # Dataset should come here
+    # string << pad_with_single_quotes(0)+', '
+    # (6) And the comment field will be here.
+    # ======================================================================= #
+    string << pad_with_single_quotes(0)+', '
+    # ======================================================================= #
+    # (7) filesize: the size of the file in question
+    # ======================================================================= #
+    string << fasta.filesize.to_s+', '
+    # ======================================================================= #
+    # (8) modification_time
+    # ======================================================================= #
+    string << pad_with_single_quotes(fasta.modification_time.to_s)+', '
+    # ======================================================================= #
+    # (9) n_accession_numbers
+    # ======================================================================= #
+    string << fasta.n_entries.to_s+', '
+    # ======================================================================= #
+    # (10) path - the filepath in question
+    # ======================================================================= #
+    string << pad_with_single_quotes(info.corresponding_datafile)
+    # ======================================================================= #
+    # Now we can insert into the postgresql Database.
+    # ======================================================================= #
+    string = InsertInto[
+      'fasta',
+      'name, taxid, type, lineage_ids, lineage_scientific_name, comment_field, filesize, modification_time, n_accession_numbers, path', # accession_number, dataset, 
+       string
+    ]
+    e 'Now storing into '+sfile(sql_filename) if be_verbose?
+    write_what_into(string, sql_filename)
+    if be_verbose?
+      e 'Next, we will attempt to read in this file into the '
+        'Postgresql localome (fasta) table.'
+    end
+    cmd = POSTGRE_LOGIN_COMMAND+' -f '+sql_filename
+    esystem(cmd)
+    if be_verbose?
+      e 'Done! All should have been well by now. '+
+        'The Taxonomic ID was '+info.taxid
+    end
+  end
+
+  # ========================================================================= #
+  # === insert_into
+  # ========================================================================= #
+  def insert_into(i = :nodes)
+    i = i.to_s
+    case i
+    when 'fasta'
+      create_fasta_table
+    when 'nodes'
+      populate_nodes_table(:be_verbose)
+    when 'names'
+      populate_names_table(:be_verbose)
+    end
+  end
+
+  # ========================================================================= #
+  # === which_database_to_use?
+  # ========================================================================= #
+  def which_database_to_use?
+    File.read(PROJECT_YAML_DIR+'use_this_database.yml')
+  end
+
+  # ========================================================================= #
+  # === show_configuration
+  # ========================================================================= #
+  def show_configuration
+    e which_database_to_use?
+  end
+
+  # ========================================================================= #
+  # === names_sql
+  # ========================================================================= #
+  def names_sql
+    store_here = AUTOGENERATED_SQL_FILES_DIR+'names.sql'
+    File.delete(store_here) if File.exist? store_here
+    e 'We will populate the names-table next. This will take a while.'
+    populate_names_table :be_verbose, store_here
+  end
+
+  # ========================================================================= #
+  # === nodes_sql
+  #
+  # Use this method to generate the nodes.sql file.
+  # ========================================================================= #
+  def nodes_sql
+    store_here = AUTOGENERATED_SQL_FILES_DIR+'nodes.sql'
+    File.delete(store_here) if File.exist? store_here
+    e 'We will populate the nodes-table next. This will take a while.'
+    populate_nodes_table :be_verbose, store_here
+  end
+
+  # ========================================================================= #
+  # === set_database
+  # ========================================================================= #
+  def set_database(i)
+    i = i.to_s.chomp.delete('"')
+    if i.empty?
+      e 'Please provide the type of the database you wish to '\
+        'use, such as "postgresql".'
+    else
+      case i
+      when 'postgre'
+        i = 'postgresql'
+      end
+      i = i.downcase
+      e 'Storing '+i+' into '+sfile(FILE_USE_THIS_DATABASE)+'.'
+      write_what_into(i, FILE_USE_THIS_DATABASE)
+    end
+  end
+
+  # ========================================================================= #
+  # === create_fasta_table
+  #
+  # This method generates the fasta table into either postgresql or
+  # whatever else you stored things into.
+  # ========================================================================= #
+  def create_fasta_table
+    remove(FASTA_SQL)
+    # e 'Now storing into fasta.sql (Fasta-Format).'
+    create_and_save_table('fasta', true) # true for verbose
+    cat FASTA_SQL # Also display it, after creation.
