bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb

@@ -17,7 +17,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta/fasta_to_yaml/fasta_to_yaml.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb

@@ -26,7 +26,7 @@
 # =========================================================================== #
 # require 'bioroebe/fastq_and_fastq/fastq_format_explainer.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb

@@ -15,7 +15,7 @@
 # require 'bioroebe/fasta_and_fastq/length_modifier/simplify_fasta_header.rb'
 # Bioroebe::LengthModifier.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb

@@ -20,7 +20,7 @@
 # Bioroebe.parse_fasta
 # Bioroebe.sizeseq
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -834,7 +834,7 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
     i = [i].flatten.compact.first.to_s.dup
     if File.exist? i.to_s # First try to read in from a file.
       if be_verbose?
-        opnn; erev "Will read from the file `#{sfile(i)}#{rev}`."
+        opnerev "Will read from the file `#{sfile(i)}#{rev}`."
       end
       i = File.readlines(i)
       if @is_a_genbank_file
@@ -849,8 +849,8 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
     end
     if i.nil? or i.empty?
       i = DEFAULT_FASTA
-      opnn; erev 'No input was provided. Thus a default FASTA '\
-                 'sequence will be used instead.'
+      opnerev 'No input was provided. Thus a default FASTA '\
+              'sequence will be used instead.'
     end
     i = sanitize_data(i)
     i = i.split(N) if i.is_a? String
@@ -979,17 +979,17 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
             result < 'FASTA '
           end
           result << 'file was found in this directory ('+sfile(file)+').'
-          opnn; erev result
-          opnn; erev 'We will use it.'
+          opnerev result
+          opnerev 'We will use it.'
         end
         i = file
       end
       unless Dir['*.{fa,fasta}'].empty?
         file = Dir['*.{fa,fasta}'].first
         if be_verbose?
-          opnn; erev "We have found a file in this "\
-                     "directory (#{sfile(file)}#{rev})."
-          opnn; erev 'We will use it.'
+          opnerev "We have found a file in this "\
+                  "directory (#{sfile(file)}#{rev})."
+          opnerev 'We will use it.'
         end
         i = file
       end
@@ -1072,7 +1072,7 @@ TGGGAACCTGCGGGCAGTAGGTGGAAT'
       write_what_into(what, into)
       return File.absolute_path(into) # And return the file we saved into.
     else
-      opnn; erev 'No @data variable exists.'
+      opnerev 'No @data variable exists.'
     end
   end; alias do_save_the_file save_into_a_fasta_file # === do_save_the_file
 
@@ -1451,7 +1451,7 @@ end
 #
 # Invocation example:
 #
-#   Bioroebe.genbank_to_fasta('/home/x/DATA/PROGRAMMING_LANGUAGES/RUBY/src/bioroebe/lib/bioroebe/data/genbank/sample_file.genbank')
+#   Bioroebe.genbank_to_fasta('/home/x/programming/ruby/src/bioroebe/lib/bioroebe/data/genbank/sample_file.genbank')
 #
 # =========================================================================== #
 def self.genbank_to_fasta(
@@ -1521,6 +1521,32 @@ def self.parse_fasta(
   ::Bioroebe::ParseFasta.new(i) { use_this_hash }
 end; self.instance_eval { alias fasta parse_fasta } # === Bioroebe.fasta
 
+# =========================================================================== #
+# === Bioroebe.sanitize_this_fasta_file
+#
+# This method will modify a .fasta file's sequence header, by appending
+# the number of aminoacids to this header.
+#
+# Usage example:
+#
+#   Bioroebe.sanitize_this_fasta_file('/root/Bioroebe/fasta/IFNB1-P01574.fasta')
+#
+# =========================================================================== #
+def self.sanitize_this_fasta_file(i)
+  if File.exist? i
+    dataset = File.readlines(i).map(&:strip)
+    header = dataset.first.dup
+    aminoacid_sequence = Bioroebe::ParseFasta.new(i) { :be_silent }.return_n_aminoacids
+    header << ", #{aminoacid_sequence} aminoacids"
+    dataset[0] = header
+    # ===================================================================== #
+    # Now we can save it again.
+    # ===================================================================== #
+    e 'Storing the modified data into '+sfile(i)+'.'
+    write_what_into(dataset.join(N), i)
+  end
+end
+
 end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb

@@ -13,7 +13,7 @@
 # =========================================================================== #
 # require 'biroebe/fastq/parse_fastq.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -72,7 +72,7 @@ e 'The .fastq file is valid.'
   # ========================================================================= #
   # === Bioroebe::ParseFastq[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb

@@ -7,7 +7,7 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/toplevel_methods/e.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   # ========================================================================= #
   # === Bioroebe.return_fasta_subsection_of_this_file

data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb

@@ -13,17 +13,12 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/show_fasta_headers.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFastaHeaders
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === BASE_DIR
   #
@@ -49,14 +44,11 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
-    # === @be_verbose
-    # ======================================================================= #
-    @be_verbose = true
-    # ======================================================================= #
-    # === @namespace
+    # === :be_verbose
     # ======================================================================= #
-    @namespace = NAMESPACE
+    set_be_verbose
   end
 
