bioroebe 0.10.80 → 0.11.25

data/lib/bioroebe/aminoacids/aminoacid_substitution.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe::AminoacidSubstitution
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -49,10 +44,7 @@ class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/aminoacids/codon_percentage.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::CodonPercentage
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -45,10 +40,7 @@ class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::Codon
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb

@@ -38,11 +38,6 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
   require 'bioroebe/misc/ruler.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_SEQUENCE
   #
@@ -73,10 +68,7 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/display_aminoacid_table.rb

@@ -79,6 +79,7 @@ class DisplayAminoacidTable < Bioroebe::CommandlineApplication # === Bioroebe::D
     if i.is_a? Array
       i = i.join(' ').strip
     end
+    i = ::Bioroebe.filter_away_invalid_aminoacids(i)
     @input = i
   end
 

data/lib/bioroebe/aminoacids/show_hydrophobicity.rb

@@ -27,11 +27,6 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
     HYDROPATHY_TABLE = YAML.load_file(FILE_HYDROPATHY_TABLE)
   end
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -142,7 +137,7 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
   # ========================================================================= #
   def opnn(i = nil)
     hash = {}
-    hash.merge!(namespace: NAMESPACE)
+    hash.merge!(namespace: namespace?)
     hash.merge!(i) if i
     super(hash)
   end

data/lib/bioroebe/base/colours_for_base/colours_for_base.rb

@@ -209,14 +209,6 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     return i
   end
 
-  # ========================================================================= #
-  # === sfancy
-  # ========================================================================= #
-  def sfancy(i = '')
-    return powderblue(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
-    return i
-  end
-
   # ========================================================================= #
   # === simp
   # ========================================================================= #
@@ -272,4 +264,22 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     @use_colours = true
   end
 
+  # ========================================================================= #
+  # === efancy
+  # ========================================================================= #
+  def efancy(i)
+    e sfancy(i)
+  end
+
+  # ========================================================================= #
+  # === sfancy
+  # ========================================================================= #
+  def sfancy(
+      i           = '',
+      use_colours = use_colours?
+    )
+    return powderblue(i) if use_colours and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/commandline_arguments.rb

@@ -111,6 +111,14 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     @commandline_arguments.join(' ').strip
   end
 
+  # ========================================================================= #
+  # === first_non_hyphen_argument?
+  # ========================================================================= #
+  def first_non_hyphen_argument?
+    return_entries_without_two_leading_hyphens.first
+  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+
+
   # ========================================================================= #
   # === select_entries_starting_with_two_hyphens
   #
@@ -125,20 +133,14 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     else
       []
     end
-  end; alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
-       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
-       alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
+  end; alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
        alias return_arguments_with_leading_hyphens                  select_entries_starting_with_two_hyphens # === return_arguments_with_leading_hyphens
        alias return_commandline_arguments_starting_with_hyphens     select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_hyphens
        alias return_commandline_arguments_starting_with_two_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_two_hyphens
-       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
+       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
+       alias commandline_arguments_containing_leading_hyphens?      select_entries_starting_with_two_hyphens # === commandline_arguments_containing_leading_hyphens?
+       alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
        alias commandline_arguments_starting_with_leading_hyphens?   select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_leading_hyphens?
-
-  # ========================================================================= #
-  # === first_non_hyphen_argument?
-  # ========================================================================= #
-  def first_non_hyphen_argument?
-    return_entries_without_two_leading_hyphens.first
-  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
 
 end; end

data/lib/bioroebe/base/commandline_application/misc.rb

@@ -435,14 +435,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     return i.delete('[0-9]')
   end
 
-  require 'bioroebe/toplevel_methods/open_in_browser.rb'
-  # ========================================================================= #
-  # === open_in_browser
-  # ========================================================================= #
-  def open_in_browser(this_url)
-    ::Bioroebe.open_in_browser(this_url)
-  end
-
   # ========================================================================= #
   # === load_bioroebe_yaml_file
   #
@@ -482,4 +474,22 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
   end; alias three_aminoacid_letter_code_to_one_aminoacid_letter_code three_to_one # === three_aminoacid_letter_code_to_one_aminoacid_letter_code
        alias three_letters_to_one_letter                              three_to_one # === three_letters_to_one_letter
 
