bioroebe 0.10.80 → 0.11.25

data/lib/bioroebe/taxonomy/interactive.rb

@@ -59,6 +59,9 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
 
   # ========================================================================= #
   # === FASTA_SQL
+  #
+  # This constant will point towards a location such as
+  # "/home/Temp/bioroebe/autogenerated_sql_files/fasta.sql".
   # ========================================================================= #
   FASTA_SQL = AUTOGENERATED_SQL_FILES_DIR+'fasta.sql'
 
@@ -124,6 +127,69 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     @run_standalone = true
   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(:default_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
+
+  # ========================================================================= #
+  # === create_and_save_table
+  # ========================================================================= #
+  def create_and_save_table(
+      i, be_verbose = false
+    )
+    case i
+    # ======================================================================= #
+    # === :default_fasta
+    # ======================================================================= #
+    when :default_fasta
+      i = FASTA_SQL
+    end
+    require 'roebe/sql_paradise/commands.rb'
+    Roebe::SqlParadise::Commands.create_and_save_table(i, be_verbose)
+  end
+
+  # ========================================================================= #
+  # === update_local_localomes
+  #
+  # Update the local collection. This will overwrite the old dataset
+  # completely, so be careful when using this.
+  #
+  # To invoke this method via the interactive menu, do:
+  #
+  #   update databases
+  #
+  # ========================================================================= #
+  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
+
   # ========================================================================= #
   # === get                                                         (get tag)
   #
@@ -204,34 +270,13 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     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
+  def try_to_display_the_status(
+      i = nil
+    )
+    if i and !i.empty? # if an argument was provided
       StatFile.new(i) if Object.const_defined?(:StatFile)
     else
       Taxonomy.status?
@@ -333,6 +378,42 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     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'
+    # ======================================================================= #
+    # === download --ncbi
+    # ======================================================================= #
+    when /^-?-?ncbi/i,
+         '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
+
   # ========================================================================= #
   # === report_lineage_ids_and_lineage_scientific_name
   # ========================================================================= #
@@ -378,24 +459,34 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   # the localomes entry.
   # ========================================================================= #
   def lupdate(i = :ncbi)
-    i = i.to_s
+    i = i.to_s # Use a String past this point.
     case i
-    when 'all','everything','both'
-      update_ncbi_database
-      update_local_localomes
-      update_lineage
+    # ======================================================================= #
+    # === localomes
+    # ======================================================================= #
+    when 'localomes',
+         'local','loc','localome','2',
+         'fasta',
+         'database',
+         'databases'
+      update_local_localomes # This will overwrite the old dataset completely, be careful.
     # ======================================================================= #
     # === ncbi_database
     # ======================================================================= #
-    when /^ncbi(-|_| )?database$/, 'ncbi','1',
+    when /^ncbi(-|_| )?database$/,
+         'ncbi',
+         '1',
          'update_ncbi'
       update_ncbi_database
     # ======================================================================= #
-    # === localomes
+    # === lupdate all
     # ======================================================================= #
-    when 'localomes','local','loc','localome','2',
-         'fasta','database','databases'
-      update_local_localomes # This will overwrite the old dataset completely, be careful.
+    when 'all',
+         'everything',
+         'both'
+      update_ncbi_database
+      update_local_localomes
+      update_lineage
     # ======================================================================= #
     # === lineage
     # ======================================================================= #
@@ -478,8 +569,9 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   # ========================================================================= #
   # === update_ncbi_database
   # 
-  # We will update the NCBI Taxonomy database with this method. This
-  # includes a download, extracting it, generating the .sql files,
+  # This method can be used to update the NCBI Taxonomy database.
+  #
+  # This includes a download, extracting it, generating the .sql files,
   # and then populating the postgresql database.
   # ========================================================================= #
   def update_ncbi_database
@@ -673,7 +765,9 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   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 '  '+sfile(
+        Bioroebe::Taxonomy.project_base_dir?+'databases/postgresql_login_command.rb'
+      )
     e
     show_port # Show the port as well here.
   end
@@ -682,7 +776,7 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   # === return_shared_code
   # ========================================================================= #
   def return_shared_code
-    return PROJECT_BASE_DIR2+'shared/shared'
+    return Bioroebe::Taxonomy.project_base_dir?+'shared/shared'
   end
 
