bioroebe 0.10.80

data/lib/bioroebe/taxonomy/menu.rb

@@ -0,0 +1,905 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This file keeps the user-menu for the taxonomy submodule.
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module Taxonomy # === Bioroebe::Taxonomy
+
+class Interactive < ::Bioroebe::CommandlineApplication
+
+  require 'bioroebe/taxonomy/taxonomy.rb'
+
+  begin
+    require 'rcfiles'
+  rescue LoadError; end
+
+  include ::Bioroebe::Taxonomy::Shared
+  include ::Bioroebe
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  #
+  # The first argument to this method is the action we wish to check
+  # against the menu.
+  #
+  # It constitutes the main menu interface of the Taxonomy project.
+  # The taxonomy commandline program calls this method here simply
+  # menu().
+  # ========================================================================= #
+  def menu(
+      instruction        = user_input?,
+      optional_this_file = nil
+    )
+    i = instruction.to_s.chomp
+    # ======================================================================= #
+    # Next we make sure that the temp-dir and the download-dir will exist.
+    # ======================================================================= #
+    ensure_that_temp_dir_exists
+    ensure_that_download_dir_exists
+    record_last_command(i, first_argument?) # Record the last command.
+    case i # (case tag)
+    # ======================================================================= #
+    # === disable_colours
+    # ======================================================================= #
+    when 'disable_colours',
+         'nocolours',
+         'nocols',
+         'nocolour',
+         'nocol',
+         'nocolorus'
+      disable_colours
+    # ======================================================================= #
+    # === extract
+    # ======================================================================= #
+    when 'extract',
+         'ext'
+      extract(File.basename(URL_TO_TAXONOMY_ARCHIVE))
+    # ======================================================================= #
+    # === download_database
+    # ======================================================================= #
+    when /^download(_|-)?database$/i,'ncbi_down'
+      download_ncbi_database
+    # ======================================================================= #
+    # === download
+    # ======================================================================= #
+    when 'download'
+      download(f)
+    # ======================================================================= #
+    # === exit
+    # ======================================================================= #
+    when *VALID_WAYS_TO_EXIT
+      exit_program
+    # ======================================================================= #
+    # === set_be_verbose
+    # ======================================================================= #
+    when /^set(-|_| )?be(-|_| )?verbose$/,
+         'verbose',
+         'be_verbose'
+      @be_verbose = true
+      e 'We will now be verbose.'
+    # ======================================================================= #
+    # === last?
+    # ======================================================================= #
+    when 'last?',
+         'show_last_command'
+      show_last_command
+    # ======================================================================= #
+    # === query_localome
+    # ======================================================================= #
+    when 'query_localome',
+         'querylocalome',
+         'qlocalome',
+         'available?',
+         'available',
+         'query?',
+         'localomes?',
+         'loc?'
+      query_localome_including_path
+    # ======================================================================= #
+    # === lineageid
+    # ======================================================================= #
+    when 'lineageid',
+         'lineage_id',
+         'lineage_ids',
+         'lineageids', # Query the localome database directly.
+         'show_lineage_from_localome_table',
+         'slocalome'
+      show_lineage_from_localome_table(f)
+    # ======================================================================= #
+    # === query
+    # ======================================================================= #
+    when 'query','qu'
+      query(f)
+    # ======================================================================= #
+    # === name_path
+    # ======================================================================= #
+    when 'name_path',
+         'namepath'
+      e run_sql('select name,path from fasta;',false, :tuples)
+    # ======================================================================= #
+    # === sql
+    # ======================================================================= #
+    when 'sql',
+        'seql'
+      sql(f)
+    # ======================================================================= #
+    # === basedir?
+    # ======================================================================= #
+    when 'projectbasedir',
+         'basedir?',
+         'project_base_dir'
+      e PROJECT_BASE_DIR
+    # ======================================================================= #
+    # === grep
+    # ======================================================================= #
+    when 'grep'
+      esystem 'grep -r '+f.to_s+' '+MODULE_PATH+'*'
+    # ======================================================================= #
+    # === set_database
+    # ======================================================================= #
+    when 'set_database','setdatabase','database'
+      set_database(f) # Set a new database
+    # ======================================================================= #
+    # === enable
+    # ======================================================================= #
+    when /^enable/
+      enable(i) # Pass all enable instructions into the method.
