Class: Bioroebe::FastqFormatExplainer

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

Overview

Bioroebe::FastqFormatExplainer

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, #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(i = nil, run_already = true) ⇒ FastqFormatExplainer

#

initialize

#


38
39
40
41
42
43
44
45
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 38

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

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::FastqFormatExplainer[]

#


123
124
125
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 123

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

Instance Method Details

#parse_input(i = first?) ) ⇒ Object

#

parse_input

#


65
66
67
68
69
70
71
72
73
74
75
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 65

def parse_input(i = first?)
  if i and File.exist?(i)
    dataset = File.read(i)
    splitted = dataset.split("\n")
    @header = splitted[0]
    @sequence = splitted[1]
    @quality_score = splitted[3]
  else
    e "No file exists at #{sfile(i)}."
  end
end

#report_result ⇒ Object Also known as: report

#

report_result (report tag)

#


104
105
106
107
108
109
110
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 104

def report_result
  if @sequence
    report_the_header
    report_the_sequence
    report_the_quality_score
  end
end

#report_the_header ⇒ Object

#

report_the_header

#


96
97
98
99
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 96

def report_the_header
  erev ('Header: ').ljust(@ljust_value)+
       orange(@header)
end

#report_the_quality_score ⇒ Object

#

report_the_quality_score

#


80
81
82
83
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 80

def report_the_quality_score
  erev ('Quality score: ').ljust(@ljust_value)+
       slateblue(@quality_score)
end

#report_the_sequence ⇒ Object

#

report_the_sequence

#


88
89
90
91
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 88

def report_the_sequence
  erev ('Sequence: ').ljust(@ljust_value)+
       lightblue(@sequence+' # '+@sequence.size.to_s+' nucleotides')
end

#reset ⇒ Object

#

reset (reset tag)

#


50
51
52
53
54
55
56
57
58
59
60
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 50

def reset
  super()
  # ======================================================================= #
  # === @sequence
  # ======================================================================= #
  @sequence = nil
  # ======================================================================= #
  # === @ljust_value
  # ======================================================================= #
  @ljust_value = 20
end

#run ⇒ Object

#

run (run tag)

#


115
116
117
118
 
# File 'lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb', line 115

def run
  parse_input
  report_result
end