Class: Bioroebe::ParseFastq
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::ParseFastq
- Defined in:
- lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb
Overview
Bioroebe::ParseFastq
Constant Summary
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Class Method Summary collapse
-
.[](i = '') ⇒ Object
# === Bioroebe::ParseFastq[] ========================================================================= #.
Instance Method Summary collapse
-
#check_whether_the_fastq_format_is_valid(i) ⇒ Object
# === check_whether_the_fastq_format_is_valid.
-
#initialize(commandline_arguments = nil, run_already = true) ⇒ ParseFastq
constructor
# === initialize ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
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) ⇒ ParseFastq
#
initialize
#
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# File 'lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb', line 25 def initialize( commandline_arguments = nil, run_already = true ) reset set_commandline_arguments( commandline_arguments ) run if run_already end |
Class Method Details
.[](i = '') ⇒ Object
#
Bioroebe::ParseFastq[]
#
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# File 'lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb', line 75 def self.[](i = '') new(i) end |
Instance Method Details
#check_whether_the_fastq_format_is_valid(i) ⇒ Object
#
check_whether_the_fastq_format_is_valid
This method will try to determine whether the FASTQ format at hand is valid or whether it is not.
#
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# File 'lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb', line 49 def check_whether_the_fastq_format_is_valid(i) unless i =~ /^\@(\S*)\s?(.*)$/ raise InvalidFastqFormat, "Invalid FASTQ format: a '@' must be at the beginning of the line" end end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb', line 39 def reset super() end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb', line 59 def run _ = first_argument? if File.exist? _ dataset = File.read(_) check_whether_the_fastq_format_is_valid(dataset) e 'DEBUG' pp dataset e 'The .fastq file is valid.' else e 'No file could be found at '+sfile(_.to_s)+'.' end end |