   # ========================================================================= #
@@ -698,7 +792,7 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   # === return_login_file
   # ========================================================================= #
   def return_login_file
-    return PROJECT_BASE_DIR2+'postgresql_login_command.rb'
+    return Bioroebe::Taxonomy.project_base_dir?+'postgresql_login_command.rb'
   end
 
   # ========================================================================= #
@@ -974,18 +1068,21 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     return result
   end; alias get_lineage_ids_and_lineage_scientific_name obtain_full_lineage_for
 
+  require 'bioroebe/constants/database_constants.rb'
   # ========================================================================= #
   # === drop_table                                                 (drop tag)
   #
   # Use this method when you wish to drop a table.
   # ========================================================================= #
-  def drop_table(i = DROP_FASTA_TABLE)
+  def drop_table(
+      i = Bioroebe::Postgresql::DROP_FASTA_TABLE
+    )
     case i.to_s
     when 'nodes'
     when 'fasta',
          'localomes',
          'localome'
-      i = DROP_FASTA_TABLE
+      i = Bioroebe::Postgresql::DROP_FASTA_TABLE
     end
     ::Bioroebe.run_sql_query(i)
   end
@@ -1645,24 +1742,6 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     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
   # ========================================================================= #
@@ -1846,41 +1925,6 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
     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
   # ========================================================================= #

data/lib/bioroebe/taxonomy/menu.rb

@@ -44,6 +44,28 @@ class Interactive < ::Bioroebe::CommandlineApplication
     record_last_command(i, first_argument?) # Record the last command.
     case i # (case tag)
     # ======================================================================= #
+    # === update
+    # ======================================================================= #
+    when 'update',
+         'lupdate',
+         'upd'
+      lupdate(f)
+    # ======================================================================= #
+    # === download
+    # ======================================================================= #
+    when 'download'
+      download(f)
+    # ======================================================================= #
+    # === status?
+    # ======================================================================= #
+    when 'status?',
+         'status',
+         'stat',
+         'stats',
+         'data?',
+         'try_to_display_the_status'
+      try_to_display_the_status(f)
+    # ======================================================================= #
     # === disable_colours
     # ======================================================================= #
     when 'disable_colours',
@@ -65,11 +87,6 @@ class Interactive < ::Bioroebe::CommandlineApplication
     when /^download(_|-)?database$/i,'ncbi_down'
       download_ncbi_database
     # ======================================================================= #
-    # === download
-    # ======================================================================= #
-    when 'download'
-      download(f)
-    # ======================================================================= #
     # === exit
     # ======================================================================= #
     when *VALID_WAYS_TO_EXIT
@@ -448,11 +465,6 @@ class Interactive < ::Bioroebe::CommandlineApplication
     # ======================================================================= #
     # === 
     # ======================================================================= #
-    when 'update','lupdate','upd'
-      lupdate(f)
-    # ======================================================================= #
-    # === 
-    # ======================================================================= #
     when 'be'
       be(f)
     # ======================================================================= #
@@ -589,12 +601,6 @@ class Interactive < ::Bioroebe::CommandlineApplication
     # ======================================================================= #
     # === 
     # ======================================================================= #
-    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)
@@ -647,7 +653,9 @@ class Interactive < ::Bioroebe::CommandlineApplication
     # ======================================================================= #
     when 'lafo','loadup_localomes','loaduplocalomes','goloc',
          'localomes_go','localomesgo','golocal','goloco',
-         'localgo','update_local_localomes','update2',
+         'localgo',
+         'update_local_localomes',
+         'update2',
          'default'
       update_local_localomes
     # ======================================================================= #
@@ -796,7 +804,8 @@ class Interactive < ::Bioroebe::CommandlineApplication
     # === update_database
     # ======================================================================= #
     when 'update_database','ud','updatedatabases','update_databases',
-         'update_ncbi_database','updatencbidatabase','update_ncbi',
+         'update_ncbi_database',
+         'updatencbidatabase','update_ncbi',
          'main' # This is the main action (main tag).
       update_ncbi_database
     # ======================================================================= #

