bioroebe 0.10.80

data/lib/bioroebe/codons/sanitize_codon_frequency.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::SanitizeCodonFrequency
+#
+# This class can be used to turn a codon frequency chart into the
+# corresponding yaml datastructure. In order to do so the dataset
+# can also be displayed on a per-line basis.
+#
+# The idea behind this was to convert the dataset stored in
+# plain text files, into proper yaml files.
+#
+# See the test string below for an example.
+#
+# Usage example:
+#
+#   Bioroebe::SanitizeCodonFrequency.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/codons/sanitize_codon_frequency.rb'
+# =========================================================================== #
+require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
+class SanitizeCodonFrequency < Base # === Bioroebe::SanitizeCodonFrequency
+
+  # ========================================================================= #
+  # === TEST_STRING
+  #
+  # This string can be used as our default test-data.
+  # ========================================================================= #
+  TEST_STRING = '# UUU 26.1(170666)  UCU 23.5(153557)  UAU 18.8(122728)  UGU  8.1( 52903)
+# UUC 18.4(120510)  UCC 14.2( 92923)  UAC 14.8( 96596)  UGC  4.8( 31095)
+# UUA 26.2(170884)  UCA 18.7(122028)  UAA  1.1(  6913)  UGA  0.7(  4447)
+# UUG 27.2(177573)  UCG  8.6( 55951)  UAG  0.5(  3312)  UGG 10.4( 67789)
+# 
+# CUU 12.3( 80076)  CCU 13.5( 88263)  CAU 13.6( 89007)  CGU  6.4( 41791)
+# CUC  5.4( 35545)  CCC  6.8( 44309)  CAC  7.8( 50785)  CGC  2.6( 16993)
+# CUA 13.4( 87619)  CCA 18.3(119641)  CAA 27.3(178251)  CGA  3.0( 19562)
+# CUG 10.5( 68494)  CCG  5.3( 34597)  CAG 12.1( 79121)  CGG  1.7( 11351)
+# 
+# AUU 30.1(196893)  ACU 20.3(132522)  AAU 35.7(233124)  AGU 14.2( 92466)
+# AUC 17.2(112176)  ACC 12.7( 83207)  AAC 24.8(162199)  AGC  9.8( 63726)
+# AUA 17.8(116254)  ACA 17.8(116084)  AAA 41.9(273618)  AGA 21.3(139081)
+# AUG 20.9(136805)  ACG  8.0( 52045)  AAG 30.8(201361)  AGG  9.2( 60289)
+# 
+# GUU 22.1(144243)  GCU 21.2(138358)  GAU 37.6(245641)  GGU 23.9(156109)
+# GUC 11.8( 76947)  GCC 12.6( 82357)  GAC 20.2(132048)  GGC  9.8( 63903)
+# GUA 11.8( 76927)  GCA 16.2(105910)  GAA 45.6(297944)  GGA 10.9( 71216)
+# GUG 10.8( 70337)  GCG  6.2( 40358)  GAG 19.2(125717)  GGG  6.0( 39359)
+'
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = TEST_STRING,
+      run_already = true
+    )
+    reset
+    set_input(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i = TEST_STRING)
+    i = i.first if i.is_a? Array
+    i = TEST_STRING if i.nil?
+    i = i.to_s.dup
+    @input = i
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end
+
+  # ========================================================================= #
+  # === report_result
+  # ========================================================================= #
+  def report_result(i = input?)
+    i.each {|entry|
+      splitted = entry.split(' ')
+      splitted[1] = splitted[1].rjust(4)
+      entry = splitted.join(' ')
+      e entry
+    } if i
+  end
+
+  # ========================================================================= #
+  # === sanitize_input
+  # ========================================================================= #
+  def sanitize_input
+    @input = input?.split(N)
+    input?.map! {|entry| entry.delete('#') } # Get rid '#' next.
+    input?.map!(&:strip)
+    input?.reject!(&:empty?)
