bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/electron_microscopy/flipy.rb

@@ -0,0 +1,83 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# ========================================================================= #
+# === Bioroebe::ElectronMicroscopy::FlipY
+#
+# This class will flip the coordinates in the y-axis direction. It will
+# work on .mrc files.
+#
+# Usage example:
+#
+#   Bioroebe::ElectronMicroscopy/FlipY.new
+#
+# ========================================================================= #
+# require 'bioroebe/electron_microscopy/flipy.rb'
+# ========================================================================= #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class FlipY < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::FlipY
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil,
+      run_already = true
+    )
+    reset
+    set_commandline_arguments(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    infer_the_namespace
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(i)
+    case i
+    # ======================================================================= #
+    # === --help
+    # ======================================================================= #
+    when /^-?-?help$/i
+      opnn; e 'Input a .mrc file.'
+      exit
+    end
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    this_image = first_argument?
+    if this_image.is_a? Array
+      this_image = this_image.first
+    end
+    this_image = this_image.to_s
+    output_location = (
+      File.dirname(this_image)+'/'+File.basename(this_image)
+    ).squeeze('/')
+    if output_location.include? 'BACKUP/'
+      output_location.gsub!(/BACKUP\//, '')
+    end
+    @cmd = 'xmipp_transform_mirror --flipY -i '+this_image+' -o '+output_location
+    menu(this_image)
+    esystem @cmd
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ElectronMicroscopy::FlipY.new(ARGV)
+end # flipy

data/lib/bioroebe/electron_microscopy/parse_coordinates.rb

@@ -19,12 +19,7 @@ module Bioroebe
 
 module ElectronMicroscopy
 
-class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ParseCoordinates.new
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ParseCoordinates
 
   # ========================================================================= #
   # === DEFAULT_FILE
@@ -58,10 +53,7 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @dataset
     # ======================================================================= #

data/lib/bioroebe/electron_microscopy/read_file_xmd.rb

@@ -22,11 +22,6 @@ module ElectronMicroscopy
 
 class ReadFileXMD < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ReadFileXMD
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   #
@@ -51,10 +46,7 @@ class ReadFileXMD < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronM
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @header
     # ======================================================================= #

data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb

@@ -22,10 +22,8 @@ module ElectronMicroscopy
 
 class SimpleStarFileGenerator < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::SimpleStarFileGenerator
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+  require 'bioroebe/electron_microscopy/electron_microscopy_module.rb'
+  include Bioroebe::ElectronMicroscopy
 
   # ========================================================================= #
   # === SAVE_HERE
@@ -62,14 +60,11 @@ _rlnMicrographName #1'+N
   end
 
   # ========================================================================= #
-  # === reset
+  # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @save_here
     # ======================================================================= #

data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb

@@ -11,9 +11,13 @@ module Bioroebe
   # ========================================================================= #
   # === Bioroebe.has_this_restriction_enzyme?
   #
-  # Determine whether we have a specific restriction enzyme or whether
-  # we do not. We will downcase all keys in use to simplify finding
-  # a matching entry.
+  # This method will determine whether we have a specific restriction
+  # enzyme registered in the yaml file restriction_enzymes.yml or
+  # whether we do not. That way we can query whether a restriction
+  # enzyme is registered (and thus available) or whether it is not.
+  #
+  # The method will downcase all keys in use to simplify finding a
+  # matching entry.
   #
   # Usage example:
   #
@@ -21,6 +25,9 @@ module Bioroebe
   #   Bioroebe.has_this_restriction_enzyme? 'EcoRI'   # => true
   #   Bioroebe.has_this_restriction_enzyme? 'EcoRII'  # => true
   #   Bioroebe.has_this_restriction_enzyme? 'EcoRIII' # => false
+  #   Bioroebe.has_this_restriction_enzyme? 'PvuI'    # => true
+  #   Bioroebe.has_this_restriction_enzyme? 'PvuII'   # => true
+  #   Bioroebe.has_this_restriction_enzyme? 'PvuIII'  # => false
   #
   # ========================================================================= #
   def self.has_this_restriction_enzyme?(

data/lib/bioroebe/enzymes/restriction_enzyme.rb

@@ -152,7 +152,7 @@ class RestrictionEnzyme < ::Bioroebe::CommandlineApplication # === Bioroebe::Res
   # ========================================================================= #
   # === Bioroebe::RestrictionEnzyme[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 
@@ -184,6 +184,28 @@ def self.restriction_enzyme(i)
   _[i]
 end
 
+# =========================================================================== #
+# === Bioroebe.restriction_sites?
+#
+# Usage examples:
+#
+#   x = Bioroebe.restriction_sites?('EcoRI') # => "GAATTC"
+#   x = Bioroebe.restriction_sites?('SacI')  # => "GAGCTC"
+#   x = Bioroebe.restriction_sites?('KpnI')  # => "GGTACC"
+#   x = Bioroebe.restriction_sites?('XmaI')  # => "CCCGGG"
+#   x = Bioroebe.restriction_sites?('BamHI') # => "GGATCC"
+#   x = Bioroebe.restriction_sites?('XbaI')  # => "TCTAGA"
+#   x = Bioroebe.restriction_sites?('SalI')  # => "GTCGAC"
+#
+# =========================================================================== #
+def self.restriction_sites?(i)
+  if i.is_a? Array
+    i = i.join(' ').strip
+  end
+  i = i.dup if i.frozen?
+  return restriction_enzyme(i)
+end
+
 end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb

