bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/shell/enzymes.rb

@@ -1,310 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# Enzyme-related components of the BioShell will be stored here.
-# =========================================================================== #
-# require 'bioroebe/shell/enzymes.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  require 'bioroebe/enzymes/has_this_restriction_enzyme.rb'
-  require 'bioroebe/enzymes/restriction_enzymes_file.rb'
-
-  # ========================================================================= #
-  # === return_random_restriction_enzyme
-  #
-  # This method will return a random restriction enzyme, such as:
-  #
-  #   ["EgeI", "GGCGCC 3"]
-  #
-  # ========================================================================= #
-  def return_random_restriction_enzyme(be_verbose = false)
-    splitted = ::Bioroebe.restriction_enzymes.sample
-    _ = splitted[1].split(' ')[0]
-    if be_verbose
-      erev 'Now adding restriction site `'+red(splitted[0])+
-           '` (cuts at '+simp(_)+').'
-    end
-    return _
-  end
-
-  # ========================================================================= #
-  # === find_restriction_enzymes_that_cut_at
-  #
-  # A wrapper over find_restriction_sites().
-  # ========================================================================= #
-  def find_restriction_enzymes_that_cut_at(i)
-    erev 'Trying to find restriction enzymes that '\
-         'cut at `'+sfancy(i)+rev+'`.'
-    result = find_restriction_sites(i)
-    unless result
-      erev 'Found no result for this sequence.'
-    end
-  end
-
-  # ========================================================================= #
-  # === show_restriction_enzymes
-  #
-  # Display the available restriction enzymes here.
-  #
-  # If we pass an argument, then we assume that we wish to show only
-  # these restriction enzymes that cut at n bp.
-  #
-  # Invocation example:
-  #
-  #   show_restriction_enzymes(:show_all)
-  #
-  # ========================================================================= #
-  def show_restriction_enzymes(optional_input = nil)
-    case optional_input
-    when nil, :show_all # This means to show everything.
-      ::Bioroebe.show_restriction_enzymes # Defined in module_methods.rb
-    else # Ok we gave input then.
-      _ = ::Bioroebe.restriction_enzymes
-      _.select! {|entry|
-        last = entry.last
-        last = last.split(' ').last
-        if last == optional_input
-          true
-        else
-          false
-        end
-      }
-      if _.empty?
-        erev 'We found no match for '+optional_input+'.'
-      else # else display the cutters.
-        erev 'These enzymes cut at `'+sfancy(optional_input)+rev+'` nucleotides.'
-        _.each {|entry|
-          entry[0] = entry[0].rjust(15)
-          entry[1] = entry[1].gsub(/ (.+)/, swarn(' \\1')+rev)
-          e "  #{entry.join(' -> ')}"
-        }
-        erev 'These are '+simp(_.size.to_s)+rev+' restriction enzymes.'
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === try_to_find_this_restriction_enzyme
-  #
-  # Use this method to find a specific restriction enzyme.
-  #
-  # The restriction enzymes are stored in this yaml file here:
-  #
-  #   bl $BIOROEBE/yaml/restriction_enzymes/restriction_enzymes.yml
-  #
-  # Usage example:
-  #
-  #   MvnI?
-  #
-  # ========================================================================= #
-  def try_to_find_this_restriction_enzyme(i)
-    i = i.dup if i.frozen?
-    i.delete!('?') # We do not need any '?' characters.
-    original_input = i.dup
-    # i = i.downcase # No longer downcase since as of June 2018.
-    if i.include? 'restriction'
-      i.sub!(/restriction/,'')
-    end
-    if i.include? '.site' # Assume a syntax such as: Restriction.EcoRI.site
-      e ::Bioroebe.restriction_enzyme(i)
-    else # else it will be more verbose
-      i.delete!('.') if i.include? '.'
-      if i.end_with?('1') and !::Bioroebe.has_this_restriction_enzyme?(i) # Is invalid. 