+    # Next, drop the old Fasta table. But we must set the password before.
+    e 'Trying to drop the fasta table next.'
+    drop_table :fasta
+    # And now, read in the new one.
+    read_sql :fasta
+  end
+
+  # ========================================================================= #
+  # === set_commandline_arguments
+  # ========================================================================= #
+  def set_commandline_arguments(i = nil)
+    i = [i] unless i.is_a? Array
+    @commandline_arguments = i # Must be an Array.
+  end
+
+  # ========================================================================= #
+  # === do_startup_actions
+  # ========================================================================= #
+  def do_startup_actions
+    if be_verbose?
+      e Colours.rev+'Welcome to interactive Taxonomy.'+N+N
+      e 'We will show the help menu now (on startup).'+N+N
+      show_help
+      e 'Please input your command(s). ("help" for help, '+
+        '"quit", "exit" or "q" to exit.)'
+      nohelp if at_home? # At home I won't use this here.
+    end
+    check_commandline_arguments
+  end
+
+  # ========================================================================= #
+  # === check_commandline_arguments
+  #
+  # We check the commandline.
+  # ========================================================================= #
+  def check_commandline_arguments
+    @commandline_arguments.each {|entry|
+      case entry
+      when :run_connected
+        do_run_connected # This mode is for when we embed it in the BioroebeShell.
+      end
+    }
+  end
+
+  # ========================================================================= #
+  # === fetch_user_input_via_loop
+  # ========================================================================= #
+  def fetch_user_input_via_loop
+    loop {
+      begin
+        obtain_user_input # This sets the @user_input variable.
+      rescue Interrupt
+        if be_verbose?
+          e 'Sigint occurred by user interrupt, exiting gracefully now.'
+        end
+        exit_program
+      end
+      if run_connected? 
+        break if VALID_WAYS_TO_EXIT.include? @user_input
+      end
+    }
+  end
+
+  # ========================================================================= #
+  # === run_standalone?
+  # ========================================================================= #
+  def run_standalone?
+    @run_standalone
+  end
+
+  # ========================================================================= #
+  # === run_connected?
+  # ========================================================================= #
+  def run_connected?
+    ! run_standalone?
+  end
+
+  # ========================================================================= #
+  # === exit_program
+  #
+  # Use this method when exiting.
+  # ========================================================================= #
+  def exit_program
+    exit if run_standalone?
+  end
+
+  # ========================================================================= #
+  # === show_sql_commands                                           (sql tag)
+  #
+  # This method will feedback the SQL commands to create our postgre
+  # table and also show the Insert commands used.
+  # ========================================================================= #
+  def show_sql_commands
+    e N+'The three commands to create the '+
+      simp('PostgreSQL database')+' are:'+N+N
+    e '  (1) names table:'+N+N
+    efancy '  '+create_table(:names).to_s
+    e N+'  (2) nodes table:'+N+N
+    efancy '  '+create_table(:nodes).to_s
+    e N+'  (3) fasta table:'+N+N
+    efancy '  '+create_table(:fasta).to_s
+  end; alias sql?         show_sql_commands # === sql?
+       alias table_names? show_sql_commands # === table_names?
+
+  # ========================================================================= #
+  # === create_table
+  #
+  # A wrapper over class CreateTable.
+  # ========================================================================= #
+  def create_table(i)
+    i = i.to_s
+    case i
+    when 'fasta'
+      create_fasta_table
+    else
+      i << '.sql' # Append .sql in this case.
+      result = ::SqlParadise::Commands.create_table(i)
+      store_here = AUTOGENERATED_SQL_FILES_DIR+'create_table_'+i
+      e 'Next creating a table for '+simp(i)+'. Will '+
+        'store into '+sfile(store_here)
+      save_what_into(result, store_here)
+      e result
+    end
+  end
+
+  # ========================================================================= #
+  # === enable
+  # ========================================================================= #
+  def enable(i)
+    i = i.to_s
+    if i.start_with? 'enable'
+      i.gsub!(/^enable/,'')
+    end
+    i.strip!
