bioroebe 0.10.80

data/lib/bioroebe/parsers/parse_embl.rb

@@ -0,0 +1,76 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ParseEMBL
+#
+# This class can be used to parse EMBL files.
+# =========================================================================== #
+# require 'bioroebe/parsers/parse_embl.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class ParseEMBL < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseEMBL
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    _ = first_argument?
+    if _ and File.exist?(_)
+      dataset = File.readlines(_).select {|line|
+        line.start_with? '     '
+      }.map {|entry|
+        splitted = entry.strip.split(' ')
+        splitted.pop # Remove the last element.
+        splitted.join.strip
+      }
+      if dataset.is_a? Array
+        dataset = dataset.join
+      end
+      @sequence = dataset.upcase
+    end
+  end
+
+  # ========================================================================= #
+  # === sequence?
+  # ========================================================================= #
+  def sequence?
+    @sequence
+  end; alias coding_sequence? sequence? # === coding_sequence?
+       alias cds              sequence? # === cds
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  _ = Bioroebe::ParseEMBL.new(ARGV)
+  pp _.sequence?
+end # parseembl $BIOROEBE_YAML/blosum/blosum45.yml

data/lib/bioroebe/parsers/stride_parser.rb

@@ -0,0 +1,117 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::StrideParser
+#
+# This class will parse a file that has been generated by the program
+# called "stride".
+#
+# The homepage of stride can be found here:
+#
+#   http://webclu.bio.wzw.tum.de/stride/
+#
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class StrideParser < ::Bioroebe::CommandlineApplication # === Bioroebe::StrideParser
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= # 
+  def initialize(
+      i, run_already = true
+    )
+    reset
+    set_this_file(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @dataset
+    # ======================================================================= #
+    @dataset = {}
+    # ======================================================================= #
+    # === :total_surface_area
+    # ======================================================================= #
+    @dataset[:total_surface_area] = 0 # Initialize it here.
+  end
+
+  # ========================================================================= #
+  # === set_this_file
+  # ========================================================================= #
+  def set_this_file(i)
+    @dataset[:main_file] = i
+  end
+
+  # ========================================================================= #
+  # === main_file?
+  # ========================================================================= #
+  def main_file?
+    @dataset[:main_file]
+  end
+
+  # ========================================================================= #
+  # === parse_report
+  # ========================================================================= #
+  def parse_report(i = main_file?)
+    i = File.read(i) if File.exist? i
+    i.split("\n").each { |line|
+      case line
+      when /^ASG/
+        asg = line.split(/\s+/)
+        # =================================================================== #
+        # Obtain solvent-accessible area for each residue next
+        # =================================================================== #
+        @dataset[:total_surface_area] += asg[9].to_f
+      end
+    }
+    if @dataset[:total_surface_area] == 0
+      @dataset[:total_surface_area] = nil
+    end
+  end; private :parse_report
+
+  # ========================================================================= #
+  # === tot_surf_area?
+  # ========================================================================= #
+  def tot_surf_area?
+    @dataset[:total_surface_area]
+  end; alias tot_surf_area tot_surf_area? # === tot_surf_area
+  
+  # ========================================================================= #
+  # === report_result
+  # ========================================================================= #
+  def report_result
+    opnn; erev "The total surface area is: "\
+               "#{simp(tot_surf_area?.to_s)}"
+  end; alias report report_result # === report
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    parse_report
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  stride = Bioroebe::StrideParser.new(ARGV.first)
+  stride.report_result
+end # ruby_stride

data/lib/bioroebe/patterns/README.md

@@ -0,0 +1,5 @@
+This directory, created in May 2020, is used to find certain patterns
+in aminoacid-sequences or DNA/RNA nucleotides.
+
+The primary focus is on patterns in proteins (thus, the aminoacid
+sequence).

