bioroebe 0.10.80

data/lib/bioroebe/utility_scripts/consensus_sequence.rb

@@ -0,0 +1,374 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ConsensusSequence
+#
+# This class will generate a consensus sequence.
+#
+# You have to input several sequences to this class - at the least
+# two.
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/consensus_sequence.rb'
+# Bioroebe::ConsensusSequence.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::ConsensusSequence
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(*i)
+    reset
+    run_already = true # This is the default value.
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded # case tag
+      # ===================================================================== #
+      # === :do_not_run_yet_and_be_quiet
+      # ===================================================================== #
+      when :do_not_run_yet_and_be_quiet
+        run_already = false
+        @be_verbose = false
+        @report_the_frequencies = false
+      # ===================================================================== #
+      # === :do_not_run_yet
+      # ===================================================================== #
+      when :do_not_run_yet
+        run_already = false
+      # ===================================================================== #
+      # === :be_quiet
+      # ===================================================================== #
+      when :be_quiet
+        @be_verbose = false
+        @report_the_frequencies = false
+      end
+    end
+    set_input_sequences(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @array_consensus_positions
+    # ======================================================================= #
+    @array_consensus_positions = []
+    # ======================================================================= #
+    # === @be_verbose
+    # ======================================================================= #
+    @be_verbose = true
+    # ======================================================================= #
+    # === @report_the_frequencies
+    # ======================================================================= #
+    @report_the_frequencies = true
+  end
+
+  # ========================================================================= #
+  # === input_sequences?
+  # ========================================================================= #
+  def input_sequences?
+    @input_sequences
+  end
+
+  # ========================================================================= #
+  # === set_input_sequences(i)
+  # ========================================================================= #
+  def set_input_sequences(i)
+    @input_sequences = [i].flatten
+  end
+
+  # ========================================================================= #
+  # === iterate_over_the_sequences
+  # ========================================================================= #
+  def iterate_over_the_sequences
+    size = @input_sequences.first.size
+    0.upto(size - 1) {|n|
+      mapped = @input_sequences.map {|line| line[n,1] }
+      frequencies = calculate_frequencies_of(mapped)
+      # ===================================================================== #
+      # max_value has two values:
+      #
+      #   (1) the nucleotide
+      #   (2) the amount of times that nucleotide occurs
+      #
+      # We can not use .max_by because it returns only one result; so we
+      # have to use .group_by instead.
+      # ===================================================================== #
+      # max_value = frequencies.max_by {|key, value| value }
+      max_value = frequencies.group_by {|key, value| value }.max.last # => [2, 5]
+      _ = max_value.map {|first, last| first }
+      if _.size > 1
+        append_this = '['+_.join('/')+']'
+      else
+        append_this = _.join
+      end
+      if @report_the_frequencies
+        erev "The #{mediumslateblue('frequencies')}#{rev} "\
+             "for #{lightgreen(mapped.join)}#{rev} "+
+             '(at '+colourize_nucleotide_position("nucleotide position #{n+1}")+
+             rev+') were:'
+        e
+        print '  '; pp frequencies
+        erev "\nThe associated max-value for "+
+             colourize_nucleotide_position("nucleotide position #{n+1}")+
+             "#{rev} was: "+
+             simp(
+               max_value.map {|a| a.join(': ') }.join('; ')
+             )
+        e
+      end
+      @array_consensus_positions << append_this
+    }
+  end; alias determine_the_consensus_sequences iterate_over_the_sequences # === determine_the_consensus_sequences
+
+  # ========================================================================= #
+  # === colourize_nucleotide_position
+  # ========================================================================= #
+  def colourize_nucleotide_position(i)
+    seagreen(i)
+  end
+
+  # ========================================================================= #
+  # === random_nucleotide_for_this_IUPAC_code
+  # ========================================================================= #
+  def random_nucleotide_for_this_IUPAC_code(i)
+    case i
+    when 'H'
+      return_A_or_T_or_C
+    when 'M'
+      return_A_or_C
+    end
+  end
+
+  # ========================================================================= #
+  # === return_A_or_C
+  # ========================================================================= #
+  def return_A_or_C
+    %w( A C ).sample
+  end
+
+  # ========================================================================= #
+  # === return_A_or_T
+  # ========================================================================= #
+  def return_A_or_T
+    %w( A T ).sample
+  end
+
+
+  # ========================================================================= #
+  # === return_A_or_T_or_C
+  # ========================================================================= #
+  def return_A_or_T_or_C
+    %w( A T C ).sample
+  end
+
+  # ========================================================================= #
+  # === consensus_sequence?