+    input?.map! {|entry| entry.split(')') }
+    input?.flatten!
+    input?.map!(&:strip)
+    input?.map! {|entry|
+      if entry.include? '('
+        entry = entry[0..(entry.index('(')-1)]
+      end
+      entry.squeeze! ' '
+      if entry.include? ' '
+        entry.gsub!(/ /,': ')
+      end
+      entry
+    }
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    sanitize_input
+    report_result
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::SanitizeCodonFrequency[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::SanitizeCodonFrequency.new(ARGV)
+end # sanitizecodonfrequency

data/lib/bioroebe/codons/show_codon_tables.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ShowCodonTables
+#
+# This small convenience class can be used to quickly show the various
+# codon tables used by different organisms/species.
+# =========================================================================== #
+# require 'bioroebe/codons/show_codon_tables.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCodonTables
+
+  require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/codons/codon_table.rb'
+  require 'bioroebe/codons/codon_tables.rb'
+  require 'bioroebe/codons/show_this_codon_table.rb'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      show_what = ARGV
+    )
+    reset
+    if show_what.is_a? Array
+      if show_what.empty?
+        show_what << :default
+      end
+    end
+    if show_what.is_a? Array
+      first = show_what.first
+    else
+      first = show_what
+    end
+    case first.to_sym
+    # ======================================================================= #
+    # === :human
+    # ======================================================================= #
+    when :human
+      Bioroebe::ShowThisCodonTable.new
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
+    when :default,
+         :everything
+      do_display_all_available_codon_tables
+    # ======================================================================= #
+    # === Show the headers
+    # ======================================================================= #
+    when :only_names,
+         :headers,
+         '--headers'
+      ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
+        e number.to_s.rjust(3)+') '+long_name.ljust(70)
+      }
+    end
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === print_this_line_of_a_codon_table
+  # ========================================================================= #
+  def print_this_line_of_a_codon_table(codon, aminoacid)
+    print "#{codon}: #{simp(aminoacid)}   #{rev}"
+  end
+
+  # ========================================================================= #
+  # === do_display_all_available_codon_tables
+  # ========================================================================= #
+  def do_display_all_available_codon_tables
+    # ======================================================================= #
+    # Display the human CodonTable first.
+    # ======================================================================= #
+    Bioroebe::ShowThisCodonTable.new(ARGV)
+    e
+    erev 'The above is the human CodonTable. We will next show all'
+    erev 'available codon tables.'
+    e
+    ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
+      e long_name
+      e '=' * 42
+      # ===================================================================== #
+      # Obtain the very important dataset for that particular codon next:
+      # ===================================================================== #
+      dataset = ::Bioroebe::CodonTable[number]
+      sliced  = dataset.to_a.each_slice(5)
+      sliced.each {|array|
+        array.each {|codon, aminoacid|
+          print_this_line_of_a_codon_table(codon, aminoacid)
+        }; e
+      }
+      e
+    }
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.show_codon_tables
+#
+# Here, the default input argument is reversed.
+# =========================================================================== #
+def self.show_codon_tables(how = :headers)
+  ShowCodonTables.new(how)
+end
+
+# =========================================================================== #
+# === Bioroebe.available_codon_tables?
+# =========================================================================== #
+def self.available_codon_tables?
+  ::Bioroebe::CodonTables.definitions?.values # Do not sort this.
+end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ShowCodonTables.new(ARGV)
+end # showcodontables
+    # showcodontables human

data/lib/bioroebe/codons/show_codon_usage.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ShowCodonUsage
+#
+# This class will keep track of the codon usage of a given DNA string.
+# It will count the codons as well.
+#
+# You can pass an existing file as input.
+#
+# Usage example:
+#
+#   Bioroebe::ShowCodonUsage.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/codons/show_codon_usage.rb'
+# Bioroebe::ShowCodonUsage.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCodonUsage
+
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil,
+      run_already = true
+    )
+    reset
+    set_input(i)
+    # ======================================================================= #
+    # === Handle blocks given to this method next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      when :be_quiet
+        do_not_be_verbose
+      end
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i = '')
+    i = i.first if i.is_a? Array
+    i = i.to_s.dup
+    @input = i
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end; alias string? input? # === string?