+    # ======================================================================= #
+    # === password?
+    # ======================================================================= #
+    when 'password?',
+         'password',
+         'show_password',
+         'spassword',
+         'spass',
+         'showpassword'
+      show_password
+    # ======================================================================= #
+    # === show_sql_commands_only
+    # ======================================================================= #
+    when 'show_sql_commands_only',
+         'showsqlcommandsonly',
+         'show2'
+      show_sql_commands_only
+    # ======================================================================= #
+    # === commands?
+    # ======================================================================= #
+    when 'commands?',
+         'commands',
+         'show_sql_commands',
+         'sql?',
+         'sqlinfo',
+         'tables?',
+         'stored?',
+         'databases?',
+         'database?',
+         'sql_commands?'
+      show_sql_commands
+    # ======================================================================= #
+    # === autogenerated_sql_files_dir
+    # ======================================================================= #
+    when 'AUTOGENERATED_SQL_FILES_DIR','autogenerated_sql_files_dir'
+      e AUTOGENERATED_SQL_FILES_DIR
+    # ======================================================================= #
+    # === usewhichdatabase?
+    # ======================================================================= #
+    when 'use_which_database?',
+         'which_database?',
+         'd??',
+         'datenbank?',
+         'usewhichdatabase?',
+         'usewhichdatabase',
+         'whichdatabase?'
+      e File.read(FILE_USE_THIS_DATABASE)
+    # ======================================================================= #
+    # === populatenodestable
+    # ======================================================================= #
+    when /^populate(_|-)?nodes(_|-)?table$/i,
+         'nodestable',
+         'nodes.sql'
+      nodes_sql
+    # ======================================================================= #
+    # === populatenamestable
+    # ======================================================================= #
+    when 'populate_names_table','populatenamestable','namestable',
+         'names.sql'
+      names_sql
+    # ======================================================================= #
+    # === create_database
+    # ======================================================================= #
+    when /^create(_|-)?database/,
+         'cdata'
+      create_database
+    # ======================================================================= #
+    # === generatesql
+    # ======================================================================= #
+    when 'make_sql',
+         'makesql',
+         'msql',
+         'do_sql',
+         'dosql',
+         'generatesql'
+      nodes_sql
+      names_sql
+    # ======================================================================= #
+    # === config?
+    # ======================================================================= #
+    when 'config?'
+      show_configuration
+    # ======================================================================= #
+    # === dirs?
+    # ======================================================================= #
+    when 'dirs?','feedback','d?','dir?','home?'
+      show_important_directories # Defined in this file here.
+    # ======================================================================= #
+    # === last_update
+    # ======================================================================= #
+    when 'last_update',
+         'last_update?',
+         'lup',
+         'lup?',
+         'lupd',
+         'lupdate?',
+         'lastupdate',
+         'lupd?',
+         'lastupdate?',
+         'lastupdated?',
+         'last_upd?'
+      try_to_show_when_the_last_update_has_happened
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'create_fasta_table',
+         'ftable',
+         'fff',
+         'cfasta',
+         'createfastatable'
+      create_fasta_table
+    # ======================================================================= #
+    # === names
+    # ======================================================================= #
+    when 'names',
+         'nodes',
+         'fasta2',
+         'names_db',
+         'nodes_db',
+         'fasta_db'
+      # ===================================================================== #
+      # We default to the directory SHARED_HOME, unless the user did
+      # input any other arg.
+      # ===================================================================== #
+      cd SHARED_HOME unless f
+      i = i.gsub(/_db/,'') # Get rid of possible _db entries.
+      this_file = i+'.sql'
+      remove(i+'.sql', true) if File.exist? this_file
+      if be_verbose?
+        e 'In '+sdir(Dir.pwd+'/')+', we will now generate the '+
+          sfile(this_file)+' file anew. This may take'
+        e 'a while, please be patient.'
+      end
+      create_and_save_table(i)
+      # ===================================================================== #
+      # Next, fill in that .sql file with INSERT INTO statements.