-        erev 'The input `'+simp(i)+rev+'` ends with the number 1. This '\
-             'is not possible, so'
-        erev 'we replace the trailing 1 with a capital I.'
-        i[-1,1] = 'i' # Ok not a capital one, because we store in a downcased variant.
-        original_input[-1,1] = 'I'
-      end
-      if ::Bioroebe.has_this_restriction_enzyme? i
-        target_sequence_data = ::Bioroebe.return_restriction_enzyme_sequence_and_cut_position(i)
-        # =================================================================== #
-        # Tap into the method Bioroebe.restriction_enzyme
-        # =================================================================== #
-        _ = ::Bioroebe.restriction_enzyme(i) # bl $BIOROEBE/module_methods.rb
-        erev "We have found a restriction enzyme called "\
-             "#{sfancy(original_input)}#{rev}."
-        e
-        e "#{rev}The sequence this #{mediumorchid(_.size.to_s+'-cutter')}#{rev}"\
-          " relates to is: `"\
-          "#{sfancy(five_prime+simp(_)+rev)}"\
-          "#{sfancy(three_trailer)}#{rev}`"
-        e
-        # =================================================================== #
-        # The variable target_sequence_data will look like this:
-        #   ["GCCNNNNNGGC", "7", "7"]
-        # =================================================================== #
-        if target_sequence_data.last == :blunt
-          erev "This restriction enzyme will produce a "\
-               "#{seagreen('blunt')}#{rev} overhang."
-          e
-        else
-          erev "This restriction enzyme will produce a "\
-               "#{seagreen('sticky-end')}#{rev} overhang."
-          e
-        end
-        # =================================================================== #
-        # Next, show the exact cut that will be made.
-        # =================================================================== #
-        sequence = ::Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme(i)
-        erev 'It will specifically cut between:     '+
-              sfancy(five_prime)+rev+
-              simp(sequence)+
-              sfancy(three_trailer)+rev
-        # =================================================================== #
-        # And the complementary sequence follows next. The colour used
-        # is swarn().
-        # =================================================================== #
-        complementary_sequence = reverse(
-          Colours.remove_escape_sequences(sequence)
-        )
-        # =================================================================== #
-        # We must insert a | at the right position.
-        # =================================================================== #
-        target_sequence_data = target_sequence_data[1].to_i
-        complementary_sequence[-target_sequence_data,0] = swarn('|')+rev
-        erev ''.ljust(38)+sfancy(leading_three_prime)+rev+
-             complementary_sequence+rev+
-             sfancy(five_prime_trailer)+rev
-      else
-        erev 'We were unable to find a restriction enzyme called '\
-             '`'+sfancy(i)+'`'+rev
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === try_to_find_restriction_enzymes_for
-  #
-  # This method name is a slight misnomer; we can simply find any
-  # target sequence.
-  #
-  # The method can also handle some Symbols as input, such as the symbol
-  # :shine_dalgarno, which will be replaced accordingly to the SD
-  # sequence.
-  # ========================================================================= #
-  def try_to_find_restriction_enzymes_for(
-      i
-    )
-    # ======================================================================= #
-    # === We always have to work with an Array as input
-    # ======================================================================= #
-    unless i.is_a? Array
-      i = [i]
-    end
-    i.map! {|entry|
-      case entry # Use special sequences.
-      when :shine_dalgarno
-        entry = 'AGGAGGT'
-      end
-      # ===================================================================== #
-      # Past this point, we will assume a String as input. But we will have
-      # to make sure, still.
-      # ===================================================================== #
-      entry = entry.to_s unless entry.is_a? String
-      entry.delete!('-') if entry.include? '-'
-      entry
-    }
-    i.each {|entry|
-      report_main_sequence(entry) { :with_ruler }
-      possible_results = dna_string?.scan(/#{entry}/)
-      unless possible_results.empty?