+  # ========================================================================= #
+  def consensus_sequence?
+    @array_consensus_positions.join
+  end
+
+  # ========================================================================= #
+  # === calculate_frequencies_of
+  # ========================================================================= #
+  def calculate_frequencies_of(array)
+    hash = {}
+    hash['A'] = array.count('A')
+    hash['T'] = array.count('T')
+    hash['C'] = array.count('C')
+    hash['G'] = array.count('G')
+    return hash
+  end
+
+  # ========================================================================= #
+  # === report_on_which_sequences_we_will_operate
+  # ========================================================================= #
+  def report_on_which_sequences_we_will_operate(
+      be_verbose = @be_verbose
+    )
+    case be_verbose
+    when :be_verbose
+      be_verbose = true
+    end
+    if be_verbose
+      e
+      erev "#{rev}Working on the following "\
+           "#{steelblue(@input_sequences.size)} "\
+           "#{rev}sequences next:"
+      e
+      @input_sequences.each_with_index {|this_sequence, index| index += 1
+        e "  #{sfancy(this_sequence)} #{steelblue(index.to_s.rjust(3))}"
+      }; e
+    end
+  end
+
+  # ========================================================================= #
+  # === report_the_consensus_sequence
+  # ========================================================================= #
+  def report_the_consensus_sequence
+    if @be_verbose
+      the_consensus_sequence = consensus_sequence?
+      erev 'The consensus sequence is: '
+      e
+      e "  #{simp(the_consensus_sequence)}"
+      e
+      if the_consensus_sequence.include? '/'
+        # =================================================================== #
+        # In this case, we can perhaps simplify it via the IUPAC code.
+        # =================================================================== #
+        try_to_find_and_report_a_simpler_consensus_sequence(
+          the_consensus_sequence
+        )
+        # =================================================================== #
+        # And this here will just pick any even simpler consensus
+        # sequence. We assume that this would imply equal likelihood
+        # for a given sequence.
+        # =================================================================== #
+        try_to_find_and_report_an_even_simpler_consensus_sequence(
+          the_consensus_sequence
+        )
+        if @be_verbose
+          erev 'Finally, we will display the above findings in a'
+          erev 'shorter variant:'
+          report_on_which_sequences_we_will_operate
+          display_an_even_simpler_consensus_sequence
+          e
+        end
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === display_an_even_simpler_consensus_sequence
+  # ========================================================================= #
+  def display_an_even_simpler_consensus_sequence(
+      i = consensus_sequence?
+    )
+    this_sequence = orange(return_an_even_simpler_consensus_sequence(i))
+    erev "  #{this_sequence}#{rev} "\
+         "# ← a very likely consensus sequence"
+  end
+
+  # ========================================================================= #
+  # === return_an_even_simpler_consensus_sequence
+  # ========================================================================= #
+  def return_an_even_simpler_consensus_sequence(
+      i = consensus_sequence?
