Class: Bioroebe::RestrictionEnzyme

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/enzymes/restriction_enzyme.rb

Overview

Bioroebe::RestrictionEnzyme

Constant Summary collapse

HASH_ALL_RESTRICTION_ENYMES =
#

HASH_ALL_RESTRICTION_ENYMES

#
Bioroebe.restriction_enzymes(:hash)

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(commandline_arguments = nil, run_already = true) ⇒ RestrictionEnzyme

#

initialize

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 46

def initialize(
    commandline_arguments = nil,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::RestrictionEnzyme[]

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 155

def self.[](i = ARGV)
  new(i)
end

Instance Method Details

#can_cut_this_sequence?(i) ⇒ Boolean

#

can_cut_this_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 115

def can_cut_this_sequence?(i)
  i.include? @cuts_at
end

#cuts_at? ⇒ Boolean Also known as: recognizes_which_sequence?

#

cuts_at?

This method will return at which sequence to cut.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 88

def cuts_at?
  @cuts_at
end

#do_cut_the_sequence(this_sequence = 'GGGGATTCATGCCAAGGGGAATTCGATTCATGCCAAAAAAAAATGAATTCTTTTTAAAAAACCCCCGGGGGGTTT') ⇒ Object Also known as: cut_the_sequence

#

do_cut_the_sequence

This method can take a sequence and cut it. Note that the individual fragments return are not the final digestion - we still have to find out where the restriction enzyme really cuts.

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 135

def do_cut_the_sequence(
    this_sequence = 'GGGGATTCATGCCAAGGGGAATTCGATTCATGCCAAAAAAAAATGAATTCTTTTTAAAAAACCCCCGGGGGGTTT'
  )
  if can_cut_this_sequence?(this_sequence)
    splitted = this_sequence.split(/#{@cuts_at}/)
    return splitted
  else
    [this_sequence]
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 60

def reset
  super()
  # ======================================================================= #
  # === @type
  # ======================================================================= #
  @type = nil
  # ======================================================================= #
  # === @cuts_at
  #
  # Denote where the restriction enzyme will cut at.
  # ======================================================================= #
  @cuts_at = ''
end

#return_original_sequence ⇒ Object

#

return_original_sequence

This method will return the original sequence as-is.

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 124

def return_original_sequence
  HASH_ALL_RESTRICTION_ENYMES[@name_of_the_restriction_enzyme]
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 149

def run
end

#set_cuts_at(i = @dataset.first) ⇒ Object

#

set_cuts_at

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 77

def set_cuts_at(
    i = @dataset.first
  )
  @cuts_at = i
end

#set_name_of_the_restriction_enzyme(i) ⇒ Object

#

set_name_of_the_restriction_enzyme

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 95

def set_name_of_the_restriction_enzyme(i)
  @name_of_the_restriction_enzyme = i.to_s
end

#use_this_restriction_enzyme=(i = :EcoRI) ⇒ Object

#

use_this_restriction_enzyme=

#


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# File 'lib/bioroebe/enzymes/restriction_enzyme.rb', line 102

def use_this_restriction_enzyme=(i = :EcoRI)
  set_name_of_the_restriction_enzyme(i)
  @dataset = HASH_ALL_RESTRICTION_ENYMES[i.to_s]
  if @dataset.include? ' '
    set_cuts_at(@dataset.split(' ').first)
  else
    set_cuts_at(@dataset.first)
  end
end