bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/www/sinatra/sinatra.rb

@@ -14,7 +14,6 @@ module Bioroebe
 class Sinatra < ::Sinatra::Base
 
   require 'bioroebe/www/embeddable_interface.rb'
-
   set :port, ::Bioroebe::EmbeddableInterface::USE_THIS_PORT
 
   # ========================================================================= #
@@ -47,16 +46,25 @@ class Sinatra < ::Sinatra::Base
     Cyberweb.try_to_open_this_URL_via_the_browser(target, use_this_port) { :be_quiet }
   end
 
+  # ========================================================================= #
+  # === p
+  # ========================================================================= #
+  def p(
+      i, hash = {}
+    )
+    return HtmlTags.p(i, hash)
+  end
+
   # ========================================================================= #
   # === Convert into DNA                    (2 tag, second entry, reverse_complement tag)
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4567/reverse_complement
+  #   http://localhost:4568/reverse_complement
   #
   # Example:
   #
-  #   http://localhost:4567/reverse_complement/ATGCUUUUUUUUUU
+  #   http://localhost:4568/reverse_complement/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
   get('/reverse_complement/*') {
@@ -68,19 +76,28 @@ class Sinatra < ::Sinatra::Base
       the_params = params['user_input']
     end
     the_params = the_params.strip.upcase if the_params
-    the_result = ::Bioroebe.reverse_complement(the_params)
+    if the_params.is_a? Array
+      the_params = the_params.flatten.first
+    end
+    the_reverse_complement = ::Bioroebe.reverse_complement(the_params)
+    if the_reverse_complement.is_a? Array
+      the_reverse_complement = the_reverse_complement.first.to_s
+    end
+    the_result = ''.dup
     if the_params.empty?
-      the_result = return_intro_for_reverse_complement_conversion+
-      p(
-        '<b> Please input a DNA sequence which will be '\
-        'reverse-complemented into DNA.</b>'
-      )+
-      return_paragraph_of_hyperlinks
+      the_result << return_intro_for_reverse_complement_conversion+
+        p(
+          '<b> Please input a DNA sequence which will be '\
+          'reverse-complemented into DNA.</b>'
+        )+
+        return_paragraph_of_hyperlinks
     else
-      the_result = embeddable_interface?.return_intro_for_reverse_complement_conversion+
-      p('The reverse complement of <b>'+the_params+'</b> is:')+
-      p(
-        '<b>'+the_result+'</b>',
+      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
+      the_result << _+p(
+        "The reverse complement of <b>5'-#{the_params.to_s}</b> is:"
+      )
+      the_result << p(
+        "<b>5'-#{the_reverse_complement}</b>",
         css_style: 'margin:1em; font-size: larger; color: blueviolet'
       )
     end
@@ -90,13 +107,14 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/to_dna_source
+  # http://localhost:4568/to_dna_source
   # ========================================================================= #
   get([
         '/to_dna_source',
         '/to_aa_source'
       ]){
-    sanitized_URL_part = request.path_info.to_s.sub('_source','').delete('/').to_sym
+    sanitized_URL_part = request.path_info.to_s.sub('_source','').
+                         delete('/').to_sym
     file, line_number = ::Bioroebe.method(sanitized_URL_part).source_location
     if File.exist? file
       readlines = File.readlines(file)
@@ -121,7 +139,7 @@ class Sinatra < ::Sinatra::Base
   # =========================================================================== #
   # Example:
   #
-  #   http://localhost:4567/shuffleseq
+  #   http://localhost:4568/shuffleseq
   #
   # =========================================================================== #
   get('/shuffleseq'){
@@ -131,14 +149,14 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === /shuffleseq
   #
-  # http://localhost:4567/shuffleseq
+  # http://localhost:4568/shuffleseq
   # ========================================================================= #
   ['/shuffleseq'].each {|target|
     get(target) {
       Cyberweb::HtmlTemplate[
         title: 'Shuffleseq - Shuffle a sequence',
         body:  '<pre>'+
-               ::Bioroebe.shuffleseq(method(:method_reverse_complement))+
+               ::Bioroebe.shuffleseq(method(:reverse_complement))+
                '</pre>'+
                footer
       ].to_s
@@ -224,24 +242,13 @@ class Sinatra < ::Sinatra::Base
   end
 