+      # ===================================================================== #
+      populate(i, false, this_file) # in file commands.rb
+      finished 'Generated '+i.to_s+'.' if File.exist? this_file
+    # ======================================================================= #
+    # === cat
+    # ======================================================================= #
+    when 'cat'
+      cat(f)
+    # ======================================================================= #
+    # === cd
+    # ======================================================================= #
+    when 'cd'
+      cd(f, :be_verbose)
+    # ======================================================================= #
+    # === colours?
+    # ======================================================================= #
+    when 'colours?'
+      e 'Will we use colours: '+@use_colours.to_s
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'BASE?','base'
+      cd working_directory?
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'url?'
+      e NCBI_URL
+    # ======================================================================= #
+    # === date
+    # ======================================================================= #
+    when 'date',
+         'time',
+         'date?',
+         'time?',
+         'show_current_time_and_date'
+      show_current_time_and_date
+    # ======================================================================= #
+    # === populate
+    # ======================================================================= #
+    when 'populate',
+         'pop',
+         'loadup', # This will loadup dataset from a fasta file into the fasta table.
+         'create_sql_file_from_local_fasta_entry'
+      create_sql_file_from_local_fasta_entry(f)
+    # ======================================================================= #
+    # === create?
+    # ======================================================================= #
+    when 'create?'
+      e 'We can create:'
+      e '  names'
+      e '  nodes'
+    # ======================================================================= #
+    # === ctable
+    # ======================================================================= #
+    when 'create_table','ctable','createtable','create'
+      create_table(first_argument?)
+    # ======================================================================= #
+    # === create_dirs
+    # ======================================================================= #
+    when 'create_dirs','cdirs'
+      create_dirs(:be_verbose)
+    # ======================================================================= #
+    # === verify
+    # ======================================================================= #
+    when 'verify?','verify','ver','v','debug','debug?'
+      verify_proper_sql_structures
+    # ======================================================================= #
+    # === show_help
+    # ======================================================================= #
+    when 'help','hlep',
+         'subhelp',
+         'shelp',
+         'helps',
+         '?',
+         'hlp',
+         '--help',
+         '-help'
+      show_help
+    # ======================================================================= #
+    # === instructions?
+    # ======================================================================= #
+    when 'instructions?','instruction','ins','ins?',
+         'inst?','instruction?'
+      try_to_show_instructions
+    # ======================================================================= #
+    # === test
+    # ======================================================================= #
+    when 'test','batch','batch_process','batch_read_info_files',
+         'batch?','batchprocess'
+      ParseFasta.batch_process # Run them all.
+    # ======================================================================= #
+    # === parentid
+    # ======================================================================= #
+    when 'parent_id','pid','parentid','pid?','parentof',
+         'get_parent_id_of','parent'
+      e 'The parent id of Tax ID '+sfancy(f)+' is: '+simp(
+           get_parent_id_of(f)
+         )
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'get_scientific_name_of','getscientificnameof', # Obtain the scientific name here.
+         'science','sciname','sci','sciid','scif',
+         'show_scientific_name_of','scientific_name_of',
+         'name_of',
+         'scientific_name',
+         'scientificname'
+      show_scientific_name_of(f)
+    # ======================================================================= #
+    # === insert_into
+    # ======================================================================= #
+    when 'insert_into','insertinto','iinto'
+      insert_into(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'postgres_size?','show_postgres_size','showpostgressize',
+         'showsize','size?','table_size?','tablesize?'
+      show_postgres_size
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'fasta_table?','fastatable?'