+  require 'bioroebe/toplevel_methods/open_in_browser.rb'
+  # ========================================================================= #
+  # === open_in_browser
+  # ========================================================================= #
+  def open_in_browser(this_url)
+    ::Bioroebe.open_in_browser(this_url)
+  end; alias open_in_browser_tab open_in_browser # === open_in_browser_tab
+
+  require 'bioroebe/toplevel_methods/verbose.rb'
+  # ========================================================================= #
+  # === verbose_truth
+  #
+  # Delegate towards the module Bioroebe::VerboseTruth here.
+  # ========================================================================= #
+  def verbose_truth(i)
+    ::Bioroebe::VerboseTruth[i]
+  end
+
 end; end

data/lib/bioroebe/base/misc.rb

@@ -91,4 +91,20 @@ class Base
     ::Bioroebe.project_yaml_directory?
   end; alias yaml_directory? project_yaml_directory? # === yaml_directory?
 
+  # ========================================================================= #
+  # === infer_the_namespace
+  #
+  # This will assume the true namespace from the inspectable name.
+  # ========================================================================= #
+  def infer_the_namespace
+    _ = inspect.to_s.delete('<')
+    if _.include? ' '
+      _ = _.split(' ').first.delete('#')
+      if _.include? ':'
+        _ = _.split(':')[0 .. -2].reject {|entry| entry.empty? }.join('::')
+      end
+    end
+    @namespace = _ # And assign it here.
+  end
+
 end; end

data/lib/bioroebe/base/prototype/misc.rb

@@ -18,7 +18,7 @@ class Base
   # ========================================================================= #
   def is_on_roebe?
     ::Bioroebe.is_on_roebe?
-  end
+  end; alias on_roebe? is_on_roebe? # === on_roebe?
 
   # ========================================================================= #
   # === main_encoding?

data/lib/bioroebe/codons/show_codon_tables.rb

@@ -37,6 +37,7 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
     else
       first = show_what
     end
+    first = first.to_s.delete('-')
     case first.to_sym
     # ======================================================================= #
     # === :human
@@ -56,7 +57,9 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
          :headers,
          '--headers'
       ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
-        e number.to_s.rjust(3)+') '+long_name.ljust(70)
+        e turquoise(number.to_s.rjust(3))
+          +') '+
+          long_name.ljust(70)
       }
     end
   end
@@ -127,4 +130,5 @@ end
 if __FILE__ == $PROGRAM_NAME
   Bioroebe::ShowCodonTables.new(ARGV)
 end # showcodontables
-    # showcodontables human
+    # showcodontables human
+    # showcodontables everything

data/lib/bioroebe/codons/show_codon_usage.rb

@@ -133,7 +133,8 @@ class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCo
   # ========================================================================= #
   def report_the_top_five_codons(from_this_dataset)
     e
-    e 'The top five codons in use, sorted, are:'
+    erev 'The '+mediumpurple('top five codons')+
+         rev+' in use, sorted by frequency, are:'
     e
     top_five = from_this_dataset.sort_by {|key, values| values }.reverse[0..4]
     top_five.each {|name_of_codon, how_many_of_them|

data/lib/bioroebe/constants/aminoacids_and_proteins.rb

@@ -3,6 +3,7 @@
 # frozen_string_literal: true
 # =========================================================================== #
 # require 'bioroebe/constants/aminoacids_and_proteins.rb'
+# Bioroebe.filter_away_invalid_aminoacids
 # =========================================================================== #
 module Bioroebe
 

data/lib/bioroebe/constants/database_constants.rb

@@ -89,7 +89,7 @@ module Postgresql # === Bioroebe::Postgresql
   DROP_TABLE_FASTA = 'DROP TABLE fasta;'
 
   # ========================================================================= #
-  # === POSTGRE_DROP_FASTA_COMMAND
+  # === Bioroebe::Postgresql::POSTGRE_DROP_FASTA_COMMAND
   # ========================================================================= #
   POSTGRE_DROP_FASTA_COMMAND = DROP_FASTA_TABLE = DROP_TABLE_FASTA
 

data/lib/bioroebe/constants/files_and_directories.rb

@@ -165,15 +165,16 @@ module Bioroebe
   end
 
   # ========================================================================= #
-  # === FILE_FASTQ_QUALITY_SCHEMES
+  # === Bioroebe.file_fastq_quality_schemes
   #
   # This constant will point to a location such as this one here:
   #
   #   /Programs/Ruby/2.6.4/lib/ruby/site_ruby/2.6.0/bioroebe/yaml/fastq_quality_schemes.yml
   #
   # ========================================================================= #
-  FILE_FASTQ_QUALITY_SCHEMES =
-    "#{project_yaml_directory?}fastq_quality_schemes.yml"
+  def self.file_fastq_quality_schemes
+    "#{project_yaml_directory?}fasta_and_fastq/fastq_quality_schemes.yml"
+  end
 
