Class: Bioroebe::ShowFastaStatistics

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

Overview

Bioroebe::ShowFastaStatistics

Constant Summary

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, #opne, #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, #set_be_verbose, #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 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_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?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #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

Constructor Details

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

#

initialize

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 26

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

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::ShowFastaStatistics[]

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 171

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

Instance Method Details

#add_these_entries_to_the_fasta_files(i) ⇒ Object

#

add_these_entries_to_the_fasta_files

This method can be used to append to our Array keeping track of the FASTA files.

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 118

def add_these_entries_to_the_fasta_files(i)
  @array_fasta_files << i
  @array_fasta_files.flatten!
end

#determine_all_local_fasta_files ⇒ Object

#

determine_all_local_fasta_files

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 54

def determine_all_local_fasta_files
  # ======================================================================= #
  # === @array_fasta_files
  #
  # We will populate the Array next. First we will try via .fa files,
  # but if this is empty, we will try via .fasta as well.
  # ======================================================================= #
  @array_fasta_files = Dir['*.fa']
  if @array_fasta_files.empty?
    @array_fasta_files = Dir['*.fasta']
  end
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 70

def menu(
    i = commandline_arguments?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --help
    # ===================================================================== #
    when /help/
      show_help
      exit
    # ===================================================================== #
    # === show_fasta_statistics --start-with
    #
    # This entry point allows us to restrict to only certain .fa 
    # filenames.
    #
    # Usage example on the commandline:
    #
    #   show_fasta_statistics --start-with=ncrna
    #   show_fasta_statistics --fasta-stats=ncrna
    #
    # ===================================================================== #
    when /^-?-?start(_|-)?with=(.+)$/i, # $2
         /^-?-?fasta(-|_)?stats=(.+)$/i
      starts_with = $2.to_s.dup
      @array_fasta_files.select! {|line|
        line.start_with? starts_with
      }
    else
      if File.directory? i
        _ = Dir[rds(i+'/**.fa')]
        _ << Dir[rds(i+'/**.fasta')]
        _.flatten!
        add_these_entries_to_the_fasta_files(_)
      end
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 40

def reset
  super()
  determine_all_local_fasta_files
  # ======================================================================= #
  # === @pad_filename_to
  #
  # This variable keeps track how much we should pad things.
  # ======================================================================= #
  @pad_filename_to = 35 
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 136

def run
  menu
  regex_to_use = /(\d+)/
  sorted = @array_fasta_files.sort_by {|line|
    line =~ regex_to_use
    match = $1.to_s.dup.to_i
    if match == 0
      match = 999 # This is just so that we sort entries such as "foo.MT.fa" last.
    end
    match
  }
  sorted.each_with_index {|this_file, index| index += 1
    show_this_filename = this_file.sub(/\.fa$/,'')
    padded_index = index.to_s.rjust(4)
    # ===================================================================== #
    # Next colourize the index a little bit.
    # ===================================================================== #
    result = lightgreen(padded_index)+' '+
             sfile(
               show_this_filename.ljust(@pad_filename_to) # Pad the name of the file.
             )
    if File.exist? this_file
      n_entries = ' '+File.readlines(this_file).select {|line|
        line.start_with? '>'
      }.size.to_s.rjust(5)
      colourized_n_entries = seagreen("#{n_entries.to_s} different entries")
      result << colourized_n_entries
    end
    e result
  }
end

#show_help ⇒ Object

#

show_help (help tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb', line 126

def show_help
  e
  e '  --start-with= # consider only these file names '\
    'that start with that substring'
  e
end