@@ -0,0 +1,65 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::RestrictionEnzymes::Statistics
+#
+# Statistics-related information is stored in this file.
+# =========================================================================== #
+# require 'statistics.rb'
+# =========================================================================== #
+module Bioroebe
+
+module RestrictionEnzymes
+
+module Statistics # === Bioroebe::RestrictionEnzymes::Statistics
+
+  require 'bioroebe/constants/files_and_directories.rb'
+
+  alias e puts
+
+  # ========================================================================= #
+  # === Bioroebe::RestrictionEnzymes::Statistics.erev
+  # ========================================================================= #
+  def self.erev(i = '')
+    ::Bioroebe.erev(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::RestrictionEnzymes::Statistics.show
+  # ========================================================================= #
+  def self.show
+    require 'yaml'
+    require 'bioroebe/colours/rev.rb'
+    dataset = YAML.load_file(Bioroebe.file_restriction_enzymes)
+    erev 'A total of '+dataset.keys.size.to_s+' restriction enzymes '\
+         'are registered in this project.'
+    array = []
+    dataset.each_pair {|key, value|
+      if value.include? ' '
+        value = value.split(' ').first.to_s
+      end
+      array << value.size
+    }
+    hash = Hash.new
+    hash.default = 0
+    array.each {|entry|
+      hash[entry] += 1
+    }
+    sorted = hash.sort_by {|key, value| key }
+    e
+    erev 'The composition is:'
+    e
+    sorted.each {|key, value|
+      erev '  Restriction size '+key.to_s.rjust(2)+' is encountered '+
+        value.to_s.rjust(3)+' times.'
+    }
+    e
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  include Bioroebe::RestrictionEnzymes::Statistics
+  Bioroebe::RestrictionEnzymes::Statistics.show
+end # statistics.rb

data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb

@@ -23,11 +23,6 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
 
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -47,10 +42,7 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb

@@ -21,9 +21,9 @@ module Bioroebe
 class CompactFastaFile < ::Bioroebe::CommandlineApplication # === Bioroebe::CompactFastaFile
 
   # ========================================================================= #
-  # === NAMESPACE
+  # === SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE
   # ========================================================================= #
-  NAMESPACE = inspect
+  SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE = true
 
   # ========================================================================= #
   # === initialize
@@ -72,10 +72,7 @@ class CompactFastaFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Comp
   # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @user_configuration
     # ======================================================================= #
@@ -83,7 +80,8 @@ class CompactFastaFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Comp
     # ======================================================================= #
     # === :do_upcase_the_sequence
     # ======================================================================= #
-    @user_configuration[:do_upcase_the_sequence] = false
+    @user_configuration[:do_upcase_the_sequence] =
+      SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE
     enable_colours
   end
 
@@ -99,7 +97,7 @@ class CompactFastaFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Comp
   # ========================================================================= #
   def do_upcase_the_sequence?
     @user_configuration[:do_upcase_the_sequence]
-  end
+  end; alias shall_we_upcase_the_sequence? do_upcase_the_sequence? # === shall_we_upcase_the_sequence?
 
   # ========================================================================= #
   # === menu                                                       (menu tag)
@@ -131,7 +129,7 @@ class CompactFastaFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Comp
     )
     _ = Bioroebe::ParseFasta.new(this_file) { :be_quiet }
     what = '> '+_.header?+"\n".dup
-    if do_upcase_the_sequence?
+    if shall_we_upcase_the_sequence?
       what << _.body?.upcase.delete(' ')
     else
       what << _.body?.delete(' ')

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

@@ -23,11 +23,6 @@ module Bioroebe
 
 class FastaDefline < ::Bioroebe::CommandlineApplication # === Bioroebe::FastaDefline
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -47,6 +42,7 @@ class FastaDefline < ::Bioroebe::CommandlineApplication # === Bioroebe::FastaDef
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
   end
 
   # ========================================================================= #

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

@@ -0,0 +1,81 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::FastaToYaml
+#
+# This class can turn a FASTA sequence, such as one stored in .fasta,
+# into a .yml file.
+#
+# Usage example:
+#
+#   Bioroebe::FastaToYaml.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/fasta/fasta_to_yaml/fasta_to_yaml.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class FastaToYaml < ::Bioroebe::CommandlineApplication # === Bioroebe::FastaToYaml
+
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    infer_the_namespace
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    _ = first?
+    if _ and File.exist?(_)
+      dataset = Bioroebe.parse_fasta_file(_)
+      opne 'Converting the dataset from '+sfile(_)
+      opne 'into a standalone .yml file next.'
+      hash = {}
+      hash[:filename] = _
+      hash[:identifier] = File.read(_).split("\n").first.delete('>').lstrip
+      hash[:identifier] = return_the_first_line_of_this_file(_).
+                          delete('>').delete(':').
+                          lstrip
+      hash[:sequence] = dataset.sequence?
+      what = YAML.dump(hash)
+      into = _.delete_suffix(File.extname(_))+'.yml'
+      opne 'Storing into the file `'+sfile(into)+rev+'` next.'
+      write_what_into(what, into)
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::FastaToYaml[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::FastaToYaml.new(ARGV)
+end # fastatoyaml