Class: Bioroebe::CompactFastaFile

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb

Overview

Bioroebe::CompactFastaFile

Constant Summary collapse

SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE =
#

SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE

#
true

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

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(i = ARGV, run_already = true, &block) ⇒ CompactFastaFile

#

initialize

#


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 31

def initialize(
    i           = ARGV,
    run_already = true,
    &block
  )
  reset
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # First handle Symbols.
    # ===================================================================== #
    case yielded
    # ===================================================================== #
    # === :be_verbose
    # ===================================================================== #
    when :be_verbose,
         :verbose
      set_be_verbose_and_report_the_sequence
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet,
         :be_silent
      be_quiet
    end
  end
  set_commandline_arguments(i)
  case run_already
  # ======================================================================= #
  # === :dont_run_yet
  # ======================================================================= #
  when :dont_run_yet
    run_already = false
  end
  run if run_already
end

Instance Method Details

#do_upcase_the_sequence ⇒ Object

#

do_upcase_the_sequence

#


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 91

def do_upcase_the_sequence
  @user_configuration[:do_upcase_the_sequence] = true
end

#do_upcase_the_sequence? ⇒ Boolean Also known as: shall_we_upcase_the_sequence?

#

do_upcase_the_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 98

def do_upcase_the_sequence?
  @user_configuration[:do_upcase_the_sequence]
end

#menu(i = commandline_arguments_starting_with_leading_hyphens? ) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 105

def menu(
    i = commandline_arguments_starting_with_leading_hyphens?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === compactfile --upcase small_proline_rich_protein_4.fasta
    # ===================================================================== #
    when /^-?-?upcase$/i
      do_upcase_the_sequence
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 74

def reset
  infer_the_namespace
  # ======================================================================= #
  # === @user_configuration
  # ======================================================================= #
  @user_configuration = {}
  # ======================================================================= #
  # === :do_upcase_the_sequence
  # ======================================================================= #
  @user_configuration[:do_upcase_the_sequence] =
    SHALL_WE_UPCASE_THE_SEQUENCE_IN_THE_NEWLY_GENERATED_FILE
  enable_colours
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb', line 124

def run
  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
  this_file = first_non_hyphened_argument?.to_s
  menu(
    commandline_arguments_starting_with_leading_hyphens?
  )
  _ = Bioroebe::ParseFasta.new(this_file) { :be_quiet }
  what = '> '+_.header?+"\n".dup
  if shall_we_upcase_the_sequence?
    what << _.body?.upcase.delete(' ')
  else
    what << _.body?.delete(' ')
  end
  into = this_file
  opne 'Storing into the file:'
  e
  e "  #{sfile(into)}"
  e
  write_what_into(what, into)
end