   # ========================================================================= #
-  # === /random_aminoacids
-  #
-  # http://localhost:4567/random_aminoacids
-  # ========================================================================= #
-  ['/random_aminoacids'].each {|target|
-    get(target) {
-      embeddable_interface?.method_random_aminoacids
-    }
-  }
-
-  # ========================================================================= #
-  # http://localhost:4567/reverse_complement_source
+  # http://localhost:4568/reverse_complement_source
   # ========================================================================= #
   ['/reverse_complement_source'].each {|target|
     get(target) {
       body = HtmlTags.p('The source is:')+
              '<pre>'+
-             ::Bioroebe.return_source_code_of_this_method(method(:method_reverse_complement))+
+             ::Bioroebe.return_source_code_of_this_method(method(:reverse_complement))+
              '</pre>'+
              footer
       Cyberweb::HtmlTemplate[
@@ -254,18 +261,18 @@ class Sinatra < ::Sinatra::Base
   # =========================================================================== #
   # Example:
   #
-  #   http://localhost:4567/reverse_complement
+  #   http://localhost:4568/reverse_complement
   #
   # =========================================================================== #
   get('/reverse_complement'){
-    method_reverse_complement
+    embeddable_interface?.method_reverse_complement
   }
 
   # =========================================================================== #
   # Example:
   #
-  #   http://localhost:4567/n_stop_codons_in_this_sequence
-  #   http://localhost:4567/n_stop
+  #   http://localhost:4568/n_stop_codons_in_this_sequence
+  #   http://localhost:4568/n_stop
   #
   # =========================================================================== #
   %w( 
@@ -291,7 +298,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === /palindromes
   #
-  # http://localhost:4567/palindromes
+  # http://localhost:4568/palindromes
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.each {|target|
     get(target) {
@@ -314,7 +321,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === view
   #
-  # http://localhost:4567/view
+  # http://localhost:4568/view
   # ========================================================================= #
   get('/view') { # view tag
     embeddable_interface?.return_view_string
@@ -332,13 +339,13 @@ class Sinatra < ::Sinatra::Base
     ].to_s
   }
   # ========================================================================= #
-  # http://localhost:4567/random_aminoacids_source
+  # http://localhost:4568/random_aminoacids_source
   # ========================================================================= #
   ['/random_aminoacids_source'].each {|target|
     get(target) {
       body = HtmlTags.p('The source is:')+
              '<pre>'+
-             ::Bioroebe.return_source_code_of_this_method(method(:method_random_aminoacids))+
+             ::Bioroebe.return_source_code_of_this_method(method(:random_aminoacids))+
              '</pre>'+
              footer
       Cyberweb::HtmlTemplate[
@@ -349,7 +356,7 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/random_aminoacids/33
+  # http://localhost:4568/random_aminoacids/33
   # ========================================================================= #
   ['/random_aminoacids/*'].each {|target|
     get(target) {
@@ -392,11 +399,11 @@ class Sinatra < ::Sinatra::Base
   #
   # This method will try to discover palindromes.
   #
-  #   http://localhost:4567/palindromes
+  #   http://localhost:4568/palindromes
   #
   # Example:
   #
-  #   http://localhost:4567/palindromes/30
+  #   http://localhost:4568/palindromes/30
   #
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.each {|target|
@@ -443,11 +450,11 @@ class Sinatra < ::Sinatra::Base
   # This method will determine how many stop codons are in the given
   # sequence.
   #
-  #   http://localhost:4567/n_stop_codons_in_this_sequence
+  #   http://localhost:4568/n_stop_codons_in_this_sequence
   #
   # Example:
   #
-  #   http://localhost:4567/n_stop_codons_in_this_sequence/ATGCUUUUUUUUUTAG
+  #   http://localhost:4568/n_stop_codons_in_this_sequence/ATGCUUUUUUUUUTAG
   #
   # ========================================================================= #
   %w(
@@ -490,7 +497,7 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/is_palindrome
+  # http://localhost:4568/is_palindrome
   # ========================================================================= #
   get('/is_palindrome') {
     return_header_for_palindromes('Is palindrome')+
@@ -507,7 +514,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/is_palindromes/ATTA
+  #   http://localhost:4568/is_palindromes/ATTA