data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb

@@ -0,0 +1,149 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::AnalyseGlycosylationPattern
+#
+# This class can analyse a given sequence for glycosylation patterns.
+#
+# Usage example:
+#
+#   Bioroebe::AnalyseGlycosylationPattern.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/pattern/analyse_glycosylation_pattern.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class AnalyseGlycosylationPattern < ::Bioroebe::CommandlineApplication # === Bioroebe::AnalyseGlycosylationPattern
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    case run_already
+    when :do_not_run_yet
+      run_already = false
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = return_commandline_arguments_starting_with_hyphens
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # case tag
+      # ===================================================================== #
+      # === --help
+      # ===================================================================== #
+      when /^-?-?help/
+        show_help
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === report_how_many_asparagines_are_in_this_sequence
+  # ========================================================================= #
+  def report_how_many_asparagines_are_in_this_sequence(
+      i = @sequence
+    )
+    erev 'This sequence contains '+
+          steelblue(
+            i.to_s.count('N').to_s.rjust(2)
+          )+rev+
+          ' asparagine residues. '+could_be(:N_linked)+
+          rev+'.'
+  end
+
+  # ========================================================================= #
+  # === could_be
+  # ========================================================================= #
+  def could_be(i = :N_linked)
+    case i
+    when :O_linked
+      'These could be sites for '+
+      steelblue('O-linked glycosylation')+
+      rev
+    when :N_linked
+      'These could be sites for '+
+      steelblue('N-linked glycosylation')+
+      rev
+    end
+  end
+
+  # ========================================================================= #
+  # === report_how_many_serines_are_in_this_sequence
+  # ========================================================================= #
+  def report_how_many_serines_are_in_this_sequence(
+      i = @sequence
+    )
+    erev 'This sequence contains '+
+          steelblue(
+            i.to_s.count('S').to_s.rjust(2)
+          )+rev+
+          ' serine residues.     '+could_be(:O_linked)+
+          '.'
+  end
+
+  # ========================================================================= #
+  # === report_how_many_threonines_are_in_this_sequence
+  # ========================================================================= #
+  def report_how_many_threonines_are_in_this_sequence(
+      i = @sequence
+    )
+    erev 'This sequence contains '+
+          steelblue(
+            i.to_s.count('T').to_s.rjust(2)
+          )+rev+
+         ' threonines residues. '+could_be(:O_linked)+
+         '.'
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    menu
+    @sequence = first_argument?
+    erev 'The sequence '
+    e  "  #{colourize_nucleotides(@sequence)}"
+    erev 'will now be analysed.'
+    report_how_many_asparagines_are_in_this_sequence
+    report_how_many_serines_are_in_this_sequence
+    report_how_many_threonines_are_in_this_sequence
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::AnalyseGlycosylationPattern[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::AnalyseGlycosylationPattern.new(ARGV)
+end # glycopattern QLSLMSRAITMHAPSGPNARTNPPALYHVDRSVRWLIACLLLRGKWSPLPVPHLSLSSDAPRRSFLPIVLLYNASGTEQSCSQYGLYTQQATVLDRSNLVLGRPGCYP

data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb

@@ -0,0 +1,66 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/pattern/find_EGF2_pattern.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+
+  # =========================================================================== #
+  # === Bioroebe.is_this_sequence_a_EGF2_pattern?
+  #
+  # This method makes use of a "special" syntax, which will be explained
+  # next.
+  #
+  # An 'x' represents any amino acid.
+  #
+  # [ALV] represents any of the 3 amino acids (Ala, Leu, Val).
+  #
+  # A(2,4) - represents 2 to 4 Ala.
+  #
+  # x(2,4) - represents 2 to 4 amino acids (any).
+  #
+  # The pattern for the EGF-like domain signature 2 is:
+  #
+  #   C-x-C-x(2)-[GP]-[FYW]-x(4,8)-C
+  #
+  # This means cystein, any aminoacid, cystein, two any aminoacids,
+  # either G or P, either F or Y o W, then 4 up to 8 any aminoacid,
+  # followed by C.
+  # =========================================================================== #
+  def self.is_this_sequence_a_EGF2_pattern?(
+      this_sequence,
+      use_this_pattern = :default
+    )
+    result = false
+    if this_sequence.is_a? Array
+      this_sequence = this_sequence.first
+      if this_sequence.nil?
+        this_sequence = 'XXCXCXXGFXXXXCXX'
+      end
+    end
+    case use_this_pattern
+    when :default
+      use_this_pattern = 'C-x-C-x(2)-[GP]-[FYW]-x(4,8)-C'
+    end
+    # ======================================================================= #
+    # See this on rubular: https://rubular.com/r/1DSfXLyuCy1QSi
+    # ======================================================================= #
+    use_this_regex =
+      /(C[ACDEFGHIKLMNPQRSTVWY]C[ACDEFGHIKLMNPQRSTVWY]{2}[GP][FYW][ACDEFGHIKLMNPQRSTVWY]{4,8}C)/
+    this_sequence =~ use_this_regex
+    if $1
+      result = true
+    end
+    return result
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  puts Bioroebe.is_this_sequence_a_EGF2_pattern?(ARGV)
+end # EGF2pattern GKCDCPPGFGGDDCAE
+    # EGF2pattern XXCXCXXGFXXXXCXX
+    # EGF2pattern XXCXCXXQFXXXXCXX

