bioroebe 0.10.80 → 0.11.32

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/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