bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java

@@ -0,0 +1,34 @@
+package bioroebe;
+
+/*
+ * class Codons
+ *
+ * This class will include codon-related code.
+ *
+ * It is currently very unfinished, but should ideally
+ * be useable for some toplevel method calls such as:
+ *
+ *   Codons.is_valid_start_codon("UUU") # => true or false
+ *
+ */
+class Codons extends Base {
+
+  /* Designate the main start codon to use. */
+  public static String start_codon = "ATG";
+
+  /*
+   * Codons.display_start_codons()
+   *
+   * This shall simply display all valid start codons.
+   *
+   * We currently miss reporting GTG and another one;
+   * this has to be fixed eventually.
+   */
+  public static void display_start_codons() {
+    e(start_codon);
+  }
+  public static String return_start_codon() {
+    return start_codon;
+  }
+
+}

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java

@@ -0,0 +1,101 @@
+/*
+ * This class will handle commandline-given input.
+ */
+package bioroebe;
+
+import bioroebe.*;
+
+public class Commandline {
+
+  /*
+   * Main constructor (def initialize)
+   */
+  String[] commandline_arguments;
+  public Commandline(String[] args) {
+    commandline_arguments = args;
+    run();
+  }
+  /*
+   * show_help()                                                     (help tag)
+   *
+   * show help instructions for this class.
+   */
+  void show_help() {
+    en("The following commandline options are available:");
+    en("");
+    en("  --partner             # complement via partner molecules");
+    en("  --random-dna-sequence # output a random DNA sequence");
+    en("");
+  }
+  /*
+   * run()
+   */
+  void run() {
+    if (commandline_arguments.length > 0) {
+      for (String entry : commandline_arguments) {
+        /* --help */
+        if (entry.matches("help|--help")) {
+          show_help();
+        }
+        /* java bioroebe/Commandline --is-palindrome */
+        else if (entry.matches("is[\s_-]*palindrome|--is_palindrome")) {
+          System.out.println(
+            IsPalindrome.isPalindrome("OTTO")
+          );
+        }
+        /* java bioroebe/Commandline --random-dna-sequence */
+        else if (entry.matches("random-dna-sequence|--random-dna-sequence")) {
+          new GenerateRandomDnaSequence(250);
+        }
+        /* java bioroebe/Commandline --base-composition */
+        else if (entry.matches("base-composition|--base-composition")) {
+          new toplevel_methods.BaseComposition(entry);
+        }
+        /* java bioroebe/Commandline --start-codons */
+        else if (entry.matches("start-codons|--start-codons")) {
+          Codons.display_start_codons();
+        }
+        /* java bioroebe/Commandline --esystem */
+        else if (entry.matches("esystem|--esystem")) {
+          Esystem.esystem("ls");
+        }
+        /* java bioroebe/Commandline --bisulfite */
+        else if (entry.matches("bisulfite|--bisulfite")) {
+          en(
+            BisulfiteTreatment.bisulfite_treatment("ATGCCCCCCCC")
+          );
+        }
+        /* java bioroebe/Commandline --remove-numbers */
+        else if (entry.matches("remove-numbers|--remove-numbers")) {
+          en(
+            RemoveNumbers.remove_numbers("123A")
+          );
+        }
+        else if (entry.matches("partner|--partner")) {
+          en(
+            PartnerNucleotide.return_partner_nucleotide("A")
+          );
+        }
+        else {
+          en("Unsure what to do with: "+entry);
+        }
+      }
+    }
+    else {
+      en("Please provide input to this class.");
+    }
+  }
+
+  public static void e(String i) {
+    System.out.print(i);
+  }
+
+  public static void en(String i) {
+    System.out.println(i);
+  }
+
+  public static void main(String[] args) {
+    Commandline x = new Commandline(args);
+  }
+
+}

data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/main/java/bioroebe/GenerateRandomDnaSequence.java}

@@ -9,10 +9,16 @@ class GenerateRandomDnaSequence extends Base {
 
   private String dna_sequence = null;
 
-  /* The constructer for GenerateRandomDnaSequence.
+  /*
+   * The constructor for GenerateRandomDnaSequence.
    *
    * You input a number, such as 20, and this class
    * will generate a DNA string of length 20.
+   *
+   * Usage example:
+   *
+   *   new GenerateRandomDnaSequence(250);
+   *
    */
   public GenerateRandomDnaSequence(int n_characters) {
 
@@ -26,7 +32,7 @@ class GenerateRandomDnaSequence extends Base {
       dna_sequence += alphabet.charAt(r.nextInt(alphabet.length()));
     }
 