data/lib/bioroebe/patterns/profile_pattern.rb

@@ -0,0 +1,182 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ProfilePattern
+#
+# This class can be used to generate specific patterns, based on a 
+# per-position likelihood chance. Every time it is called it should
+# give another (weighted) output as result.
+#
+# Usage example:
+#
+#   Bioroebe::ProfilePattern.new
+#
+# =========================================================================== #
+# require 'profile_pattern.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class ProfilePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::ProfilePattern
+
+  # ========================================================================= #
+  # === PER_POSITION_HASH
+  #
+  # This hash can be used to specify the likelihood per position.
+  # ========================================================================= #
+  PER_POSITION_HASH = {
+    'A': [  61,  16, 352,   3, 354, 268, 360, 222, 155,  56,  83,  82,  82,  68,  77 ],
+    'C': [ 145,  46,   0,  10,   0,   0,   3,   2,  44, 135, 147, 127, 118, 107, 101 ],
+    'G': [ 152,  18,   2,   2,   5,   0,  10,  44, 157, 150, 128, 128, 128, 139, 140 ],
+    'T': [  31, 309,  35, 374,  30, 121,   6, 121,  33,  48,  31,  52,  61,  75,  71 ]
+  }
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    case run_already
+    when :do_not_run_yet
+      run_already = false
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @hash_profiles
+    #
+    # This Hash can be used to specify a particular profile for each
+    # nucleotide position. The default is 25, which  means 25% chance
+    # for each individual nucleotide.
+    # ======================================================================= #
+    @hash_profiles = {
+      A: 25,
+      T: 25,
+      C: 25,
+      G: 25
+    }
+    # ======================================================================= #
+    # === @per_position_hash
+    # ======================================================================= #
+    @per_position_hash = PER_POSITION_HASH
+  end
+
+  # ========================================================================= #
+  # === generate_sequence_based_on_this_profile
+  # ========================================================================= #
+  def generate_sequence_based_on_this_profile(
+      i = @per_position_hash
+    )
+    @string = ''.dup
+    n_times = i.values.first.size
+    n_times.times {|position|
+      # ===================================================================== #
+      # Determine the max values for the four nucleotides next:
+      # ===================================================================== #
+      max_value_for_A = i[:A][position]
+      max_value_for_C = i[:C][position]
+      max_value_for_G = i[:G][position]
+      max_value_for_T = i[:T][position]
+      sum = max_value_for_A+
+            max_value_for_C+
+            max_value_for_G+
+            max_value_for_T
+      match_with_this_number = rand(sum)+1
+      case match_with_this_number
+      when 1..(max_value_for_A)
+        this_nucleotide = 'A'
+      when (max_value_for_A)..(max_value_for_A+max_value_for_C)
+        this_nucleotide = 'C'
+      when (max_value_for_A+max_value_for_C)..(max_value_for_A+max_value_for_C+max_value_for_G)
+        this_nucleotide = 'G'
+      when (max_value_for_A+max_value_for_C+max_value_for_G)..(max_value_for_A+max_value_for_C+max_value_for_G+max_value_for_T)
+        this_nucleotide = 'T'
+      else
+        e tomato('Value of '+match_with_this_number.to_s+' is not registered.')
+      end
+      # GTATAAAAGGC
+      @string << this_nucleotide
+    }
+    display @string
+  end
+
+  # ========================================================================= #
+  # === determine_the_dna_sequence_based_on_the_main_hash_profile
+  # ========================================================================= #
+  def determine_the_dna_sequence_based_on_the_main_hash_profile
+    @string = Bioroebe.generate_random_dna_sequence(30, @hash_profiles)
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = return_commandline_arguments_starting_with_hyphens
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # case tag
+      # ===================================================================== #
+      # === --debug
+      # ===================================================================== #
+      when /^-?-?debug/
+        show_debug_information
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === show_debug_information
+  #
+  # Right now this will only display the profile in use.
+  # ========================================================================= #
+  def show_debug_information
+    erev 'The profile in use is:'; print '  '
+    pp @hash_profiles
+  end
+
+  # ========================================================================= #
+  # === display
+  # ========================================================================= #
+  def display(i = @string)
+    erev i
+  end; alias report display # === report
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    menu
+    determine_the_dna_sequence_based_on_the_main_hash_profile
+    display
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::ProfilePattern[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  _ = Bioroebe::ProfilePattern.new(ARGV, :do_not_run_yet)
+  _.menu
+  _.generate_sequence_based_on_this_profile
+end # profilepattern