+      result = run_sql(
+        'select * from fasta limit 0;',
+      false).strip.gsub(/\(0 rows\)/,'')
+      e 'The fasta table has these entries: '+N+'   '+result
+    # ======================================================================= #
+    # === search_by_name
+    # ======================================================================= #
+    when 'search_by_name','search_in_database_for_name','sname',
+         'search','name','searchfor','sfor','search_for'
+      result = search_in_database_for_name(f).strip.split(N)
+      result.each {|entry|
+        entry = entry.split('|'); e entry[0]+' '+entry[1]
+      }
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'find_highest',
+         'latest','current','akt'
+      find_highest_entries_in_sql
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'fullhelp','fhelp'
+      begin
+        require 'case_parser'
+        CaseParser.parse(__FILE__).each {|entry|
+          e "  - #{entry}"
+        }
+      rescue LoadError
+      end
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'enable_colours','enablecolours','yescolours',
+         'ecolours'
+      enable_colours
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'update','lupdate','upd'
+      lupdate(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'be'
+      be(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'dropper'
+      drop_nodes_and_names_database_tables
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'read_in_names_and_nodes_sql_files','readinnamesandnodessqlfiles'
+      read_in_names_and_nodes_sql_files
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'verbose?'
+      e be_verbose?.to_s
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'open','open_project_files'
+      open_project_files
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'set_path','setpath','spath','path','update_path'
+      set_path(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'info?','i?','info','info2','inf','nfo',
+         'parse_info','parseinfo','pinfo'
+      if f # If given a single .INFO file, continue here.
+        cliner {
+          _ = Info.new(f)
+          _.show_info(false) # false so we don't use cliner.
+          _.show_likely_fasta_file_if_it_can_be_found
+          if _.location.include? 'incoming/'
+            e 'We found the string incoming/ as being part of the location of the .INFO file.'
+            e '(The full location is: '+sfile(_.location?)+')'
+            e 'We thus assume that you wish to automatically load this dataset into '
+            e 'the localome table, and we will do so now.'
+            create_sql_file_from_local_fasta_entry(f)
+          end
+        }
+      else
+        cliner {
+          report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
+        }
+      end
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'obtain_full_lineage_for','obtainfulllineagefor'
+      pp obtain_full_lineage_for(f)
+      e 'This has also built the two lineage IDs:'+N+N
+      efancy '  '+@lineage_ids.to_s
+      efancy '  '+@lineage_scientific_name.to_s
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'search_in_localomes','searchinlocalomes','sin',
+         'searchlocalomes','slocal','slocalomes'
+      search_in_localomes(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'query_localomes_by_modtime','mod_time','modtime',
+         'modtime?'
+      query_localomes_by_modtime
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'get_all_info_entries_with_tax_id','getallinfoentrieswithtaxid',
+         'ginfo','get_all_info_entries_with_taxid'
+      get_all_info_entries_with_tax_id
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'fasta?','table?'
+      e 'We use these values for the fasta table:'
+      e '  '+FASTA_ENTRIES
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'type','types','type?','types?',
+         'show_type_of_all_info_files','showtypeofallinfofiles'
+      show_type_of_all_info_files(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'name,taxid','names,taxid'
+      run_sql 'select name,taxid from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'get_id','id','id?','getid','idof?','gid','getidof',
+         'get_id_of','showid'
+      get_id_of(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'edit','edit_login'
+      edit(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'lineage','get_lineage','getlineage','get_parent_ids',
+         'getparentids','gpids','pids','pids_of','pidsof',
+         'allids','linage'
+      return_full_lineage_of(f)
+      report_lineage_of(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'login?','login_information?','linfo?','login',
+         'show_login_information','showlogininformation'
+      show_login_information
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'nodes?','show_nodes_table','shownodestable'
+      show_nodes_table
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'store_where?','storewhere?'
+      e 'We will store at '+sdir(TEMP_DIR)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'generate'
+      generate(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'status?','status','stat','stats','data?',
+         'try_to_display_the_status'
+      try_to_display_the_status(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'remove','remove_taxid_from_localome_table',
+         'remove_id'
+      remove_taxid_from_localome_table(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'drop_table','droptable','drop','dropt'
+      drop_table(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'disable'
+      disable(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'where','where?'
+      e TAXONOMY_DIR+'names.dmp'
+      e TAXONOMY_DIR+'nodes.dmp'
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'taxtree','taxtree?','tree','treetax','tax_tree'
+      taxtree(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'query_whether_we_have_this_id','has_id?','hasid','hasid?'
+      query_whether_we_have_this_id(f)
+    # ======================================================================= #
+    # === update_lineage
+    # ======================================================================= #
+    when 'update_lineage','updatelineage','ulineage'
+      update_lineage # Only update the lineage, nothing else.
