Class: Bioroebe::ParseFasta

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

Overview

Bioroebe::ParseFasta

Constant Summary collapse

REGEX_NON_NUCLEOTIDES =
#

REGEX_NON_NUCLEOTIDES

All non-nucleotides will be handled here via this regex.

N is excluded because it may stand for “any” nucleotide too, at the least for a purine.

#
/BDEFHIJKLMOPQRSVWXYZ/
DEFAULT_FASTA =
#

DEFAULT_FASTA

This String can be used to quickly test code depending on FASTA entries.

#
'>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT'
DEFAULT_ROUND_TO =
#

DEFAULT_ROUND_TO

#
2

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, #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, #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_FASTA, run_already = true, &block) ⇒ ParseFasta

#

initialize

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 66

def initialize(
    i           = DEFAULT_FASTA,
    run_already = true,
    &block
  )
  reset
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # First handle Symbols.
    # ===================================================================== #
    case yielded
    # ===================================================================== #
    # === :be_verbose
    # ===================================================================== #
    when :be_verbose,
         :verbose
      set_be_verbose_and_report_the_sequence
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet,
         :be_silent
      be_quiet
    # ===================================================================== #
    # === :sizeseq
    # ===================================================================== #
    when :sizeseq
      @sort_by_size = true
    end
    # ===================================================================== #
    # === Handle Hashes next
    # ===================================================================== #
    if yielded.is_a? Hash
      # =================================================================== #
      # === :be_verbose
      # =================================================================== #
      if yielded.has_key? :be_verbose
        set_be_verbose(yielded.delete(:be_verbose))
        @internal_hash[:report_the_sequence] = true
      end
      # =================================================================== #
      # === :use_colours
      # =================================================================== #
      if yielded.has_key? :use_colours
        set_use_colours(
          yielded.delete(:use_colours)
        )
      end
      # =================================================================== #
      # === :sizeseq
      # =================================================================== #
      if yielded.has_key? :sizeseq
        @sort_by_size = true
      end
    end
  end
  set_commandline_arguments(i)
  case run_already
  # ======================================================================= #
  # === :dont_run_yet
  # ======================================================================= #
  when :dont_run_yet,
       :do_not_run_yet
    run_already = false
  end
  run if run_already
end

Class Method Details

.[](i) ⇒ Object

#

Bioroebe::ParseFasta[]

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1222

def self.[](i)
  _ = new(i)
  _.sequences?
end

Instance Method Details

#[](i) ⇒ Object

#

[]

This is a simpler query-interface for obtaining the DNA/RNA sequence of the FASTA file (or aminoacid sequence, if we have a protein at hand here).

Using the method sequences? here, which in turn works on @hash, is ok because Hashes are kept in a sorted manner in ruby since some time.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1215

def [](i)
  sequences?[i]
end

#add_length_information_to_the_header ⇒ Object

#

add_length_information_to_the_header

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1099

def add_length_information_to_the_header
  _ = header?.strip
  _ << ' length='+sequence_size?.to_s+';'
  # ======================================================================= #
  # Next, designate where to store this file.
  # ======================================================================= #
  into = 'new_fasta_file.fasta'
  if overwrite_the_original_file?
    into = @input_file
  end
  what = ''.dup
  what << "> "+_+"\n"
  what << raw_body?
  if what and into
    erev 'Storing into `'+sfile(into)+rev+'`.'
    write_what_into(what, into)
  end
end

#calculate_gc_content ⇒ Object

#

calculate_gc_content

Calculate the gc content through this method, which is called from within the method run().

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 722

def calculate_gc_content
  _ = @hash.values.join.delete(N)
  if is_polynucleotide? _
    @hash.each_pair {|key, content|
      # =================================================================== #
      # Delegate towards the method Bioroebe.gc_content next, including
      # to round towards 5 positions:
      # =================================================================== #
      gc_content = ::Bioroebe.gc_content(content.upcase, round_to?)
      gc_content = gc_content.first if gc_content.is_a? Array
      gc_content = gc_content.to_s
      minimal_key = key.to_s
      if minimal_key.include? '|'
        minimal_key = minimal_key.split('|').last.strip
      end
      if be_verbose?
        _ = minimal_key.strip
        if _.size > 40 # Shorten the content a bit if it is too long.
          _ = _[0 .. 40]+' [...]'
        end
        erev 'GC content of "'+simp(_)+rev+'" is: '+
             "#{sfancy(gc_content)}#{rev} %"
      end
    }
  else
    erev '`'+simp(_)+rev+'` is not a polynucleotide.' if be_verbose?
  end
end

#condense_the_sequence_onto_a_single_line? ⇒ Boolean

#

condense_the_sequence_onto_a_single_line?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 888

def condense_the_sequence_onto_a_single_line?
  @internal_hash[:condense_the_sequence_onto_a_single_line]
end

#current_key? ⇒ Boolean Also known as: id?, sequence_id?, title, title?

