Class: Bioroebe::ElectronMicroscopy::FixPosFile

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

Overview

Bioroebe::ElectronMicroscopy::FixPosFile

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

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(fix_this_pos_file = nil, run_already = true) ⇒ FixPosFile

#

initialize

#


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# File 'lib/bioroebe/electron_microscopy/fix_pos_file.rb', line 24

def initialize(
    fix_this_pos_file = nil,
    run_already       = true
  )
  reset
  set_fix_this_pos_file(
    fix_this_pos_file
  )
  run if run_already
end

Instance Method Details

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/electron_microscopy/fix_pos_file.rb', line 38

def reset
  super()
  set_fix_this_pos_file
  infer_the_namespace
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/electron_microscopy/fix_pos_file.rb', line 54

def run
  if File.exist? @fix_this_pos_file
    dataset = File.read(@fix_this_pos_file)
    unless dataset.include? '_pickingMicrographState' # In this case we assume it to be incorrect.
      parse_coordinates = ParseCoordinates.new(@fix_this_pos_file)
      _ = '# XMIPP_STAR_1 *
#
data_header
loop_
 _pickingMicrographState
 _autopickPercent
 _cost
Manual         50     0.000000
data_particles
loop_
 _xcoor
 _ycoor'+N
      coordinates = parse_coordinates.coordinates?
      # If we wish to sort this dataset, we can do, but this did lead
      # to an error:
      # coordinates.sort_by! {|x_axis, y_axis|
      #   x_axis.to_i 
      # }
      coordinates.each {|x_axis, y_axis|
        _ << '    '+x_axis.to_s.rjust(6)+'     '+y_axis.to_s.rjust(6)+N
      }
    end
    new_file = File.dirname(@fix_this_pos_file)+
              '/fixed_coordinates_'+File.basename(@fix_this_pos_file)
    opnerev 'Now storing new dataset into '+sfile(new_file)+'.'
    write_what_into(_, new_file)
  else
    opnn; no_file_exists_at(@fix_this_pos_file)
  end
end

#set_fix_this_pos_file(i = nil) ⇒ Object

#

set_fix_this_pos_file

#


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# File 'lib/bioroebe/electron_microscopy/fix_pos_file.rb', line 47

def set_fix_this_pos_file(i = nil)
  @fix_this_pos_file = i
end