+    # ======================================================================= #
+    # === ll
+    # ======================================================================= #
+    when 'll','LL','l',
+         'lll',
+         'show_directory_content',
+         'directory_paradise'
+      show_directory_content
+    # ======================================================================= #
+    # === load_from_info
+    # ======================================================================= #
+    when 'load_from_info','linfo','loadinfo'
+      load_from_info(f)
+    # ======================================================================= #
+    # === lafo
+    # ======================================================================= #
+    when 'lafo','loadup_localomes','loaduplocalomes','goloc',
+         'localomes_go','localomesgo','golocal','goloco',
+         'localgo','update_local_localomes','update2',
+         'default'
+      update_local_localomes
+    # ======================================================================= #
+    # === show_all_eukarya
+    # ======================================================================= #
+    when 'show_all_eukarya','eukarya?','eukarya','eucarya?','eucarya',
+         'eukaryota','seu','euk'
+      show_all_eukarya(f)
+    # ======================================================================= #
+    # === repeat_last
+    # ======================================================================= #
+    when 'repeat_last','last_command','lastcommand','last' # We will repeat the last command here.
+      repeat_last_command
+    # ======================================================================= #
+    # === deepfasta
+    # ======================================================================= #
+    when 'deepfasta' # The difference here is that we will also report the sequence.
+      _ = Taxonomy::ParseFasta.new(f)
+      e 'The (at least one) sequence is: '+sfancy(_.sequence.first)
+      e 'The status for '+sfile(_.location)+' is as follows:'
+      _.report_status
+      pp _.hash
+    # ======================================================================= #
+    # === isdna
+    # ======================================================================= #
+    when 'isdna','is_dna','isdna?'
+      Taxonomy::IsDNA.new(f).report
+    # ======================================================================= #
+    # === nohelp
+    # ======================================================================= #
+    when 'nohelp','nhelp','nh','silence'
+      nohelp
+    # ======================================================================= #
+    # === silent
+    # ======================================================================= #
+    when 'silent','be_silent','besilent'
+      be_silent
+      nohelp
+    # ======================================================================= #
+    # === taxid
+    # ======================================================================= #
+    when 'taxid','t','taxid?','tid'
+      get_id_of(f)
+      e 'http://www.ncbi.nlm.nih.gov/taxonomy/?term='+f.to_s
+    # ======================================================================= #
+    # === silently_update_ncbi_database
+    # ======================================================================= #
+    when 'silently_update_ncbi_database'
+      silently_update_ncbi_database
+    # ======================================================================= #
+    # === n_info?
+    # ======================================================================= #
+    when 'n_info?','ninfo'
+      report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
+    # ======================================================================= #
+    # === taxid,name,path
+    # ======================================================================= #
+    when 'taxid,name,path'
+      run_sql 'SELECT taxid,name,path from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === name,path,taxid
+    # ======================================================================= #
+    when 'name,path,taxid'
+      run_sql 'SELECT name,path,taxid from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === taxid,name,path,filesize
+    # ======================================================================= #
+    when 'taxid,name,path,filesize'
+      run_sql 'SELECT taxid,name,path,filesize from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === dependencies?
+    # ======================================================================= #
+    when 'dependencies?','deps?','dep?'
+      try_to_show_dependencies
+    # ======================================================================= #
+    # === taxid,path
+    # ======================================================================= #
+    when 'taxid,path'
+      run_sql 'SELECT taxid,path from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === name,path
+    # ======================================================================= #
+    when 'name,path'
+      run_sql 'SELECT name,path from fasta ORDER BY name;'
+    # ======================================================================= #
+    # === name,taxid,path
+    # ======================================================================= #
+    when 'name,taxid,path'
+      run_sql 'SELECT name,taxid,path from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === taxid,name
+    # ======================================================================= #
+    when 'taxid,name'
+      run_sql 'SELECT taxid,name from fasta ORDER BY taxid;'
+    # ======================================================================= #
+    # === edit_instructions
+    # ======================================================================= #
+    when 'edit_instructions'
+      edit_instructions
+    # ======================================================================= #
+    # === make_taxonomy_gem
+    # ======================================================================= #
+    when 'make_taxonomy_gem','make_gem','gem','makegem',
+         'make','gemmer'
+      make_taxonomy_gem
+    # ======================================================================= #
+    # === check_available
+    # ======================================================================= #
+    when 'check_available','checkavailable','cavail',
+         'cavailable','cava'
+      Taxonomy::CheckAvailable.new
+    # ======================================================================= #
+    # === www?