-        e
-        erev "Start nucleotide position is at: "\
-             "#{simp((dna_string?.index(entry)+1))}#{rev}"
-        e
-      end
-    }
-  end; alias find_this_sequence    try_to_find_restriction_enzymes_for # === find_this_sequence
-       alias find_in_main_sequence try_to_find_restriction_enzymes_for # === find_in_main_sequence
-
-  # ========================================================================= #
-  # === restriction_enzyme_digest
-  #
-  # This method allows us to simulate a restriction digest, on a
-  # DNA polymer.
-  #
-  # You can either give the matching DNA nucleotides or you can
-  # use the name of a restriction enzyme instead, such as 'EcoRI'.
-  #
-  # Usage examples:
-  #
-  #   random 750; digest_at TTGC
-  #   random 750; digest_at EcoRI
-  #   random 2000; [33,0] = GAATTC; digest_at EcoRI
-  #
-  # ========================================================================= #
-  def restriction_enzyme_digest(
-      split_at = nil # Default value is nil.
-    )
-    _ = dna_sequence? # Keep a copy of the DNA sequence.
-    # ======================================================================= #
-    # === Grab the first entry if we have an Array
-    # ======================================================================= #
-    split_at = split_at.first if split_at.is_a? Array
-    split_at = 'TTG' if split_at.nil?
-    split_at = split_at.to_s # Work on Strings past this point here.
-    split_at.sub!(/^first_/,'') if split_at.include? 'first_ATG'
-    # ======================================================================= #
-    # === Chop off all '?' in the sequence
-    # ======================================================================= #
-    split_at.delete!('?') if split_at.include? '?'
-    # ======================================================================= #
-    # Next, allow the user to substitute for names of restriction enzymes.
-    # How do we determine that a restriction enzyme was given to this
-    # method? Simple - we first remove all instances of 'A','T','C','G'
-    # in our DNA sequence string. If the string is then still not empty,
-    # we will assume that it is the name of a restriction enzyme.
-    # ======================================================================= #
-    unless (_.delete('ATGC').size > 0)
-      erev 'Assumingly a restriction enzyme was given as input.'
-      target_sequence = ::Bioroebe.restriction_enzyme(split_at)
-      # Must check for nil values still
-      if target_sequence
-        erev "Substituting with `#{simp(target_sequence)}#{rev}` next (for #{split_at})."
-        split_at = target_sequence
-      else
-        erev 'No substitute could be found for `'+sfancy(split_at)+rev+'`.'
-      end
-    end
-    if _.include? split_at
-      splitted = _.split(split_at)
-      e
-      erev 'We will next display all '+simp(splitted.size.to_s)+rev+
-           ' segments that were found (in orange is the part that '\
-           'is cut-out):'
-      e
-      splitted.each_with_index {|sequence, index|
-        index += 1
-        erev lpad?+lead_five_prime+sfancy(sequence)+rev+
-             trail_three_prime+' (size: '+
-             violet(sequence.size.to_s)+rev+')'
-        unless index > (splitted.size-1)
-          erev lpad?+lead_five_prime+orange(split_at)+rev+
-            trail_three_prime+rev
-        end
-      }
-      e
-      erev 'Note that this will NOT be the actual DNA fragments, '\
-           'because the restriction'
-      erev 'enzyme may cut differentially within that orange sequence.'
-    else # The target sequence was not included in this case.
-      erev "No target match for `"\
-           "#{simp(target_sequence)}#{rev}` was "\
-           "found in the given DNA sequence."
-    end
-  end; alias digest restriction_enzyme_digest # === digest
-
-  # ========================================================================= #
-  # === restriction_enzymes_run
-  # ========================================================================= #
-  def restriction_enzymes_run
-    require 'bioroebe/gui/gtk2/restriction_enzymes/restriction_enzymes.rb'
-    ::Bioroebe::GUI::Gtk::RestrictionEnzymes.start_gui_application
-  end
-
-end; end

data/lib/bioroebe/shell/fasta.rb

@@ -1,345 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/fasta.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === handle_fasta
-  #
-  # Use this method to properly handle a fasta file.