#

current_key?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 688

def current_key?
  @current_key
end

#data? ⇒ Boolean Also known as: input?, dataset?

#

data?

This will contain the full content of the (whole) .fasta file, including the header.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 791

def data?
  @data
end

#do_process_the_commandline_arguments_that_are_files(these_files = commandline_arguments_that_are_files? ) ⇒ Object

#

do_process_the_commandline_arguments_that_are_files

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 421

def do_process_the_commandline_arguments_that_are_files(
    these_files = commandline_arguments_that_are_files?
  )
  unless these_files.is_a? Array
    these_files = [these_files].flatten.compact
  end
  these_files.each {|this_file|
    set_input_file(this_file)
    set_data # This will use the default file.
    split_into_proper_sections
    report_the_FASTA_header if @show_the_header
    if @sort_by_size
      run_sizeseq_comparison
    else
      # =================================================================== #
      # === Handle cases where the input is a protein
      # =================================================================== #
      if is_the_sequence_a_polypeptide?
        if be_verbose?
          erev "This sequence is assumed to be a #{royalblue('protein')}#{rev}."
          report_how_many_elements_we_have_found
        end
      else # Must be a protein.
        # =================================================================== #
        # === Else it must be RNA or DNA
        # =================================================================== #
        if be_verbose?
          erev "This sequence is assumed to "\
               "be #{royalblue('DNA')}#{rev} or #{royalblue('RNA')}#{rev}."
        end
        calculate_gc_content # GC content makes only sense for nucleotides.
        report_how_many_elements_we_have_found if be_verbose?
      end
      if be_verbose?
        report_the_nucleotide_composition
        report_on_how_many_entries_we_did_work
        if report_the_sequence?
          do_report_the_sequence
        end
      end
    end
  }
end

#do_report_the_sequence ⇒ Object Also known as: display, report

#

do_report_the_sequence (report tag)

This method is used to display the main sequence at hand.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 514

def do_report_the_sequence
  _ = main_sequence?
  # ======================================================================= #
  # Honour the --limit commandline flag next.
  # ======================================================================= #
  if @internal_hash[:limit_the_display_to_n_nucleotides]
    _ = _[0 .. (@internal_hash[:limit_the_display_to_n_nucleotides] - 1)]
  end
  if @colourize_sequence
    if is_polynucleotide?
      # =================================================================== #
      # Else assume this is DNA/RNA input.
      # =================================================================== #
      _.gsub!(/A/, teal('A')+rev)
      _.gsub!(/C/, slateblue('C')+rev)
      _.gsub!(/G/, royalblue('G')+rev)
      _.gsub!(/T/, steelblue('T')+rev)
      _.gsub!(/U/, steelblue('U')+rev)
    #else
    end
  end
  if condense_the_sequence_onto_a_single_line?
    _ = _.delete("\n")
  end
  erev colourize_this_nucleotide_sequence(_)
  e if condense_the_sequence_onto_a_single_line?
  if show_the_translated_protein_sequence?
    # ===================================================================== #
    # Do show the translated protein sequence next:
    # ===================================================================== #
    translated_into_aa = Bioroebe.to_aa(_)
    translated_into_aa_and_colourized = translated_into_aa.dup
    if translated_into_aa.include? '*'
      translated_into_aa_and_colourized = translated_into_aa.gsub(/\*/,tomato('*'))
    end
    erev 'The translated aminoacid sequence of '+
         sfancy(translated_into_aa.size.to_s)+rev+
         ' aminoacids is:'
    e
    erev steelblue("  #{translated_into_aa_and_colourized}")
    e
  end
end

#do_show_the_header ⇒ Object

#

do_show_the_header

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 975

def do_show_the_header
  @show_the_header = true
end

#do_sort_by_size ⇒ Object Also known as: run_sizeseq_comparison

#

do_sort_by_size

This method will sort the hash by size of the sequence. It has been inspired by the EMBOSS sizeq functionality.