+    case i
+    when 'colours'
+      enable_colours
+    end
+  end
+
+  # ========================================================================= #
+  # === show_sql_commands_only
+  # ========================================================================= #
+  def show_sql_commands_only
+    e Commands.create_table :taxonomy_nodes
+    e
+    e Commands.create_table :taxonomy_names
+    e
+    e Commands.create_table :taxonomy_fasta
+    e
+  end
+
+  # ========================================================================= #
+  # === enable_colours
+  # ========================================================================= #
+  def enable_colours
+    @use_colours = true
+    Taxonomy.enable_colours
+  end
+
+  # ========================================================================= #
+  # === create_database
+  # ========================================================================= #
+  def create_database
+    case which_database_to_use?
+    when 'sqlite'
+      one   = 'CREATE TABLE names ( taxid int, name_txt varchar(155), unique_name varchar(100), name_class varchar(25) );'
+      two   = 'CREATE TABLE nodes ( taxid int, parent_taxid int, rank varchar(25) );'
+      three = 'CREATE TABLE fasta ( name varchar(80), taxid integer, type smallint, lineage_ids varchar(500), lineage_scientific_name varchar(2500), comment_field varchar(8000), filesize integer, modification_time varchar(25), n_accession_numbers integer, path varchar(120) );'
+      e one
+      e two
+      e three
+      _ = 'sqlite3 '+working_dir?+'names.db "'+one+'"'
+      esystem _
+      _ = 'sqlite3 '+working_dir?+'nodes.db "'+two+'"'
+      esystem _
+      _ = 'sqlite3 '+working_dir?+'fasta.db "'+three+'"'
+      esystem _
+      File.read(Taxonomy::Constants::NAMES_SQL).each_line {|line|
+        line = line.chomp
+        if line.include? '"'
+          line.gsub!(/"/,'\"')
+        end
+        _ = 'sqlite3 '+working_dir?+'names.db "'+line+'"'
+        Esystem.esystem _
+      }
+    else # default to postgresql for now.
+    end
+  end
+
+  # ========================================================================= #
+  # === download
+  #
+  # This method can be used to download the ncbi database.
+  # ========================================================================= #
+  def download(i = f?)
+    i = i.to_s
+    case i # case tag
+    # ======================================================================= #
+    # === --help
+    # ======================================================================= #
+    when 'HELP','?','--help'
+      e 'Currently we can download only the NCBI database.'
+      e
+      e 'To do so, do:'
+      e '  download ncbi'
+    # ======================================================================= #
+    # === --ncbi
+    # ======================================================================= #
+    when 'ncbi','--ncbi','database','1','' # '' is also a default here.
+      download_ncbi_database
+      if be_verbose?
+        e
+        e 'If all went well then you could now try to update the '+
+          'database, by issuing:'
+        e
+        efancy '  update databases'
+        e
+      end
+    else
+      e 'In the method download(), we do not know the given '+
+        'input `'+simp(i.to_s)+'`.'
+    end
+  end
+
+  # ========================================================================= #
+  # === download_ncbi_database
+  # ========================================================================= #
+  def download_ncbi_database
+    Taxonomy.download_ncbi_database # bl $TAXONOMY/class_methods.rb
+  end
+
+  # ========================================================================= #
+  # === add_comment                                             (comment tag)
+  #
+  # Use this method to add a comment to the localome table.
+  # ========================================================================= #
+  def add_comment(taxid)
+    if has? taxid
+      e 'Please input the comment you wish to add to the '+
+        'Taxonomy ID '+simp(taxid.to_s)+' now:'
+      add_this = $stdin.gets.chomp
+      _ = "UPDATE fasta SET comment_field='"+add_this+"' WHERE taxid='"+taxid.to_s+"'"
+      run_sql(_)
+    else
+      erev "We could not find any entry with the Taxonomy "\
+           "ID #{taxid.to_s}."
+    end
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    do_startup_actions
+    fetch_user_input_via_loop
+  end; alias run_in_interactive_mode run # === run_in_interactive_mode
+
+end
+
+  # ========================================================================= #
+  # === Taxonomy.interactive
+  #
+  # Invoke this method if you wish to directly invoke the interactive
+  # component of the Taxonomy module.
+  # ========================================================================= #
+  def self.interactive(i = nil)
+    ::Bioroebe::Taxonomy::Interactive.new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::Taxonomy::Interactive.run_interactive(ARGV)
+end # itax; Taxonomy.interactive