-  #
-  # The argument should be the (local) path to a fasta file.
-  # ========================================================================= #
-  def handle_fasta(i)
-    if i.nil?
-      if File.exist? fasta_file?.to_s
-        e sfile(fasta_file?.to_s)
-      else
-        show_my_fasta_file # As a reminder.
-      end
-    else
-      i = i.to_s unless i.is_a? String # Need a String past this point.
-      if File.exist?(i) and i.end_with?('.fasta')
-        opnn; erev 'Trying to parse the file `'+sfile(i)+rev+'` next.'
-        parse_fasta_format(i)
-      else
-        fasta_files = Dir['*.fasta']
-        unless fasta_files.empty?
-          erev 'There seems to be at least one .fasta file in this '\
-               'directory ('+sdir(return_pwd)+').'
-        end
-      end
-    end
-  end; alias assign_fasta           handle_fasta # === assign_fasta
-       alias handle_this_fasta_file handle_fasta # === handle_this_fasta_file
-
-  require 'bioroebe/fasta_and_fastq/parse_fasta/misc.rb'
-  # ========================================================================= #
-  # === parse_fasta_format
-  #
-  # Parse FASTA format here. We will delegate into class
-  # Bioroebe::ParseFasta for that.
-  #
-  # Usage example:
-  #
-  #   pfasta NM_001180897.3_Saccharomyces_cerevisiae_S288c_Aga2p_AGA2.fasta
-  #
-  # ========================================================================= #
-  def parse_fasta_format(
-      i = nil
-    )
-    if i.is_a? Array
-      i.each {|entry|
-        parse_fasta_format(entry)
-      }
-    else
-      # ===================================================================== #
-      # === If input is only numbers.
-      # ===================================================================== #
-      i = Dir['*'][i.to_i + 1] if i =~ /^\d+$/ # <- Only numbers.
-      case i
-      # ===================================================================== #
-      # === ASSIGN
-      #
-      # This entry point can be used by the user to input ad-hoc data
-      # for a FASTA sequence.
-      # ===================================================================== #
-      when /^ASSIGN$/i
-        opnn; erev 'Input your FASTA Data now (Use __ to terminate input):'
-        i = $stdin.gets('__').chomp
-      end
-      # ===================================================================== #
-      # If we did not provide an input, we scan for entries with .fa
-      # in the current directory.
-      # ===================================================================== #
-      if i.nil?
-        unless Dir['*.fa'].empty?
-          i = Dir['*.fa']
-        end
-      end
-      if i.is_a? Array
-        i = i.first
-      end
-      if i
-        erev "Now loading from `#{sfancy(i)}#{rev}`."
-      end
-      @internal_hash[:fasta_file] = i
-      parse_fasta_object = ::Bioroebe.parse_fasta(i) # bl $RSRC/bioroebe/lib/bioroebe/fasta/parse_fasta.rb
-      # ===================================================================== #
-      # === We will store all created fasta objects in an Array
-      # ===================================================================== #
-      array_fasta? << parse_fasta_object
-      this_sequence = parse_fasta_object.sequence?
-      # ===================================================================== #
-      # Handle large sequences next - we will add a timer. The purpose of
-      # this timer is to notify the user how long it took to assign to
-      # the main string. At a later point, we can optimize the speed and
-      # do the assignment in pure C rather than ruby.
-      # ===================================================================== #
-      if this_sequence.size > 1_000_000
-        add_timer_snapshot
-        erev 'The sequence is fairly large - we will time how long it takes to'
-        erev 'assign it to the main sequence.'
-      end
-      # ===================================================================== #
-      # Obtain the type next:
-      # ===================================================================== #
-      type = parse_fasta_object.type?