-    e(dna_sequence);
+    e(dna_sequence); /* And output the DNA sequence here. */
   }
 
 }

data/lib/bioroebe/java/bioroebe/{IsPalindrome.java → src/main/java/bioroebe/IsPalindrome.java}

@@ -1,10 +1,14 @@
 package bioroebe;
 
-public class IsPalindrome {
+public class IsPalindrome extends Base {
 
   /*
    * IsPalindrome.isPalindrome()
    *
+   * Usage example:
+   *
+   *   IsPalindrome.isPalindrome("OTTO")
+   *
    */
   public static boolean isPalindrome(String i) {
     String reversed = new StringBuffer(i).reverse().toString();

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java

@@ -0,0 +1,56 @@
+package bioroebe;
+
+import bioroebe.*;
+
+/*
+ * PartnerNucleotide.partner_nucleotide("A");
+ *
+ * This class will simply yield the corresponding nucleotide.
+ *
+ * Usage example:
+ *
+ *   PartnerNucleotide.partner_nucleotide("A");
+ *
+ */
+class PartnerNucleotide extends Base {
+
+  /*
+   * PartnerNucleotide.partner_nucleotide()
+   */
+  public static void partner_nucleotide(String i) {
+    switch(i) {
+      case "A": e("T"); break;
+      case "T": e("A"); break;
+      case "C": e("G"); break;
+      case "G": e("C"); break;
+      default: e("Unhandled input "+i); break;
+    }
+  }
+
+  /*
+   * PartnerNucleotide.return_partner_nucleotide()
+   */
+  public static String return_partner_nucleotide(String i) {
+    switch(i) {
+      case "A": return ("T");
+      case "T": return ("A");
+      case "C": return ("G");
+      case "G": return ("C");
+      default: return ("Unhandled input "+i);
+    }
+  }
+
+  public static void main(String[] args) {
+
+    if (args.length > 0) {
+      for (String string : args) {
+        PartnerNucleotide.partner_nucleotide(string);
+      }
+    }
+    else {
+      System.out.println("Please provide input to this class, a DNA sequence.");
+    }
+
+  }
+
+}

data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/main/java/bioroebe/RemoveFile.java}

@@ -1,6 +1,6 @@
 package bioroebe;
 
-import java.io.*; 
+import java.io.*;
 
 /*
  * RemoveFile.remove_file("A");
@@ -18,7 +18,13 @@ class RemoveFile extends Base {
     }
     else {
       e("The file at `"+this_file+"` could NOT be deleted");
-    } 
+    }
+
+  }
+}
+
+/*
 
-  } 
-}
+  RemoveFile.remove_file("/Depot/j/test.md");
+  
+*/

data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/main/java/bioroebe/RemoveNumbers.java}

@@ -1,4 +1,5 @@
 package bioroebe;
+
 import java.util.Scanner;
 
 /*

data/lib/bioroebe/java/bioroebe/{ToCamelcase.java → src/main/java/bioroebe/ToCamelcase.java}

@@ -13,13 +13,13 @@ class ToCamelcase extends Base {
    *
    * Usage example:
    *
-   *   ToCamelcase.to_camelcase("foo_bar");
-   *
+   *   ToCamelcase.to_camelcase("foo_bar"); # => "FooBar"
+   
    */
   public static String to_camelcase(String i) {
 
     StringBuilder sb = new StringBuilder();
-    
+
     for( String entry : i.toLowerCase().split("_") )
     {
       sb.append( entry.substring(0,1).toUpperCase() );

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java

@@ -0,0 +1,42 @@
+/* package ToRNA; */
+
+public class ToRNA {
+
+  static String[] commandline_arguments;
+
+  /*
+   * Main constructor (def initialize)
+   */
+  public ToRNA() {
+    run();
+  }
+  /*
+   * run()
+   */
+  void run() {
+    
+    if (commandline_arguments.length > 0) {
+      for (String entry : commandline_arguments) {
+        en(entry);
+      }
+    }
+    else {
+      en("Please provide an input to this method, a DNA sequence.");
+    }
+
+  }
+
+  public static void e(String i) {
+    System.out.print(i);
+  }
+
+  public static void en(String i) {
+    System.out.println(i);
+  }
+
+  public static void main(String[] args) {
+    commandline_arguments = args;
+    ToRNA x = new ToRNA();
+  }
+
+}