+    # ======================================================================= #
+    when 'www?','www','cgi?','cgi'
+      e 'http://localomics.imp.univie.ac.at:8666/'
+    # ======================================================================= #
+    # === sdc
+    # ======================================================================= #
+    when 'sdc'
+      begin
+        require 'show_directory_content'
+        ShowDirectoryContent.new
+      rescue; end # Silent error here.
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'all_info_files','all_info','allinfo','fa?'
+      pp Dir[AA_DIR+'*.fa']
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'localome?'
+      localome?
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'add_comment','comment','addcomment'
+      add_comment(f)
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'comments?'
+      menu 'taxid,comment_field'
+    # ======================================================================= #
+    # === update_database
+    # ======================================================================= #
+    when 'update_database','ud','updatedatabases','update_databases',
+         'update_ncbi_database','updatencbidatabase','update_ncbi',
+         'main' # This is the main action (main tag).
+      update_ncbi_database
+    # ======================================================================= #
+    # === finished
+    # ======================================================================= #
+    when 'finished'
+      finished
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when '',nil
+      show_short_help
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'ftp','start_ftp'
+      begin
+        require 'ftp_paradise'
+        FtpParadise::InteractiveFtp.new
+      rescue LoadError
+        e 'ftp is not available, it would depend on the ftp_paradise gem.'
+      end
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'prokarya?','prokarya','procarya?','procarya',
+         'show_all_prokarya','spu'
+      show_all_prokarya 
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'parse','parse_fasta','parsefasta','par','pa','paste',
+         'papa','pp','fasta','fas','-','pfasta'
+      _ = ParseFasta.new(f)
+      _.report_one_sequence
+      e 'The status for '+sfile(_.location)+' is as follows:'
+      _.report_status
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'port?','port','show_port','showport','sport?','sport',
+         '--port','-port','p?'
+      show_port
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'show_changelog','changes?','showchangelog','changelog?'
+      show_changelog
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'shared_code?','sharedcode?','show_shared_code_location',
+         'showsharedcodelocation','sshared','scode?'
+      show_shared_code_location
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'pwd','pwd?'
+      e sdir(  ( Dir.pwd+'/' ).squeeze('/') )
+    # ======================================================================= #
+    # === edit_gemspec
+    # ======================================================================= #
+    when 'edit_gemspec','gemspec','gemspec?','gspec'
+      edit_gemspec
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'show_table_names','table_names?','tablenames','tnames',
+         'table_names','tablenames?','tnames?','1'
+      show_table_names
+    # ======================================================================= #
+    # === 
+    # ======================================================================= #
+    when 'paths?'
+      menu 'taxid,name,path'
+    # ======================================================================= #
+    # === create_default_directories
+    # ======================================================================= #
+    when 'create_default_directories','cdd','simulate'
+      create_default_directories
+    else # else tag
+      if i.include? '.INFO'
+        menu 'parse_info',i
+      elsif i.include? '.fa' # Delegate to parsing a fasta file here.
+        menu 'parse_fasta',i
+      elsif i.include? AA_DIR
+        menu 'parse_fasta',i
+      elsif i.include?(',') # General pass through (an assumption however).
+        query_from_localome_table(i)
+      elsif ::Rcfiles::DirectoryAliases.does_include?(i)
+        e sdir(rds(Dir.pwd+'/'))
+      else
+        e 'In the method menu(), file '+__FILE__.to_s+':'
+        e 'We did not find the input: `'+sfancy(i.to_s)+'`'
+      end
+    end # end tag
+  end; alias check_against_menu menu # === check_against_menu
+
+  # ========================================================================= #
+  # === rds
+  # ========================================================================= #
+  def rds(i)
+    i.squeeze('/')
+  end
+
+end; end; end