-      unless type == :protein
-        set_dna_sequence(this_sequence)
-        if this_sequence.size > 1_000_000
-          add_timer_snapshot
-          n_seconds_difference = calculate_time_difference.abs.to_f.round(3).to_s
-          erev "Loading these #{springgreen(this_sequence.size.to_s)}"\
-               "#{rev}"\
-               " nucleotides "\
-               "took #{sfancy(n_seconds_difference)}#{rev} seconds."
-        end
-      end
-    end
-  end; alias parse_this_fasta_file parse_fasta_format # === parse_this_fasta_file
-
-  require 'bioroebe/toplevel_methods/delimiter.rb'
-  # ========================================================================= #
-  # === obtain_multiline_fasta
-  #
-  # If we want to obtain multiline FASTA input, that is input that includes
-  # the "\n" newline character, then we can use the following method here.
-  #
-  # We will use $stdin to obtain the input. The end-delimiter will
-  # be ___
-  # ========================================================================= #
-  def obtain_multiline_fasta
-    delimiter = ::Bioroebe.delimiter?
-    erev 'Input your Fasta format or nucleotide sequence next - '\
-         'delimit/end via "'+lightgreen(delimiter)+rev+'" (3x the _ '\
-         'character).'
-    # ======================================================================= #
-    # Chop away all newlines.
-    # ======================================================================= #
-    dataset = $stdin.gets(delimiter)
-    # ======================================================================= #
-    # Format the dataset a little.
-    # ======================================================================= #
-    dataset.chomp!
-    dataset.delete!('_')
-    dataset.delete!(N)
-    dataset.strip!
-    parse_fasta_format(dataset)
-    # assign_sequence(dataset)
-  end
-
-  # ========================================================================= #
-  # === array_fasta?
-  # ========================================================================= #
-  def array_fasta?
-    @internal_hash[:array_fasta]
-  end
-
-  require 'bioroebe/toplevel_methods/fasta_and_fastq.rb'
-  # ========================================================================= #
-  # === index_this_fasta_file
-  #
-  # This will index FASTA files (.fa or .fasta) via the samtools.
-  # ========================================================================= #
-  def index_this_fasta_file(i)
-    # ======================================================================= #
-    # === Handle blocks first
-    # ======================================================================= #
-    if block_given?
-      yielded = yield
-      case yielded
-      when :use_all_fasta_files_if_no_argument_was_given
-        if i.nil? or i.empty?
-          i = Dir['*.fasta']+
-              Dir['*.fa'].flatten.compact
-        end
-      end
-    end
-    if i.is_a? Array
-      i.each {|entry| index_this_fasta_file(entry) }
-    else
-      i = i.to_s # Need to work on a String past this point.
-      if File.exist? i
-        erev "Indexing the following file next, via "\
-             "#{steelblue('samtools')}#{rev}:"
-        Bioroebe.index_this_fasta_file(i)
-      else
-        no_file_exists_at(i)
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === try_to_display_this_fasta_entry
-  # ========================================================================= #
-  def try_to_display_this_fasta_entry(i)
-    if i.is_a? String
-      i = i.to_i - 1 # -1 because Arrays in ruby begin at 0.
-    end
-    last_entry = array_fasta?.last
-    sequence_data = last_entry[i]
-    erev sequence_data
-    if block_given?
-      yielded = yield
-      case yielded
-      # ===================================================================== #
-      # === :and_assign_it_as_well
-      # ===================================================================== #
-      when :and_assign_it_as_well
-        assign(sequence_data) # In this case it will become the new main sequence data.
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === parse_this_fasta_sequence
-  # ========================================================================= #
-  def parse_this_fasta_sequence(i)
-    if i and File.file?(i)
-      set_aminoacid(File.read(i).delete("\n"))
-    end
-  end
-
-  # ========================================================================= #
-  # === fasta?
-  #
-  # We need a query method over the main fasta object, IF it was set.