+    )
+    _ = i.dup
+    if _.include? '[A/T/C]'
+      _.gsub!(/\[A\/T\/C\]/,
+        steelblue(return_A_or_T_or_C)+
+        remove_escape_sequence(orange)
+      )
+    end
+    if _.include? '[A/C]'
+      _.gsub!(/\[A\/C\]/,
+        steelblue(return_A_or_C)+
+        remove_escape_sequence(orange)
+      )
+    end
+    if _.include? '[A/T]'
+      _.gsub!(/\[A\/T\]/,
+        steelblue(return_A_or_T)+
+        remove_escape_sequence(orange)
+      )
+    end
+    _
+  end
+
+  # ========================================================================= #
+  # === try_to_find_and_report_an_even_simpler_consensus_sequence
+  # ========================================================================= #
+  def try_to_find_and_report_an_even_simpler_consensus_sequence(
+      i = consensus_sequence?
+    )
+    erev "#{rev}And the following is an even simpler consensus "\
+         "sequence (blue"
+    erev "denotes random, equal choice):"
+    _ = return_an_even_simpler_consensus_sequence(i)
+    e
+    erev "  #{_}"
+    e
+  end
+
+  # ========================================================================= #
+  # === try_to_find_and_report_a_simpler_consensus_sequence
+  #
+  # For a list of IUPAC codes there, you can use this link:
+  #
+  #   https://www.bioinformatics.org/sms/iupac.html
+  #
+  # ========================================================================= #
+  def try_to_find_and_report_a_simpler_consensus_sequence(
+      i = consensus_sequence?
+    )
+    erev "#{rev}We will try to find - and report - a simpler consensus sequence:"
+    i = orange(i)
+    i = i.dup if i.frozen?
+    # ======================================================================= #
+    # === Handle [A/T/C]
+    # ======================================================================= #
+    if i.include? '[A/T/C]'
+      i.gsub!(/\[A\/T\/C\]/,
+        steelblue('H')+
+        remove_escape_sequence(orange)
+      )
+    end
+    # ======================================================================= #
+    # === Handle [A/C]
+    # ======================================================================= #
+    if i.include? '[A/C]'
+      i.gsub!(/\[A\/C\]/,
+        steelblue('M')+
+        remove_escape_sequence(orange)
+      )
+    end
+    e
+    erev "  #{i}"
+    e
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    report_on_which_sequences_we_will_operate
+    iterate_over_the_sequences
+    report_the_consensus_sequence
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.return_consensus_sequence_of
+#
+# This is a simpler module-method. It will just return the consensus
+# sequence of the given input sequence.
+#
+# It can be used like this:
+#
+#   Bioroebe.return_consensus_sequence_of(%w( ACTCC CACCA AGCCA AACGC CGCAT CGACC ACCGC GGCCG GGCGT GGCGT ))
+#
+# =========================================================================== #
+def self.return_consensus_sequence_of(*i)
+  ::Bioroebe::ConsensusSequence.new(i) { :be_quiet }.consensus_sequence?
+end; self.instance_eval { alias return_consensus_sequence return_consensus_sequence_of } # === Bioroebe.return_consensus_sequence
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ConsensusSequence.new(ARGV)
+end # consensussequence ACTCC CACCA AGCCA AACGC CGCAT CGACC ACCGC GGCCG GGCGT GGCGT
+    # consensussequence ACTCGATGCA ACACGCTCCA ACTTGCTCCA GCGCGGCGCA TCATGTTGCA TCGCGATCCT TCTCCATCCT CCTTGCTGCA CCGTCGTGCA CCACCTTACA

data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb

@@ -0,0 +1,130 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::CreateBatchEntrezFile
+#
+# This class can generate a file, that can be used for batch entrez,
+# at:
+#
+#   https://www.ncbi.nlm.nih.gov/sites/batchentrez
+#
+# A file will be created locally, that will have the IDs such as
+# "NZ_CP011602.1".
+#
+# Usage example:
+#
+#   Bioroebe::CreateBatchEntrezFile.new
+#
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/create_batch_entrez_file.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class CreateBatchEntrezFile < ::Bioroebe::CommandlineApplication # === Bioroebe::CreateBatchEntrezFile
+
+  # ========================================================================= #
+  # === DEFAULT_INPUT
+  #
+  # You can use this as test-input, to test the behaviour of the class.
