Class: Bioroebe::FastaToYaml

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

Overview

Bioroebe::FastaToYaml

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) ⇒ FastaToYaml

#

initialize

#

28
29
30
31
32
33
34
35
36
37
 
# File 'lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb', line 28

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::FastaToYaml[]

#

73
74
75
 
# File 'lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb', line 73

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

Instance Method Details

#reset ⇒ Object

#

reset (reset tag)

#

42
43
44
45
 
# File 'lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb', line 42

def reset
  super()
  infer_the_namespace
end

#run ⇒ Object

#

run (run tag)

#

50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
 
# File 'lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb', line 50

def run
  _ = first?
  if _ and File.exist?(_)
    dataset = Bioroebe.parse_fasta_file(_)
    opne 'Converting the dataset from '+sfile(_)
    opne 'into a standalone .yml file next.'
    hash = {}
    hash[:filename] = _
    hash[:identifier] = File.read(_).split("\n").first.delete('>').lstrip
    hash[:identifier] = return_the_first_line_of_this_file(_).
                        delete('>').delete(':').
                        lstrip
    hash[:sequence] = dataset.sequence?
    what = YAML.dump(hash)
    into = _.delete_suffix(File.extname(_))+'.yml'
    opne 'Storing into the file `'+sfile(into)+rev+'` next.'
    write_what_into(what, into)
  end
end