   # ========================================================================= #
@@ -109,7 +101,7 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
   # === report_this_header_from_that_file
   # ========================================================================= #
   def report_this_header_from_that_file(header, file)
-    if @be_verbose
+    if be_verbose?
       erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
       e
     end

data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/show_fasta_statistics.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb

@@ -21,7 +21,7 @@
 # Bioroebe.overwrite_fasta_header(ARGV)
 # Bioroebe::SimplifyFastaHeader.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb

@@ -13,14 +13,11 @@ class SplitThisFastaFileIntoChromosomes < ::Bioroebe::CommandlineApplication # =
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
-    # === @namespace
+    # === :be_verbose
     # ======================================================================= #
-    @namespace = NAMESPACE
-    # ======================================================================= #
-    # === @be_verbose
-    # ======================================================================= #
-    @be_verbose = false
+    set_be_quiet
     # ======================================================================= #
     # === @this_file
     #

data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb

@@ -16,7 +16,7 @@
 # require 'bioroebe/fasta/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb'
 # Bioroebe::SplitThisFastaFileIntoChromosomes.new
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -252,8 +252,8 @@ class SplitThisFastaFileIntoChromosomes < ::Bioroebe::CommandlineApplication # =
             # Here we have found a match, so we can simply store this
             # into the file in that event.
             # =============================================================== #
-            if @be_verbose
-              opnn; erev "The following line belongs to chromosome "\
+            if be_verbose?
+              opnerev "The following line belongs to chromosome "\
                          "number `#{sfancy(match)}#{rev}`."
               e crimson(fasta_header_string)
             end

data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb

@@ -17,7 +17,7 @@
 # =========================================================================== #
 # require 'bioroebe/genbank/genbank_flat_file_format_generator.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -78,20 +78,27 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
   def reset
     super()
     # ======================================================================= #
-    # === @be_verbose
+    # === :be_verbose
     # ======================================================================= #
-    @be_verbose = true
+    set_be_verbose
     # ======================================================================= #
     # === @shall_we_downcase
     # ======================================================================= #
     @shall_we_downcase = true
     # ======================================================================= #
-    # === @string
+    # === @internal_hash[:string]
     # ======================================================================= #
-    @string = ''.dup # This is the one that will be output.
+    @internal_hash[:string] = ''.dup # This is the one that will be output.
     set_name_of_the_locus
   end
 
+  # ========================================================================= #
+  # === shall_we_downcase?
+  # ========================================================================= #
+  def shall_we_downcase?
+    @shall_we_downcase
+  end
+
   # ========================================================================= #
   # === n_nucleotides?
   # ========================================================================= #
@@ -104,7 +111,7 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
   # ========================================================================= #
   def set_input(
       i                 = '',
-      shall_we_downcase = @shall_we_downcase
+      shall_we_downcase = shall_we_downcase?
     )
     i = i.first if i.is_a? Array
     i = i.to_s.dup.strip
@@ -151,7 +158,7 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
   # === add
   # ========================================================================= #
   def add(i)
-    @string << i
+    @internal_hash[:string] << i
   end
 
   # ========================================================================= #
@@ -176,15 +183,17 @@ class GenbankFlatFileFormatGenerator < ::Bioroebe::CommandlineApplication # ===
   # ========================================================================= #
   # === show_main_string
   # ========================================================================= #
-  def show_main_string
-    e @string if @be_verbose
+  def show_main_string(
+      be_verbose = be_verbose?
+    )
+    e string? if be_verbose
   end
 
   # ========================================================================= #
   # === string?
   # ========================================================================= #
   def string?
-    @string
+    @internal_hash[:string]
   end
 
   # ========================================================================= #
@@ -264,7 +273,7 @@ return_chunked_numbered_and_properly_spaced_sequence+
   # ========================================================================= #
   # === Bioroebe::GenbankFlatFileFormatGenerator[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/genome/genome.rb

@@ -13,7 +13,7 @@
 # =========================================================================== #
 # require 'bioroebe/genome/genome.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/genomes/genome_pattern.rb

@@ -20,7 +20,7 @@
 # =========================================================================== #
 # require 'bioroebe/genomes/genome_pattern.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -50,17 +50,14 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
     # === @hash
     # ======================================================================= #
     @hash = {}
+    # ======================================================================= #
     # === :array_genes
+    # ======================================================================= #
     @hash[:array_genes] = []
+    # ======================================================================= #
     # === :be_verbose
-    @hash[:be_verbose] = true # If true then we tell the user what we will do.
-  end
-
-  # ========================================================================= #
-  # === be_verbose?
-  # ========================================================================= #
-  def be_verbose?
-    @hash[:be_verbose]
+    # ======================================================================= #
+    set_be_verbose
   end
 
