Class: Bioroebe::AlignOpenReadingFrames

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/align_open_reading_frames.rb

Overview

Bioroebe::AlignOpenReadingFrames

Constant Summary collapse

START_CODON =
#

START_CODON

#
::Bioroebe.start_codon?
SHOW_N_NUCLEOTIDES =
#

SHOW_N_NUCLEOTIDES

#
true

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, #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(i = nil, run_already = true) ⇒ AlignOpenReadingFrames

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 52

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::AlignOpenReadingFrames[]

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 175

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

Instance Method Details

#analyze_main_sequence ⇒ Object

#

analyze_main_sequence

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 134

def analyze_main_sequence
  array = ::Bioroebe.scan_this_input_for_startcodons(input?, return_regex_with_startcodons)
  if array.empty?
    report_that_no_ORF_has_been_found
  else
    # ===================================================================== #
    # Now we have the array. We can report the sequences. We only use the
    # first dataset though for now.
    # ===================================================================== #
    report_aligned_sequences_using_this_array(
      array.map {|inner_array| inner_array.first }
    )
  end
end

#determine_n_nucleotides_in(i) ⇒ Object

#

determine_n_nucleotides_in

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 125

def determine_n_nucleotides_in(i)
  result = "(#{i.size.to_s} nucleotides)"
  result = slategrey(result) if use_colours?
  return result
end

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 81

def input?
  @input
end

#report_aligned_sequences_using_this_array(array) ⇒ Object

#

report_aligned_sequences_using_this_array

This method will report all sequences in an aligned manner.

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 97

def report_aligned_sequences_using_this_array(array)
  _ = input? # Grab the input-sequence here.
  e
  array.each_with_index {|start_position, index|
    index += 1
    sequence = _[(start_position - 1) .. -1]
    if use_colours?
      sequence.gsub!(/#{start_codon?}/,
        ::Colours.orange(start_codon?)+rev)
    end
    this_orf = 'ORF #'+index.to_s
    if this_orf.include? 'ORF #1'
      this_orf << "#{rev} (#{steelblue('longest ORF')})"
    end
    e simp(this_orf).rjust(5)+rev
    e
    result = "  #{sequence}".dup
    if SHOW_N_NUCLEOTIDES
      result << "  #{determine_n_nucleotides_in(sequence)}"
    end
    e result
    e
  }
end

#report_that_no_ORF_has_been_found ⇒ Object

#

report_that_no_ORF_has_been_found

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 152

def report_that_no_ORF_has_been_found
  this_length = input?.size
  opnerev "No valid stop-codon has been found for the given input"
  opnerev "sequence of length #{sfancy(this_length.to_s)}."
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 64

def reset
  super()
  infer_the_namespace
end

#return_regex_with_startcodons ⇒ Object

#

return_regex_with_startcodons

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 161

def return_regex_with_startcodons
  ::Bioroebe.regex_with_startcodons(start_codon?)
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 168

def run
  analyze_main_sequence
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 72

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.to_s.dup
  @input = i
end

#start_codon? ⇒ Boolean

#

start_codon?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/align_open_reading_frames.rb', line 88

def start_codon?
  START_CODON
end