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.java

@@ -0,0 +1,75 @@
+/* package BaseComposition; */
+/*package bioroebe.toplevel_methods;*/
+
+package bioroebe;
+
+public class BaseComposition {
+
+  static String[] commandline_arguments;
+
+  /*
+   * Main constructor (def initialize)
+   */
+  public BaseComposition() {
+    run();
+  }
+  /*
+   * run()
+   */
+  void run() {
+    if (commandline_arguments.length == 0) {
+      en("Please provide an input argument.");
+    }
+    else {
+      String first_argument = commandline_arguments[0];
+      en(
+        "The base composition frequencies of this sequence "+
+        "(length: "+first_argument.length()+") is as follows:"
+      );
+      en("");
+      int total_length = first_argument.length();
+      int n_A = 0;
+      int n_T = 0;
+      int n_C = 0;
+      int n_G = 0;
+
+      for (int i = 0; i < total_length; i++) {
+        char this_char = first_argument.charAt(i);
+        if (this_char == 'A') {
+          n_A += 1;
+        }
+        else if (this_char == 'T') {
+          n_T += 1;
+        }
+        else if (this_char == 'C') {
+          n_C += 1;
+        }
+        else if (this_char == 'G') {
+          n_G += 1;
+        }
+      }
+      en(
+        "  "+
+        "A: "+Math.round((n_A * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "T: "+Math.round((n_T * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "C: "+Math.round((n_C * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "G: "+Math.round((n_G * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "
+      );
+      en("");
+    }
+  }
+
+  public static void e(String i) {
+    System.out.print(i);
+  }
+
+  public static void en(String i) {
+    System.out.println(i);
+  }
+
+  public static void main(String[] args) {
+    commandline_arguments = args;
+    BaseComposition x = new BaseComposition();
+  }
+
+}

data/lib/bioroebe/misc/ruler.rb

@@ -24,6 +24,8 @@
 # variant - that one should work fine.
 # =========================================================================== #
 # require 'bioroebe/misc/ruler.rb'
+# puts Bioroebe.return_ruler('ATGCTGACAGGGGGGGEEEEEE')
+# Bioroebe.ruler_return_as_string_without_colours 'ATGCTGACAGGGGGGGEEEEEE'
 # Bioroebe::Ruler.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
@@ -54,8 +56,14 @@ class Ruler < ::Bioroebe::CommandlineApplication # === Bioroebe::Ruler
     set_group_together_n_nucleotides(
       group_together_n_nucleotides
     )
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
     if block_given?
       yielded = yield
+      # ===================================================================== #
+      # === Handle Hashes next
+      # ===================================================================== #
       if yielded.is_a? Hash
         # =================================================================== #
         # === :ruler
@@ -206,14 +214,15 @@ end
 # This will return the ruler as a String; it exists mostly for
 # convenience reasons.
 #
-# Invocation example:
+# Invocation examples:
 #
 #   puts Bioroebe.ruler_return_as_string 'ATGCTGACAGGGGGGGEEEEEE'
+#   puts Bioroebe.return_ruler('ATGCTGACAGGGGGGGEEEEEE')
 #
 # =========================================================================== #
 def self.ruler_return_as_string(i, group_together_n_nucleotides = 70)
   ::Bioroebe::Ruler.new(i, group_together_n_nucleotides).result_as_string
-end
+end; self.instance_eval { alias return_ruler ruler_return_as_string } # === Bioroebe.return_ruler
 
 # =========================================================================== #
 # === Bioroebe.ruler_return_as_string_without_colours

data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb

@@ -27,11 +27,6 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   require 'bioroebe/aminoacids/codon_percentage.rb'
   require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -63,10 +58,7 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb

@@ -475,13 +475,6 @@ class ShowNucleotideSequence < ::Bioroebe::Sequence # === Bioroebe::ShowNucleoti
     erev i
   end; alias display report # === display (display tag)
 
-  # ========================================================================= #
-  # === do_colourize_the_start_codon
-  # ========================================================================= #
-  def do_colourize_the_start_codon
-    add_this_substring('ATG')
-  end
-
   # ========================================================================= #
   # === colourize_dna_sequence
   # ========================================================================= #
@@ -529,6 +522,13 @@ class ShowNucleotideSequence < ::Bioroebe::Sequence # === Bioroebe::ShowNucleoti
   end; alias set_search_for     search_for_this_substring # === set_search_for
        alias add_this_substring search_for_this_substring # === add_this_substring
 
+  # ========================================================================= #
+  # === do_colourize_the_start_codon
+  # ========================================================================= #
+  def do_colourize_the_start_codon
+    add_this_substring('ATG')
+  end
+
   # ========================================================================= #
   # === run
   # ========================================================================= #