   # ========================================================================= #
   # === Bioroebe.file_talens
@@ -318,10 +319,17 @@ module Bioroebe
   # ========================================================================= #
   # === Bioroebe.file_restriction_enzymes
   # ========================================================================= #
-  def file_restriction_enzymes
+  def self.file_restriction_enzymes
     FILE_RESTRICTION_ENZYMES
   end
 
+  # ========================================================================= #
+  # === file_restriction_enzymes
+  # ========================================================================= #
+  def file_restriction_enzymes
+    ::Bioroebe.file_restriction_enzymes
+  end
+
   # ========================================================================= #
   # === Bioroebe.blosum_directory?
   # ========================================================================= #
@@ -553,6 +561,18 @@ module Bioroebe
     "#{project_yaml_directory?}aminoacids/molecular_weight.yml"
   end
 
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids_long_name_to_one_letter
+  #
+  # This method will return a String such as:
+  #
+  #   "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml"
+  #
+  # ========================================================================= #
+  def self.file_amino_acids_long_name_to_one_letter
+    "#{project_yaml_directory?}aminoacids/amino_acids_long_name_to_one_letter.yml"
+  end
+
 end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/constants/misc.rb

@@ -43,6 +43,26 @@ module Bioroebe
   # ========================================================================= #
   TOKEN = '|'
 
+  # ========================================================================= #
+  # === VALID_WAYS_TO_EXIT
+  #
+  # All ways to exit will be recorded here.
+  #
+  # If you need to use more ways, simply append to this Array.
+  #
+  # This constant may have to be moved into the bio-shell part eventually.
+  # ========================================================================= #
+  VALID_WAYS_TO_EXIT = %w(
+    quit q exit qq :q qt
+    bye
+    rda
+    r2
+    tq
+    sq
+    exit_program
+    exitprogram
+  )
+
   # ========================================================================= #
   # === NAMES_ENTRIES
   #

data/lib/bioroebe/count/count_amount_of_nucleotides.rb

@@ -425,6 +425,9 @@ class CountAmountOfNucleotides < ::Bioroebe::CommandlineApplication # === Bioroe
     if File.exist? i.to_s
       i = File.read(i.to_s).strip.delete(N)
     end
+    if i.is_a? Array
+      i = i.join(' ').strip
+    end
     i = i.to_s.dup if i.frozen?
     i.upcase! # Want to keep it upcased.
     @dna_string = i

data/lib/bioroebe/crystal/README.md

@@ -0,0 +1,2 @@
+This may contain experimental crystal support for the bioroebe
+project.

data/lib/bioroebe/crystal/to_rna.cr

@@ -0,0 +1,19 @@
+module Bioroebe
+
+  # ========================================================================= #
+  # === Bioroebe.to_rna
+  # ========================================================================= #
+  def self.to_rna(i = ARGV)
+    if i.is_a? Array
+      i = i.first?
+    end
+    if i.nil? || i.empty?
+      return i
+    else
+      return i.gsub("T","U")
+    end
+  end
+
+end
+
+puts Bioroebe.to_rna(ARGV)

data/lib/bioroebe/data/README.md

@@ -1,10 +1,13 @@
-This directory may contain some FASTA files or .pdb files, as
-that may be of help of people who end up using the BioRoebe
-project.
+This directory may contain some FASTA files or .pdb files, as that may 
+be of help of people who end up using the BioRoebe project.
+
+That dataset can be quickly tested and used to demonstrate how the 
+BioRoebe project works.
+
+In the pdb/ directory there is presently only one .pdb file. This 
+file is used mostly for a test .rb file in the test/ directory.
+
+The directory electron_microscopy/ is used primarily for cryo-electron
+microscopy and what not, using software such as relion.
 
-That dataset can be quickly tested and used to demonstrate how
-the BioRoebe project works.
 
-In the pdb/ directory there is presently only one .pdb file.
-This file is used mostly for a test .rb file in the test/
-directory.