+  #
+  # The URL should be to e. g. a NZ file.
+  # ========================================================================= #
+  DEFAULT_INPUT = '
+https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP011602.1
+
+https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP011636.1
+
+https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP014070.1
+
+https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP007215.2
+
+https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
+'
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = DEFAULT_INPUT,
+      run_already = true
+    )
+    reset
+    set_input(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i = DEFAULT_INPUT)
+    i = i.first if i.is_a? Array
+    i = DEFAULT_INPUT if i.nil?
+    i = i.to_s.dup.split(N)
+    @input = i
+    sanitize_input
+  end
+
+  # ========================================================================= #
+  # === sanitize_input
+  # ========================================================================= #
+  def sanitize_input
+    @input.reject! {|line| line.strip.empty? }
+    @input.map! {|line| File.basename(line) }
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end
+
+  # ========================================================================= #
+  # === store_input_into_a_file
+  # ========================================================================= #
+  def store_input_into_a_file
+    this_file = 'input_files.fasta'
+    opnn; e "Now storing into `#{sfile(this_file)}`."
+    what = @input.join(N)
+    into = this_file
+    write_what_into(what, into)
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    store_input_into_a_file
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::CreateBatchEntrezFile[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::CreateBatchEntrezFile.new(ARGV)
+end # createbatchentrezfile

data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb

@@ -0,0 +1,115 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::DetermineAntigenicAreas
+#
+# Analysis of data from experimentally determined antigenic sites on
+# proteins has revealed that the hydrophobic residues:
+#
+#   (1) Cys (C)
+#   (2) Leu (L), and
+#   (3) Val (V)
+#
+# if they occur on the surface of a protein, are more likely to be a
+# part of antigenic sites.
+#
+# The method of "Kolaskar and Tongaonkar" to predict antigenic determinants
+# in proteins is semi-empirical and makes use of physicochemical properties
+# of amino acid residues and their frequencies of occurrence in
+# experimentally known "segmental epitopes".
+#
+# Note that this class here is currently incomplete. :\ :/
+#
+# Usage example:
+#
+#   Bioroebe::DetermineAntigenicAreas.new
+#
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/determine_antigenic_areas.rb'
+# =========================================================================== #
+require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
+class DetermineAntigenicAreas < Base # === Bioroebe::DetermineAntigenicAreas.new
+
+  # ========================================================================= #
+  # === ARRAY_IMPORTANT_HYDROPHOBIC_RESIDUES
+  # ========================================================================= #
+  ARRAY_IMPORTANT_HYDROPHOBIC_RESIDUES = %w( C L V )
+
+  # ========================================================================= #
+  # === SAMPLE_INPUT
+  #
+  # Use this as example for the input.
+  # ========================================================================= #
+  SAMPLE_INPUT =
+    'MEDEIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS'\
+    'KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT'\
+    'QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL'\
+    'AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMGTAASSSSLEKSY'\
+    'ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTYNSIMKCDVDIRKDLYANTVLS'\
+    'GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ'\
+    'EYDESGPSIVHRKCF'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = SAMPLE_INPUT,
+      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 = SAMPLE_INPUT)
+    i = i.first if i.is_a? Array
+    i = SAMPLE_INPUT if i.nil? # Use default in this case.
+    i = i.to_s.dup
+    @input = i
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    erev 'The provided input had '+steelblue(@input.size.to_s)+rev+' entries.'
+    e
+    erev '  n '+lightgreen('C')+rev+':'+@input.count('C').to_s.rjust(3)
+    erev '  n '+lightgreen('L')+rev+':'+@input.count('L').to_s.rjust(3)
+    erev '  n '+lightgreen('V')+rev+':'+@input.count('V').to_s.rjust(3)
+    e
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::DetermineAntigenicAreas[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::DetermineAntigenicAreas.new(ARGV)
+end # determineantigenicareas