bioroebe 0.10.80 → 0.12.12

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

@@ -47,16 +47,25 @@ 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 +77,28 @@ 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 +108,14 @@ 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 +140,7 @@ class Sinatra < ::Sinatra::Base
   # =========================================================================== #
   # Example:
   #
-  #   http://localhost:4567/shuffleseq
+  #   http://localhost:4568/shuffleseq
   #
   # =========================================================================== #
   get('/shuffleseq'){
@@ -131,14 +150,14 @@ 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 +243,13 @@ 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 +262,18 @@ 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 +299,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === /palindromes
   #
-  # http://localhost:4567/palindromes
+  # http://localhost:4568/palindromes
   # ========================================================================= #
   Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.each {|target|
     get(target) {
@@ -314,7 +322,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   # === view
   #
-  # http://localhost:4567/view
+  # http://localhost:4568/view
   # ========================================================================= #
   get('/view') { # view tag
     embeddable_interface?.return_view_string
@@ -332,13 +340,13 @@ 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 +357,7 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # http://localhost:4567/random_aminoacids/33
+  # http://localhost:4568/random_aminoacids/33
   # ========================================================================= #
   ['/random_aminoacids/*'].each {|target|
     get(target) {
@@ -392,11 +400,11 @@ 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 +451,11 @@ 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 +498,7 @@ 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 +515,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/is_palindromes/ATTA
+  #   http://localhost:4568/is_palindromes/ATTA
   #
   # ========================================================================= #
   get('/is_palindrome/*') {
@@ -543,7 +551,7 @@ 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 +572,9 @@ 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 +588,11 @@ 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 +627,8 @@ 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 +647,7 @@ 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 +671,8 @@ 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 +684,11 @@ 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 +730,11 @@ 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 +773,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/compseq
+  #   http://localhost:4568/compseq
   #
   # =========================================================================== #
   get('/compseq'){
@@ -820,8 +828,8 @@ 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 +880,7 @@ class Sinatra < ::Sinatra::Base
   #
   # Example:
   #
-  #   http://localhost:4567/blosum
+  #   http://localhost:4568/blosum
   #
   # =========================================================================== #
   get('/blosum'){
@@ -898,11 +906,11 @@ 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 +950,7 @@ 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 +975,11 @@ 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 +1005,114 @@ 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/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/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/restriction_enzymes/restriction_enzymes.yml

@@ -49,7 +49,7 @@ AccII:     CGCG         2
 AccIII:    TCCGGA       1
 Acc16I:    TGCGCA       3
 Acc65I:    GGTACC       1
-Acc113I:   AGTACT       3
+Acc113I:   AGTACT       3 # blunt end
 AccB1I:    GGYRCC       1
 AccB7I:    CCANNNNNTGG  7
 AclI:      AACGTT       2
@@ -108,11 +108,11 @@ BalI:      TGGCCA 3
 BamHI:     GGATCC 1
 BanI:      GGYRCC 1
 BanII:     GRGCYC 5
-BanIII:    ATCGAT 2
+BanIII:    ATCGAT 2     # At CG.
 BbeI:      GGCGCC 5
 BbrPI:     CACGTG 3
 BbuI:      GCATGC 5
-Bbv12I:    GWGCWC 5
+Bbv12I:    GWGCWC      5
 BclI:      TGATCA      1
 BcnI:      CCSGG       2
 BcoI:      CYCGRG      1
@@ -495,31 +495,31 @@ Ppu10I:    ATGCAT   1
 PpuMI:     RGGWCCY  2
 PpuXI:     RGGWCCY  2
 PshAI:     GACNNNNGTC 5
-PshBI:     ATTAAT   2
-PsiI:      TTATAA   3
-Psp03I:    GGWCC    4
-Psp5II:    RGGWCCY  2
-Psp6I:     CCWGG    0
-Psp1406I:  AACGTT   2
-PspAI:     CCCGGG 1
-Psp124BI:  GAGCTC 5
-PspEI:     GGTNACC 1
-PspGI:     CCWGG 0
-PspLI:     CGTACG 1
-PspN4I:    GGNNCC 3
-PspOMI:    GGGCCC 1
-PspPI:     GGNCC 1
-PspPPI:    RGGWCCY 2
-PssI:      RGGNCCY 5
-PstI:      CTGCAG 5
-PsuI:      RGATCY 1
+PshBI:     ATTAAT    2
+PsiI:      TTATAA    3
+Psp03I:    GGWCC     4
+Psp5II:    RGGWCCY   2
+Psp6I:     CCWGG     0
+Psp1406I:  AACGTT    2
+PspAI:     CCCGGG    1
+Psp124BI:  GAGCTC    5
+PspEI:     GGTNACC   1
+PspGI:     CCWGG     0
+PspLI:     CGTACG    1
+PspN4I:    GGNNCC    3
+PspOMI:    GGGCCC    1
+PspPI:     GGNCC     1
+PspPPI:    RGGWCCY   2
+PssI:      RGGNCCY   5
+PstI:      CTGCAG    5
+PsuI:      RGATCY    1
 PsyI:      GACNNNGTC 4
-PvuI:      CGATCG 4
-PvuII:     CAGCTG 3
-RcaI:      TCATGA 1
-RsaI:      GTAC 2
-RsrII:     CGGWCCG 2
-Rsr2I:     CGGWCCG 2
+PvuI:      CGATCG    4
+PvuII:     CAGCTG    3 # will cleave at 5'-CAG/CTG-3', and generate blunt termini.
+RcaI:      TCATGA    1
+RsaI:      GTAC      2
+RsrII:     CGGWCCG   2
+Rsr2I:     CGGWCCG   2
 
 # =========================================================================== #
 # === s tig