Class: Bioroebe::CreateBatchEntrezFile

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/create_batch_entrez_file.rb

Overview

Bioroebe::CreateBatchEntrezFile

Constant Summary collapse

DEFAULT_INPUT =
#

DEFAULT_INPUT

You can use this as test-input, to test the behaviour of the class.

The URL should be to e. g. a NZ file.

#
'
https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP011602.1

https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP011636.1

https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP014070.1

https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP007215.2

https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
'

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

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(i = DEFAULT_INPUT, run_already = true) ⇒ CreateBatchEntrezFile

#

initialize

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 50

def initialize(
    i           = DEFAULT_INPUT,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::CreateBatchEntrezFile[]

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 114

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

Instance Method Details

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 89

def input?
  @input
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 62

def reset
  super()
  infer_the_namespace
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 107

def run
  store_input_into_a_file
end

#sanitize_input ⇒ Object

#

sanitize_input

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 81

def sanitize_input
  @input.reject! {|line| line.strip.empty? }
  @input.map! {|line| File.basename(line) }
end

#set_input(i = DEFAULT_INPUT) ⇒ Object

#

set_input

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 70

def set_input(i = DEFAULT_INPUT)
  i = i.first if i.is_a? Array
  i = DEFAULT_INPUT if i.nil?
  i = i.to_s.dup.split(N)
  @input = i
  sanitize_input
end

#store_input_into_a_file ⇒ Object

#

store_input_into_a_file

#

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# File 'lib/bioroebe/utility_scripts/create_batch_entrez_file.rb', line 96

def store_input_into_a_file
  this_file = 'input_files.fasta'
  opnn; e "Now storing into `#{sfile(this_file)}`."
  what = @input.join(N)
  into = this_file
  write_what_into(what, into)
end