bioroebe 0.10.80 → 0.11.12

data/doc/todo/bioroebe_todo.md

@@ -1,5 +1,24 @@
+
+GenbankParser should handle multiple genbank files
+^^^^^^^
+
+-------------------------------------------------------------------------------
+(1) → Show the frequency of codons in different tables
+
+  This works quite ok, but right now the approach is to store
+  this in a .yml file which is not ideal.
+
+  Thus, we have to add two things:
+    - The ability to store this into a SQL database
+    - The ability to batch-download all of these codons,
+      which first requires that we have a way to obtain all
+      taxonomic ids.
+Add where this can be found.
 -------------------------------------------------------------------------------
-(1) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
+(2) improve docu + tests for melting temperature analysis again
++ usage example + GUI + web-use
+-------------------------------------------------------------------------------
+(3) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
 
     ^^^ work through the above, also integrate it + write docs
 
@@ -74,7 +93,7 @@ Gibt es neue GUIs die wir kombinieren könnten? Hmmm.
 
 https://www.tbi.univie.ac.at/RNA/tutorial/
 -------------------------------------------------------------------------------
-(1) → get insulin squence frmo NCBI
+(10) → get insulin squence frmo NCBI
         human
       then apply trypsin onto it
       and try it like this:
@@ -89,12 +108,12 @@ Also add:
 Hmm. Perhaps also auto-download or something.
 
 -------------------------------------------------------------------------------
-(1) → in bioroebe: UAG?
+(11) → in bioroebe: UAG?
       ^^^ show all stop codons with that in the bioshell
       all UAG sequences... hmm. and TAG?
       Finish that.
 ..........................................................................
-(1) → The position of a symbol in a string is the total number of
+(12) → The position of a symbol in a string is the total number of
       symbols found to its left, including itself (e.g., the positions
       of all occurrences of 'U' in "AUGCUUCAGAAAGGUCUUACG" are 2, 5,
       6, 15, 17, and 18). The symbol at position i
@@ -103,10 +122,10 @@ Hmm. Perhaps also auto-download or something.
   ^^^ add a solution there, a toplevel API
   !!!!!
 -------------------------------------------------------------------------------
-(1) → http://bioruby.org/rdoc/Bio/Blast.html
+(13) → http://bioruby.org/rdoc/Bio/Blast.html
       ^^^ add support for BLAST
 ..........................................................................
-(1) → add: parse_pdb()
+(14) → add: parse_pdb()
       With this we shall just show some info, about a given
       .pdb file at hand.
       Also make it commandline based too + bioshell variant
@@ -114,18 +133,18 @@ Hmm. Perhaps also auto-download or something.
       Don't forget to document it!!!!!
       ^^^ and google a bit how others do that
 ..........................................................................
-(2) → pdb 1a6m
+(15) → pdb 1a6m
       ^^^ download this when that is used in the bioshell; we also have
           to use the download directory for this, so make sure that
           we do.
       ^^^ And then, also document this clearly.
 -------------------------------------------------------------------------------
-(3) show_string
+(16) show_string
 ^^^ slowly port this ... find out differences
     then unify into one method. right now we used
     two or something.
 -------------------------------------------------------------------------------
-(4) → Try to see if we can integrate this into our GUI:
+(17) → Try to see if we can integrate this into our GUI:
 
   https://cdn.snapgene.com/assets/7.6.11/assets/images/snapgene/homepage/homepage-hero.png
 -------------------------------------------------------------------------------
@@ -409,17 +428,6 @@ class: OptimizeCodons.new(of_this_sequence)
       information for (in mm10). Is there some service online where I can
       paste this list? ^^^ enable this
 -------------------------------------------------------------------------------
-(10) → Show the frequency of codons in different tables
-
-  This works quite ok, but right now the approach is to store
-  this in a .yml file which is not ideal.
-
-  Thus, we have to add two things:
-    - The ability to store this into a SQL database
-    - The ability to batch-download all of these codons,
-      which first requires that we have a way to obtain all
-      taxonomic ids. 
--------------------------------------------------------------------------------
 (11) → Add a way in bioroebe to store a gene into a yaml file
       or so, and to also load it up again. Perhaps simplify
       this automatically. Need some ways to describe that.
@@ -597,9 +605,7 @@ This now sorta works semi-ok.
 -------------------------------------------------------------------------------
 - Neue funktionälit rein
 -------------------------------------------------------------------------------
-- mehr doku!
--------------------------------------------------------------------------------
-- continue on bioroebe, and when it is done, write to the guy.
+- mehr doku!!!
 -------------------------------------------------------------------------------
 - Rewrite bioroebe completely - add some tests, too or so, to
   test this. ^^^
@@ -643,8 +649,6 @@ extend bioroebe sinatra interface
 also add a footer to show which entries are available or so
 → in bioroebe, mach das die postgresql datenbank wieder funktioniert ...
 