The output that should be generated might look like this:

https://www.bioinformatics.nl/cgi-bin/emboss/help/sizeseq#input.1

Invocation example:

x = Bioroebe::ParseFasta.new('/Depot/j/globins.fasta'); x.do_sort_by_size
#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 916

def do_sort_by_size
  # ======================================================================= #
  # Sort it here first, by the size of the "value", aka the sequence body.
  # ======================================================================= #
  @hash = return_size_sorted_hash(@hash)
  _ = ''.dup
  @hash.each_pair {|key, sequence|
    _ << '> ID '+sequence.size.to_s+' AA.; DE: '+key.to_s+
         ' SQ '+sequence.size.to_s+' AA'+N # ; unknown MW as of yet; '\
         #'unknown CRC64 as of yet'+N
    _ << sequence+N+N
  }
  e _
end

#entries? ⇒ Boolean

#

entries?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 491

def entries?
  @data
end

#first_key? ⇒ Boolean

#

first_key?

Obtain the very first entry.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 952

def first_key?
  headers?.first
end

#first_value ⇒ Object

#

first_value

This will return the first entry of the Fasta files.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 756

def first_value
  sequences?.first
end

#gc_content? ⇒ Boolean Also known as: gc_content

#

gc_content?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1296

def gc_content?
  return ::Bioroebe.gc_content(main_sequence?).to_f # Must be a float.
end

#hash? ⇒ Boolean

#

hash?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 799

def hash?
  @hash
end

#header? ⇒ Boolean

#

header?

This variant will always return the first entry.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 961

def header?
  headers?.first.to_s
end

#headers? ⇒ Boolean

#

headers?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 943

def headers?
  @hash.keys
end

#is_polynucleotide?(i = main_sequence?) ) ⇒ Boolean Also known as: is_a_nucleotide?

#

is_polynucleotide?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 774

def is_polynucleotide?(i = main_sequence?)
  !is_protein?(i)
end

#is_the_sequence_a_polypeptide?(i = main_sequence? ) ⇒ Boolean Also known as: is_protein?, is_a_protein?

#

is_the_sequence_a_polypeptide?

This method can be used to determine whether a given input sequence is a polypeptide (aka a protein) or whether it is not.

If this sequence is a polypeptide then this method will return true. Otherwise false will be returned.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1249

def is_the_sequence_a_polypeptide?(
    i = main_sequence?
  )
  return_value = false # Set the default return value here.
  # ======================================================================= #
  # Look at the first 120 positions to determine whether this is a protein
  # or a nucleotide sequence.
  # ======================================================================= #
  subsequence = i[0 .. 119] # Must deduct 1 at the end since Arrays in ruby start at 0.
  # ======================================================================= #
  # Build a frequency of the characters there.
  # ======================================================================= #
  hash = {}
  hash.default = 0
  subsequence.chars.each {|character|
    hash[character] += 1
  }
  keys_to_check_for = %w(
    B D E F H I J K L M O P Q R S V W X Y Z
  )

  values = hash.select {|key, value|
    if keys_to_check_for.include? key
      true
    else
      false
    end
  }.values.sum
  if values > 0
    return_value = true
  end
  return return_value
end

#is_this_sequence_a_polynucleotide_sequence? ⇒ Boolean

#

is_this_sequence_a_polynucleotide_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 781

def is_this_sequence_a_polynucleotide_sequence?
  !is_protein?
end

#main_sequence? ⇒ Boolean

#

main_sequence?

This will always return the first entry.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1289

def main_sequence?
  @hash.values.first
end

#menu(i = return_commandline_arguments_that_are_not_files) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 255