   # ========================================================================= #
@@ -88,11 +85,13 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
   # ========================================================================= #
   # === add_gene
   # ========================================================================= #
-  def add_gene(i = :foo)
+  def add_gene(
+      i = :foo
+    )
     _ = array_genes?
     unless _.include? i
       if be_verbose?
-        opnn; erev "Now adding the gene `#{sfancy(i.to_s)}#{rev}`."
+        opnerev "Now adding the gene `#{sfancy(i.to_s)}#{rev}`."
       end
       _ << i
     end
@@ -113,11 +112,11 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
   # ========================================================================= #
   def report
     if genome?.empty?
-      opnn; erev 'We have no genes stored.'
+      opnerev 'We have no genes stored.'
     else
-      opnn; erev 'We have these genes:'
+      opnerev 'We have these genes:'
       genes?.each {|entry|
-        opnn; erev '  '+sfancy(entry.to_s)
+        opnerev "  #{sfancy(entry.to_s)}"
       }
     end
   end
@@ -127,7 +126,9 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
   #
   # Use this method to remove a Gene again.
   # ========================================================================= #
-  def remove_gene(i = :foo, be_verbose = be_verbose?)
+  def remove_gene(
+      i = :foo, be_verbose = be_verbose?
+    )
     case be_verbose
     when :be_verbose
       be_verbose = true
@@ -135,7 +136,7 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
     _ = array_genes?
     if _.include? i
       if be_verbose
-        opnn; erev "Now removing the gene `#{sfancy(i.to_s)}#{rev}`."
+        opnerev "Now removing the gene `#{sfancy(i.to_s)}#{rev}`."
       end
       _.delete i
     end

data/lib/bioroebe/genomes/genome_retriever.rb

@@ -11,7 +11,7 @@
 # =========================================================================== #
 # require 'bioroebe/genomes/genome_retriever.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -46,6 +46,7 @@ class GenomeRetriever < ::Bioroebe::CommandlineApplication # === Bioroebe::Genom
   # ========================================================================= #
   def fetch(what)
     case what.to_sym
+    # === :human
     when :human,
          :humans
       open_via_the_browser 'https://www.genome.jp/dbget-bin/www_bget?hsa+20+21+22'
@@ -56,7 +57,8 @@ class GenomeRetriever < ::Bioroebe::CommandlineApplication # === Bioroebe::Genom
   # === open_via_the_browser
   # ========================================================================= #
   def open_via_the_browser(
-      url, use_this_browser = :firefox
+      url,
+      use_this_browser = :firefox
     )
     system_cmd "#{use_this_browser} --new-tab #{url}"
   end

data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb

@@ -15,10 +15,7 @@ module GUI
 
 module Gtk
 
-class Snapgene < ::Gtk::Box # === Bioroebe::GUI::Gtk::Snapgene 
-
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
+class Snapgene < ::Gtk::BaseModuleBox # === Bioroebe::GUI::Gtk::Snapgene 
 
   # ========================================================================= #
   # === NAMESPACE
@@ -99,18 +96,18 @@ class Snapgene < ::Gtk::Box # === Bioroebe::GUI::Gtk::Snapgene
   # ========================================================================= #
   def connect_skeleton
     abort_on_exception
-    left_pane  = gtk_vbox
-    right_pane = gtk_vbox
-    hbox1 = gtk_hbox
+    left_pane  = create_vbox
+    right_pane = create_vbox
+    hbox1 = create_hbox
     hbox1.minimal(text('Lane 1: '))
-    entry1 = gtk_entry
+    entry1 = create_entry
     entry1.width_height(220, 30)
     hbox1.minimal(entry1, 2)
-    entry2 = gtk_entry('cut with')
+    entry2 = create_entry('cut with')
     entry2.width_height(220, 30)
     hbox1.minimal(entry2, 2)
     right_pane.minimal(hbox1, 1)
-    left_pane.minimal(gtk_image(
+    left_pane.minimal(create_image(
       'https://i.imgur.com/Ytw7PiC.jpg'
     ))
     minimal(
@@ -122,7 +119,7 @@ class Snapgene < ::Gtk::Box # === Bioroebe::GUI::Gtk::Snapgene
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
-    create_skeleton_then_connect_skeleton
+    super()
   end
 
   # ========================================================================= #
@@ -131,12 +128,12 @@ class Snapgene < ::Gtk::Box # === Bioroebe::GUI::Gtk::Snapgene
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/app/app.rb'
+    require 'gtk_paradise/run'
     _ = ::Bioroebe::GUI::Gtk::Snapgene.new(i)
     r = ::Gtk.run
     r << _
     r.automatic_size_then_automatic_title
-    # r.enable_quick_exit
+    r.enable_quick_exit
     r.top_left_then_run
   end