Class: Bioroebe::ElectronMicroscopy::GenerateEm2emFile

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/electron_microscopy/generate_em2em_file.rb

Overview

Bioroebe::ElectronMicroscopy::GenerateEm2emFile

Constant Summary collapse

NAME_OF_NEW_FILE =
#

NAME_OF_NEW_FILE

#
'_em2em.dff'

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(name_of_input_tif_file = '1_36kx_02.tif', run_already = true) ⇒ GenerateEm2emFile

#

initialize

We require a .tif as input file.

To invoke this class, do:

gen2 1_36kx_01.tif
gen2 1_36kx_02.tif
gen2 1_36kx_03.tif
#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 36

def initialize(
    name_of_input_tif_file = '1_36kx_02.tif',
    run_already            = true
  )
  reset
  set_tif_file(
    name_of_input_tif_file
  )
  run if run_already
end

Instance Method Details

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 50

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @name_of_new_file
  # ======================================================================= #
  @name_of_new_file = NAME_OF_NEW_FILE
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 104

def run
  setup_dataset
  opnerev "Next generating file `#{sfile(@name_of_new_file)}`."
  save_dataset
end

#save_dataset ⇒ Object

#

save_dataset

#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 73

def save_dataset
  write_what_into(@_, @name_of_new_file)
end

#set_tif_file(i) ⇒ Object

#

set_tif_file

#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 62

def set_tif_file(i)
  if i.is_a? Array
    i = i.first
  end
  i = i.to_s
  @tif_file = i
end

#setup_dataset ⇒ Object

#

setup_dataset

Fill up the ivar @_.

#


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# File 'lib/bioroebe/electron_microscopy/generate_em2em_file.rb', line 82

def setup_dataset
  @_ = 
'INP_2D_OR_3D:  2D
FORMAT_INP:  TIFF
FORMAT_OUT:  MRC
IMPORT_2D_NO_EXTENSION:
OUTPUT_2D_INPUT_TYPE:  STACK_OF_IMAGES
OUTPUT_2D_SET_ROOTNAME:
ASK_SCALE_DENS:  YES
KEEP_TYPE:  RETAIN_TYPE
SINGLE_LOC_EXP_2D:  SINGLE_IMAGE_FILE
IMPORT_A_2D_SET:  NO
IMPORT_ONE_2D_WITH_EXT_TIFF:  '+@tif_file+'
OUTPUT_SINGLE_2D_WITH_EXTENSION:  '+
@tif_file.gsub(/#{File.extname(@tif_file)}/,'')+'.mrc
REVERSE_WANTED:  YES
NAME_OPTION_SINGLE:  NAME_OF_IMPORT_FILE'
end