data/lib/bioroebe/taxonomy/parse_fasta.rb

@@ -111,7 +111,9 @@ class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy::
   # ========================================================================= #
   # === try_to_locate_info_file
   # ========================================================================= #
-  def try_to_locate_info_file(i = @location)
+  def try_to_locate_info_file(
+      i = @location
+    )
     i = File.basename(i)
     # chop away the extname.
     i.gsub!(/#{File.extname(i)}/, '')

data/lib/bioroebe/taxonomy/shared.rb

@@ -16,6 +16,7 @@
 # include this module here.
 # =========================================================================== #
 # require 'bioroebe/taxonomy/shared/shared.rb'
+# =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
 
 module Bioroebe # === Bioroebe::Taxonomy::Shared

data/lib/bioroebe/taxonomy/taxonomy.rb

@@ -16,6 +16,7 @@ module Taxonomy
   require 'bioroebe/taxonomy/class_methods.rb'
   require 'bioroebe/taxonomy/chart.rb'
   require 'bioroebe/taxonomy/node.rb'
+  require 'bioroebe/constants/misc.rb'
 
   require 'bioroebe/toplevel_methods/databases.rb'
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'

data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb

@@ -129,29 +129,6 @@ module Bioroebe
     return _
   end
 
-  # ========================================================================= #
-  # === Bioroebe.remove_invalid_aminoacids
-  #
-  # This method will filter away invalid aminoacids such as "U".
-  # "U" is not a valid aminoacid.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.remove_invalid_aminoacids('LKLSUSURZZZ')
-  #
-  # ========================================================================= #
-  def self.remove_invalid_aminoacids(from_this_string)
-    if from_this_string.is_a? Array
-      from_this_string = from_this_string.first
-    end
-    all_valid_aminoacids = YAML.load_file(Bioroebe.file_amino_acids).keys
-    new_result = ''.dup
-    from_this_string.chars.each {|entry|
-      new_result << entry if all_valid_aminoacids.include?(entry)
-    }
-    return new_result
-  end
-
   # ========================================================================= #
   # === Bioroebe.colourize_aa
   #
@@ -664,6 +641,36 @@ module Bioroebe
     end
   end
 
+  # ========================================================================= #
+  # === Bioroebe.remove_invalid_aminoacids
+  #
+  # This method will filter away invalid aminoacids such as "U".
+  # "U" is not a valid aminoacid. It requires the data stored
+  # in the yaml file at:
+  # 
+  #    "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids.yml"
+  #
+  # Note that U is a valid aminoacid - it is selenocysteine.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.remove_invalid_aminoacids('LKLSUSURZZZ')
+  #
+  # ========================================================================= #
+  def self.remove_invalid_aminoacids(
+      from_this_string
+    )
+    if from_this_string.is_a? Array
+      from_this_string = from_this_string.first
+    end
+    all_valid_aminoacids = YAML.load_file(Bioroebe.file_amino_acids).keys
+    new_result = ''.dup
+    from_this_string.chars.each {|entry|
+      new_result << entry if all_valid_aminoacids.include?(entry)
+    }
+    return new_result
+  end
+
 end
 
 if __FILE__ == $PROGRAM_NAME
@@ -682,7 +689,7 @@ if __FILE__ == $PROGRAM_NAME
     input = ARGV.join(' ').strip
   end
 
-  puts 'From '+input+' to: '+Bioroebe.three_to_one(input) # => "TRH"
+  e 'From '+input+' to: '+Bioroebe.three_to_one(input) # => "TRH"
   # And more tests:
   #   p Bioroebe.is_aminoacid? 'Tryptophan' # => true
   #   p Bioroebe.is_aminoacid? 'Glycine'    # => true

data/lib/bioroebe/toplevel_methods/databases.rb

@@ -15,7 +15,7 @@ module Bioroebe
   # can pass the password for the postgreSQL database.
   # ========================================================================= #
   def self.set_pgpassword(
-      new_password = POSTGRE_PASSWORD
+      new_password = Bioroebe::Postgresql::POSTGRE_PASSWORD
     )
     ENV['PGPASSWORD'] = new_password
   end; self.instance_eval { alias set_password set_pgpassword } # === Bioroebe.set_password