   #
   # ========================================================================= #
   get('/is_palindrome/*') {
@@ -543,7 +550,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === /mirror_source
   #
-  # http://localhost:4567/mirror_source
+  # http://localhost:4568/mirror_source
   # ========================================================================= #
   get('/mirror_source'){
     file, line_number = ::Bioroebe.method(:mirror_repeat).source_location
@@ -564,9 +571,9 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/chunked_display
-  # http://localhost:4567/chunked
-  # http://localhost:4567/upcase
+  # http://localhost:4568/chunked_display
+  # http://localhost:4568/chunked
+  # http://localhost:4568/upcase
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
     get(target) {
@@ -580,11 +587,11 @@ class Sinatra < ::Sinatra::Base
   #
   # Visit:
   #
-  #   http://localhost:4567/compseq
+  #   http://localhost:4568/compseq
   #
   # Example:
   #
-  #   http://localhost:4567/compseq/ATGCUUUUUUUUUU
+  #   http://localhost:4568/compseq/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
   get('/compseq/*') {
@@ -619,8 +626,8 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/to_aa
-  # http://localhost:4567/to_aminoacids
+  # http://localhost:4568/to_aa
+  # http://localhost:4568/to_aminoacids
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.each {|target|
     get(target) {
@@ -639,7 +646,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/mirror
+  #   http://localhost:4568/mirror
   # =========================================================================== #
   get('/mirror'){
     body = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
@@ -663,8 +670,8 @@ class Sinatra < ::Sinatra::Base
   #
   # Usage Examples:
   #
-  #   http://localhost:4567/to_dna
-  #   http://localhost:4567/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
+  #   http://localhost:4568/to_dna
+  #   http://localhost:4568/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
   #
   # =========================================================================== #
   get('/to_dna'){
@@ -676,11 +683,11 @@ class Sinatra < ::Sinatra::Base
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4567/to_dna
+  #   http://localhost:4568/to_dna
   #
   # Example:
   #
-  #   http://localhost:4567/to_dna/ATGCUUUUUUUUUU
+  #   http://localhost:4568/to_dna/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
   get('/to_dna/*') {
@@ -722,11 +729,11 @@ class Sinatra < ::Sinatra::Base
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4567/chunked
+  #   http://localhost:4568/chunked
   #
   # Example:
   #
-  #   http://localhost:4567/chunked/ATGCUUUUUUUUUU
+  #   http://localhost:4568/chunked/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
@@ -765,7 +772,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/compseq
+  #   http://localhost:4568/compseq
   #
   # =========================================================================== #
   get('/compseq'){
@@ -820,8 +827,8 @@ class Sinatra < ::Sinatra::Base
   #
   # Examples:
   #
-  #   http://localhost:4567/to_aa/ATGGGGCCCGCGCCA
-  #   http://localhost:4567/to_aa/GGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTG
+  #   http://localhost:4568/to_aa/ATGGGGCCCGCGCCA
+  #   http://localhost:4568/to_aa/GGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTG
   #
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.map {|entry| "#{entry}/*" }.each {|target|
@@ -872,7 +879,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/blosum
+  #   http://localhost:4568/blosum
   #
   # =========================================================================== #
   get('/blosum'){
@@ -898,11 +905,11 @@ class Sinatra < ::Sinatra::Base
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4567/mirror
+  #   http://localhost:4568/mirror
   #
   # Example:
   #
-  #   http://localhost:4567/mirror/ATGCUUUUUUUUUU
+  #   http://localhost:4568/mirror/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
   get('/mirror/*') {
@@ -942,7 +949,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === /blosum_source
   #
-  # http://localhost:4567/blosum_source
+  # http://localhost:4568/blosum_source
   # ========================================================================= #
   get('/blosum_source'){
     file, line_number = ::Bioroebe.method(:blosum).source_location
@@ -967,11 +974,11 @@ class Sinatra < ::Sinatra::Base
   #
   # This method will show the blosum matrices.
   #
-  #   http://localhost:4567/blosum
+  #   http://localhost:4568/blosum
   #
   # Example:
   #
-  #   http://localhost:4567/blosum/42
+  #   http://localhost:4568/blosum/42
   #
   # ========================================================================= #
   get('/blosum/*') {
@@ -997,6 +1004,114 @@ class Sinatra < ::Sinatra::Base
     the_result
   }
 