+
+  # ========================================================================= #
+  # === menu
+  # ========================================================================= #
+  def menu(i = @input)
+    if i and File.file?(i)
+      # ===================================================================== #
+      # Handle locally existing files next.
+      # ===================================================================== #
+      @input = File.read(i).strip.delete("\n")
+    end
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    menu
+    codon_usage = Hash.new(0)
+    if string?.empty?
+      e rev+'Not found any string. Please "'+simp('assign')+rev+'" one first.'
+    else
+      string = string?
+      _ = string.dup
+      # ===================================================================== #
+      # Next, obtain the codons in that sequence:
+      # ===================================================================== #
+      _ = _.scan(/..?.?/) # Grab 3 pairs each here.
+      _.each { |this_codon|
+        codon_usage[this_codon] += 1
+      }
+      # ===================================================================== #
+      # Sort it next, so that the highest entries come on top. That
+      # way we simplify downstream-applications that want to show the
+      # result in a sensible manner.
+      # ===================================================================== #
+      codon_usage = codon_usage.sort_by {|key, value|
+        value
+      }.reverse
+      codon_usage = Hash[*codon_usage.flatten]
+      type = 'DNA'
+      # ===================================================================== #
+      # RNA is supported as well.
+      # ===================================================================== #
+      if string.include? 'U'
+        type = 'RNA'
+      end
+      if be_verbose?
+        erev 'The codon usage of this '+simp(type)+rev+
+             ' string ('+sfancy(string.size.to_s)+rev+
+             ' nucleotides) is as follows:'
+        e
+        print '  '; pp codon_usage # Simply report the main Hash in use here.
+        report_the_top_five_codons(codon_usage)
+      end
+      @hash = codon_usage
+    end
+  end
+
+  # ========================================================================= #
+  # === report_the_top_five_codons
+  # ========================================================================= #
+  def report_the_top_five_codons(from_this_dataset)
+    e
+    e 'The top five codons in use, sorted, are:'
+    e
+    top_five = from_this_dataset.sort_by {|key, values| values }.reverse[0..4]
+    top_five.each {|name_of_codon, how_many_of_them|
+      _ = name_of_codon.upcase
+      this_codon = codon_to_aminoacid(_)
+      colourized_this_codon = turquoise(this_codon)
+      e rev+'  - '+
+        teal(_)+
+        rev+
+        ': '+simp(how_many_of_them.to_s.rjust(2))+
+        rev+' ('+colourized_this_codon+rev+')'
+    }; e
+  end
+
+  # ========================================================================= #
+  # === codon_to_aminoacid
+  # ========================================================================= #
+  def codon_to_aminoacid(i)
+    ::Bioroebe.codon_to_aminoacid(i)
+  end
+
+  # ========================================================================= #
+  # === hash?
+  #
+  # This hash will keep the codon-usage.
+  #
+  # It may look like this:
+  #
+  #   {"GTA"=>6,
+  #    "TAC"=>5,
+  #    "ACG"=>4,
+  #    "CGT"=>4,
+  #
+  # So it is already sorted properly.
+  # ========================================================================= #
+  def hash?
+    @hash
+  end; alias result? hash? # === result?
+
+  # ========================================================================= #
+  # === Bioroebe::ShowCodonUsage[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.codon_frequencies_of_this_sequence
+# =========================================================================== #
+def self.codon_frequencies_of_this_sequence(i = ARGV)
+  Bioroebe::ShowCodonUsage.new(i) { :be_quiet }
+end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ShowCodonUsage.new(ARGV)
+end # codonusage ATGGGCGGGGTGATGGCAATGCCTTTAATGCCGCCAAAAAAAAAAAAAAAA
+    # codonusage /root/Bioroebe/fasta/sample_file.fasta