-
-
 ..........................................................................
 
 → ^^^ improve this whole project a lot
@@ -687,16 +691,6 @@ also add a footer to show which entries are available or so
   THEN UPLOAD!
   ^^^ this works now but is not documented
 
-
--------------------------------------------------------------------------------
-
-- chop to first ATG
-
-  chop :ATG
-
-  ^^^^ enable this, to chop towards the first ATG
-       sequence in the string
-  
 -------------------------------------------------------------------------------
 → http://www.biophp.org/stats/describe_data/demo.php?show=formula
 
@@ -720,11 +714,6 @@ also add a footer to show which entries are available or so
       Also, add in the documentation where this
       can be found.
 ..........................................................................
-(3) → Add aaruler, similar to "ruler"; in the bioshell.
-      But we want to do this on the dna-sequence rather
-      than the aminoacid sequence.
-      This works but the display is not ideal.
-..........................................................................
 (4) → Add some codon-usage analyzer. What shall it show? It
       should show how many codons are used, frequencies etc...
       by an organism, and compare that to other data.

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/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/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/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/files_and_directories.rb

@@ -318,10 +318,17 @@ 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?
   # ========================================================================= #

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/gui/gtk3/protein_to_DNA/protein_to_DNA.rb

@@ -107,7 +107,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_right.clear_background
     scrolled_window_right.width_height(300, 300)
     scrolled_window_right.bblack1
-    scrolled_window_right.css_class('mar2px')
+    scrolled_window_right.mar2px
     # ======================================================================= #
     # === scrolled_window_left
     # ======================================================================= #
@@ -115,7 +115,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_left.clear_background
     scrolled_window_left.width_height(300, 300)
     scrolled_window_left.bblack1
-    scrolled_window_left.css_class('mar2px')
+    scrolled_window_left.mar2px
     top_hpaned = gtk_hpaned(
       scrolled_window_left,
       scrolled_window_right
@@ -126,22 +126,6 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     @dataset[:top_hbox] = top_hpaned
   end
 
-  # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
-  # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    @main_vbox.maximal(@dataset[:top_hbox], 4)
-    @main_vbox.maximal(@middle_bar)
-    button_box = button_box(
-      @dataset[:backtrack_button],
-      @dataset[:quit_button]
-    )
-    button_box.vertical_layout
-    @main_vbox.minimal(button_box)
-    add(@main_vbox)
-  end
-
   # ========================================================================= #
   # === create_left_buffer
   # ========================================================================= #
@@ -161,6 +145,22 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     super()
   end
 
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    @main_vbox.maximal(@dataset[:top_hbox], 4)
+    @main_vbox.maximal(@middle_bar)
+    button_box = button_box(
+      @dataset[:backtrack_button],
+      @dataset[:quit_button]
+    )
+    button_box.vertical_layout
+    @main_vbox.minimal(button_box)
+    add(@main_vbox)
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::Gtk::ProteinToDNA.run
   # ========================================================================= #

data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb

@@ -143,13 +143,6 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     end
   end
 
-  # ========================================================================= #
-  # === left_buffer?
-  # ========================================================================= #
-  def left_buffer?
-    @dataset[:left_buffer]
-  end; alias left? left_buffer? # === left?
-
   # ========================================================================= #
   # === right_buffer?
   # ========================================================================= #
@@ -164,6 +157,20 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     @dataset[:left_buffer].set_text(i.to_s)
   end
 
+  # ========================================================================= #
+  # === aminoacid_sequence?
+  # ========================================================================= #
+  def aminoacid_sequence?
+    left_buffer?.to_s
+  end
+
+  # ========================================================================= #
+  # === left_buffer?
+  # ========================================================================= #
+  def left_buffer?
+    @dataset[:left_buffer]
+  end; alias left? left_buffer? # === left?
+
   # ========================================================================= #
   # === do_determine_the_backtrack_sequence                           (click tag)
   #
@@ -182,11 +189,4 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     right_buffer?.set_text(text_for_right_hand_side)
   end; alias do_determine_the_DNA_sequence do_determine_the_backtrack_sequence # === do_determine_the_DNA_sequence
 
-  # ========================================================================= #
-  # === aminoacid_sequence?
-  # ========================================================================= #
-  def aminoacid_sequence?
-    left_buffer?.to_s
-  end
-
 end; end; end