+  # ========================================================================= #
+  # === /random_aminoacids
+  #
+  # http://localhost:4568/random_aminoacids
+  # ========================================================================= #
+  ['/random_aminoacids'].each {|target|
+    get(target) {
+      embeddable_interface?.method_random_aminoacids
+    }
+  }
+
+  # ========================================================================= #
+  # === /codon_frequency_of_this_string
+  #
+  # http://localhost:4568/codon_frequency_of_this_string
+  # ========================================================================= #
+  ['/codon_frequency_of_this_string'].each {|target|
+    get(target) {
+      embeddable_interface?.method_codon_frequency_of_this_string
+    }
+  }
+
+  # ========================================================================= #
+  # === Codon Frequencies
+  #
+  # Example:
+  #
+  #   http://localhost:4568/codon_frequency_of_this_string/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/codon_frequency_of_this_string/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    if params.has_key? 'user_input'
+      the_params = params['user_input']
+    end
+    the_params = the_params.strip.upcase if the_params
+    if the_params.is_a? Array
+      the_params = the_params.flatten.first
+    end
+    the_result = ''.dup
+    if the_params.empty?
+      the_result << return_intro_for_reverse_complement_conversion+
+        p(
+          '<b> Please input a DNA sequence.'
+        )+
+        return_paragraph_of_hyperlinks
+    else
+      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
+      the_result << p(
+        Bioroebe.codon_frequency_of_this_string(the_params)
+      )
+    end
+    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+# ========================================================================= #
+  # === /codon_frequency_of_this_string
+  #
+  # http://localhost:4568/codon_frequency_of_this_string
+  # ========================================================================= #
+  ['/codon_frequency_of_this_string'].each {|target|
+    get(target) {
+      embeddable_interface?.method_codon_frequency_of_this_string
+    }
+  }
+
+  # ========================================================================= #
+  # === Codon Frequencies
+  #
+  # Example:
+  #
+  #   http://localhost:4568/frequency_per_thousand/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/frequency_per_thousand/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    if params.has_key? 'user_input'
+      the_params = params['user_input']
+    end
+    the_params = the_params.strip.upcase if the_params
+    if the_params.is_a? Array
+      the_params = the_params.flatten.first
+    end
+    the_result = ''.dup
+    if the_params.empty?
+      the_result << return_intro_for_reverse_complement_conversion+
+        p(
+          '<b>Please input a DNA sequence.</b>'
+        )+
+        return_paragraph_of_hyperlinks
+    else
+      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
+      the_result << HtmlTags.pre(
+        Bioroebe.frequency_per_thousand(the_params)
+      )
+    end
+    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+  
 end
 
 # =========================================================================== #

data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml

@@ -1,5 +1,5 @@
 # =========================================================================== #
-# x = YAML.load_file(Bioroebe.file_amino_acids_long_name_to_one_letter)
+# === amino_acids_long_name_to_one_letter.yml
 #
 # In code this will be:
 #
@@ -7,7 +7,7 @@
 #
 # Note that the file here stores both the english and the german names.
 # =========================================================================== #
-# 'amino_acids_long_name_to_one_letter.yml'
+# x = YAML.load_file(Bioroebe.file_amino_acids_long_name_to_one_letter)
 # =========================================================================== #
 