-  #
-  # Since we already have an Array that keeps track of these objects,
-  # we can simply grab the last one from that collection.
-  # ========================================================================= #
-  def fasta?
-    array_fasta?.last
-  end; alias last_fasta?       fasta? # === fasta?
-       alias last_fasta_entry? fasta? # === last_fasta_entry?
-
-  # ========================================================================= #
-  # === colourize_fasta_file
-  #
-  # Invocation example:
-  #
-  #   colourize_fasta_file /Depot/Temp/bioroebe/sequence.fasta
-  #
-  # ========================================================================= #
-  def colourize_fasta_file(i)
-    if i.is_a? Array
-      i.each {|entry| colourize_fasta_file(entry) }
-    else
-      # ===================================================================== #
-      # First, get the raw content of the fasta sequence here.
-      # ===================================================================== #
-      if File.exist? i
-        sequence = ::Bioroebe.parse_fasta_file(i).sequence?
-        # =================================================================== #
-        # Now that we have the sequence, colourize it.
-        # =================================================================== #
-        cliner {
-          ColourSchemeDemo.new(sequence)
-        }
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === to_fasta
-  #
-  # Create a Fasta format from the target sequence.
-  # ========================================================================= #
-  def to_fasta(
-      i = dna_sequence?
-    )
-    array = i.scan(/.{,80}/).reject {|entry| entry.empty? }
-    name_of_the_gene = sequence_object?.name_of_gene?.to_s
-    if name_of_the_gene.empty?
-      name_of_the_gene << 'Drosophila melanogaster chromosome'
-    end
-    array[0,0] = '>gi|671162122:c7086083-7083225 '+name_of_the_gene
-    e array.join(N)
-  end
-
-  # ========================================================================= #
-  # === fasta_file?
-  # ========================================================================= #
-  def fasta_file?(i = :fasta_file)
-    if @internal_hash[:fasta_file].has_key?(i)
-      @internal_hash[:fasta_file].fetch(i)
-    else
-      erev 'We could not find the key called `'+simp(i.to_s)+rev+'`.'
-    end
-  end
-
-  # ========================================================================= #
-  # === create_fasta_file
-  # ========================================================================= #
-  def create_fasta_file
-    set_save_file :default_fasta
-    e 'Now creating a new fasta file. Will store into `'+sfile(@save_file)+'`.'
-    _ = '>gi|12345|pir|TVHGG| some unknown protein'+N
-    _ << string?
-    save_file(_, @internal_hash[:save_file])
-  end
-
-  # ========================================================================= #
-  # === return_fasta_files_in_the_log_directory
-  # ========================================================================= #
-  def return_fasta_files_in_the_log_directory
-    Dir[::Bioroebe.log_dir?+'*.fa*']
-  end
-
-  # ========================================================================= #
-  # === use_this_fasta_file
-  #
-  # Use a fasta file based on its position.
-  #
-  # For instance, fasta file at position 2 will be the second fasta file
-  # kept in the main log directory.
-  # ========================================================================= #
-  def use_this_fasta_file(at_position = 1)
-    # ======================================================================= #
-    # We need to map the given position to the existing (local) file at hand.
-    # ======================================================================= #
-    this_fasta_file = return_fasta_files_in_the_log_directory[at_position.to_i - 1]
-    if this_fasta_file
-      assign_fasta(this_fasta_file)
-    else
-      erev 'Could not find any file at position '+simp(at_position.to_s)+rev+'.'
-      erev 'Use "'+steelblue('show_fasta_files')+rev+
-           '" to see which fasta files are available.'
-    end
-  end
-
-  # ========================================================================= #
-  # === show_my_fasta_file
-  # ========================================================================= # 
-  def show_my_fasta_file
-    e HOME_DIRECTORY_OF_USER_X+
-      'data/science/BIOINFORMATIK/DATA/FASTA/tardigrada_fasta.ffn'
-  end
-
-end; end