Class: Bioroebe::ElectronMicroscopy::CoordinateAnalyzer

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/electron_microscopy/coordinate_analyzer.rb

Overview

Bioroebe::ElectronMicroscopy::CoordinateAnalyzer

Constant Summary collapse

STORE_HERE =
#

STORE_HERE

#
"#{::Bioroebe.log_dir?}total_amount_of_particles"

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

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(run_already = true) ⇒ CoordinateAnalyzer

#

initialize

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 30

def initialize(
    run_already = true
  )
  reset
  run if run_already
end

Instance Method Details

#add(i) ⇒ Object

#

add

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 72

def add(i)
  if i.is_a? Array
    i.each {|entry| add(entry) }
  else
    if File.exist? i
      @dataset << i
    end
  end
end

#analyze_dataset ⇒ Object

#

analyze_dataset

Use this method to analyze the dataset finally.

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 87

def analyze_dataset
  if @dataset.empty?
    erev 'Can not analyze anything as the dataset (from '+
         simp(base?)+rev+') is empty.'
  else
    erev 'Analyzing the dataset.'
    @dataset.sort.each_with_index {|entry, index|
      index += 1
      index = '%02d' % index
      data = File.readlines(entry)
      data = data.select {|inner_entry| inner_entry.include? '    ' }
      n_lines = data.size
      entry = '%-41s' % entry
      erev '  '+sfile(entry)+rev+' has '+simp(n_lines.to_s)+rev+' particles.'
      # Next, we store this directly into the file.
      append_what_into('Image '+index+': '+n_lines.to_s+N, store_where?)
      @n_total_particles += n_lines
    }
  end
end

#base? ⇒ Boolean

#

base?

Which internal base directory to use.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 65

def base?
  "#{log_dir?}image*"
end

#generate_a_report ⇒ Object

#

generate_a_report

This method will generate a report status.

It will generate the file total_amount_of_particles.

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 126

def generate_a_report
  erev "Now generating a report into `#{sfile(store_where?)}#{rev}`."
  append_what_into(
    N+N+'Total: '+@n_total_particles.to_s+N,
    store_where?
  )
end

#get_all_image_directories ⇒ Object

#

get_all_image_directories

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 56

def get_all_image_directories
  @directories = Dir[base?]
end

#obtain_all_pos_files ⇒ Object

#

obtain_all_pos_files

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 163

def obtain_all_pos_files
  @directories.each {|directory|
    location = Dir[directory+'/*.pos'].reject {|entry| entry.include? 'fixed_coordinates' }.
                                       reject {|entry| entry.include? 'from' }
    add(location)
  }
end

#remove_old_log_file(this_file = store_where?) ) ⇒ Object

#

remove_old_file

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 147

def remove_old_log_file(this_file = store_where?)
  if File.exist? this_file
    remove_file(this_file)
  end
end

#report_how_many_particles_we_have_found ⇒ Object

#

report_how_many_particles_we_have_found

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 111

def report_how_many_particles_we_have_found
  n_images = @dataset.size
  unless @dataset.empty?
    opnerev 'We have found '+simp(@n_total_particles)+' particles in '+
            'a total of '+bold_blue(n_images.to_s)+' images.'
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 40

def reset
  super()
  infer_the_namespace
  # ========================================================================= #
  # === @dataset
  # ========================================================================= #
  @dataset = []
  # ========================================================================= #
  # === @n_total_particles
  # ========================================================================= #
  @n_total_particles = 0
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 174

def run
  startup_message
  remove_old_log_file
  get_all_image_directories
  obtain_all_pos_files # After this step we have all .pos files.
  analyze_dataset
  report_how_many_particles_we_have_found
  generate_a_report
end

#startup_message ⇒ Object

#

startup_message

#


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 137

def startup_message
  opnn { :no_trailing }
  e
  e
  erev 'Attempting to analyze the coordinates next.'
end

#store_where? ⇒ Boolean

#

store_where?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/coordinate_analyzer.rb', line 156

def store_where?
  STORE_HERE
end