 # =========================================================================== #

data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml

@@ -14,20 +14,20 @@
 
                                  n kDa
 ----------------------------------------------------------------------------------------
-ATP:                             0.507  # Yup, ATP has a molecular weight of about 507 Dalton. Formula is: C₁₀H₁6N5O₁3P3
-tRNAs:                           25     # This applies to mature tRNAs with an average of 76 nucleotides.
-GFP:                             26.9   # The good, old "Green Fluorescent Protein". 
-scFv:                            27     # The "scFv fragment".
-recA-Protein:                    38     # The recA Protein in Prokaryotes.
-Protein A:                       42     # Protein A from "Staphylococcus aureus".
-RUBISCO monomer:                 55     # Yes, the RUBISCO monomer has a weight of 55 kDa.
-Fab fragment:                    55     # Part of a typical antibody, e. g. IgG antibody.
-Luciferase:                      62     # Originally from the firefly.
-IgG:                            150     # IgG antibodies have a weight of approximately 150 kDa.
-IgA:                            160     # IgA antibodies have a weight of approximately 160 kDa.
-IgD:                            175     # IgD antibodies have a weight of approximately 175 kDa.
-IgE:                            190     # IgE antibodies have a weight of approximately 190 kDa.
-IgA-dimers:                     400     # IgA dimers have a MW of 400.000 Da.
-Apolipoprotein:                +500     # The Apolipoprotein is fairly large.
-ATP synthase:                 500-600   # Has a weight between ~500-600 kDa; probably species-dependent.
-IgM-pentamers:                  950     # IgM pentamers have a MW of 950.000 Da. Other sources claim 900.000 Da.
+ATP:                              0.507  # Yup, ATP has a molecular weight of about 507 Dalton. Formula is: C₁₀H₁6N5O₁3P3
+tRNAs:                           25      # This applies to mature tRNAs with an average of 76 nucleotides.
+GFP:                             26.9    # The good, old "Green Fluorescent Protein".
+scFv:                            27      # The "scFv fragment".
+recA-Protein:                    38      # The recA Protein in Prokaryotes.
+Protein A:                       42      # Protein A from "Staphylococcus aureus".
+RUBISCO monomer:                 55      # Yes, the RUBISCO monomer has a weight of 55 kDa.
+Fab fragment:                    55      # Part of a typical antibody, e. g. IgG antibody.
+Luciferase:                      62      # Originally from the firefly.
+IgG:                            150      # IgG antibodies have a weight of approximately 150 kDa.
+IgA:                            160      # IgA antibodies have a weight of approximately 160 kDa.
+IgD:                            175      # IgD antibodies have a weight of approximately 175 kDa.
+IgE:                            190      # IgE antibodies have a weight of approximately 190 kDa.
+IgA-dimers:                     400      # IgA dimers have a MW of 400.000 Da.
+Apolipoprotein:                +500      # The Apolipoprotein is fairly large.
+ATP synthase:                 500-600    # Has a weight between ~500-600 kDa; probably species-dependent.
+IgM-pentamers:                  950      # IgM pentamers have a MW of 950.000 Da. Other sources claim 900.000 Da.

data/lib/bioroebe/yaml/configuration/browser.yml

@@ -1 +1 @@
-firefox # palemoon
+firefox # chromium # palemoon

data/lib/bioroebe/yaml/configuration/temp_dir.yml

@@ -1 +1 @@
-/home/Temp/bioroebe
+/home/x/Temp/bioroebe

data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml

@@ -0,0 +1 @@
+AP1: TGA(GC)TCA # This is the AP1 binding site in DNA.

data/lib/bioroebe/yaml/genomes/README.md

@@ -1,7 +1,6 @@
-This directory is primarily intended to provide some links to 
-external resources - in particular genome information, the
-latest revisions to a genome, where it can be downloaded,
-and so forth.
+This directory is primarily intended to provide some links to external
+resources - in particular genome information, the latest revisions to
+a genome, where it can be downloaded, and so forth.
 
 As such we will focus on model organisms primarily.
 

data/lib/bioroebe/yaml/nucleotides/nucleotides.yml

@@ -32,3 +32,8 @@ Desoxyguanosin: C10H13N5O4 # See https://de.wikipedia.org/wiki/Desoxyguanosin
 # =========================================================================== #
 Thymin:           C5H6N2O2 # See https://de.wikipedia.org/wiki/Thymin
 Desoxythymidin: C10H14N2O5 # See https://de.wikipedia.org/wiki/Desoxythymidin
+
+# =========================================================================== #
+# === Uracil tag
+# =========================================================================== #
+Uracil:           C4H4N2O2 # See https://de.wikipedia.org/wiki/Uracil