def menu(
    i = return_commandline_arguments_that_are_not_files
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --to-protein
    #
    # Invocation example:
    #
    #   pfasta *.fasta --toprotein
    #
    # ===================================================================== #
    when /^-?-?to(-|_)?protein/i
      @internal_hash[:show_the_translated_protein_sequence] = true
    # ===================================================================== #
    # === --one-line
    #
    # Invocation example:
    #
    #   pfasta rpoS_NC_000913.3.fasta --one-line
    #
    # ===================================================================== #
    when /^-?-?one(-|_)?liner?/i
      @internal_hash[:condense_the_sequence_onto_a_single_line] = true
    # ===================================================================== #
    # === --limit=1000
    #
    # Invocation example:
    #
    #   pfasta --limit=1000
    #
    # ===================================================================== #
    when /^-?-?limit=(\d+)$/i
      @internal_hash[:limit_the_display_to_n_nucleotides] = $1.to_s.dup.to_i
    # ===================================================================== #
    # === --overwrite
    # ===================================================================== #
    when /^-?-?overwrite/i
      @internal_hash[:overwrite_the_original_file] = true
    # ===================================================================== #
    # === --help
    #
    # Usage example:
    #
    #   parse_fasta --help
    #
    # ===================================================================== #
    when /^-?-?help/i
      show_help
      exit
    # ===================================================================== #
    # === --save-file
    # ===================================================================== #
    when /^-?-?save(-|_)?file/i
      @internal_hash[:save_the_file] = true
    # ===================================================================== #
    # === --also-show-the-sequence
    #
    # To invoke this method try:
    #
    #   parsefasta /Depot/Bioroebe/NP_013521.3_289_aa.fasta --show
    #
    # ===================================================================== #
    when /^-?-?also(-|_)?show(-|_)?the(-|_)?sequence$/i,
         /^-?-?report$/i,
         /^-?-?show$/i
      @internal_hash[:report_the_sequence] = true
    # ===================================================================== #
    # === --header
    # ===================================================================== #
    when /^-?-?header/i
      do_show_the_header
    # ===================================================================== #
    # === --short
    #
    # This entry point can be used to show 300 nucleotides and not
    # more, by simply using the --short commandline flag.
    # ===================================================================== #
    when /^-?-?short/i
      @internal_hash[:limit_the_display_to_n_nucleotides] = 300
    # ===================================================================== #
    # === --size
    #
    # This will simply tell us how many nucleotides the given sequence 
    # has, then exit.
    #
    # To invoke this method try:
    #
    #   parsefasta /Depot/Bioroebe/NP_013521.3_289_aa.fasta --size
    #
    # ===================================================================== #
    when /^-?-?size$/i
      set_be_quiet
      do_process_the_commandline_arguments_that_are_files
      erev size? # Report the size here.
      exit
    end
  end
end

#n_nucleotides? ⇒ Boolean Also known as: return_n_aminoacids, size?, sequence_size?

#

n_nucleotides?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 934

def n_nucleotides?
  @hash.values.first.delete("\n").size
end

#nucleotides_or_aminoacids? ⇒ Boolean

#

nucleotides_or_aminoacids?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 763

def nucleotides_or_aminoacids?
  if is_polynucleotide?
    'nucleotides'
  else
    'aminoacids'
  end
end

#opnn ⇒ Object

#

opnn

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 705

def opnn
  super(namespace?) if use_opn?
end

#output_results ⇒ Object

#

output_results

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 505

def output_results
  pp @hash
end

#overwrite_the_original_file? ⇒ Boolean

#

overwrite_the_original_file?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1033

def overwrite_the_original_file?
  @internal_hash[:overwrite_the_original_file]
end

#raw_body? ⇒ Boolean

#

raw_body?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 968

def raw_body?
  @hash.values.first
end

#report_how_many_elements_we_have_found ⇒ Object

#

report_how_many_elements_we_have_found

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 590

def report_how_many_elements_we_have_found
  if @hash
    first = @hash.values.first.delete("\n")
    size = first.size.to_s
    if be_verbose?
      n_start_codons = first.count('ATG')
      # =================================================================== #
      # We upcase it since as of October 2021, as some FASTA files may
      # include the sequence in lowercased characters.
      # =================================================================== #
      n_start_codons += first.reverse.upcase.count('ATG')
      result = "This sequence contains #{simp(size.to_s)}#{rev}"\
               " #{nucleotides_or_aminoacids?}".dup
      if is_a_nucleotide?
        result << " and #{n_start_codons} "\
                  "ATG codons (on both strands) in total"
      end
      result << '.'
      if size.to_i > 1_000_000
        # ================================================================= #
        # Format the number with '_' characters.
        # ================================================================= #
        formatted = size.to_i.to_s.reverse.split(/(.{3})/).reject(&:empty?).join('_').reverse
        result = result.dup if result.frozen?
        result << ' ('+simp(formatted+' bp')+rev+')'
      end
      erev result
    end
  end
end

#report_on_how_many_entries_we_did_work ⇒ Object

#

report_on_how_many_entries_we_did_work

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 624

def report_on_how_many_entries_we_did_work
  if be_verbose?
    entry_or_entries = 'entry'
    if @hash.keys.size > 1
      entry_or_entries = 'entries'
    end
    erev "We have identified a total of #{orange(@hash.keys.size)}"\
         "#{rev} #{entry_or_entries} in this fasta dataset."
    e
  end
end

#report_the_FASTA_header ⇒ Object

#

report_the_FASTA_header

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 639

def report_the_FASTA_header
  e "#{rev}The header is: #{steelblue(header?)}"
end

#report_the_nucleotide_composition ⇒ Object Also known as: report_the_protein_composition

#

report_the_nucleotide_composition

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 562

def report_the_nucleotide_composition
  if is_this_sequence_a_polynucleotide_sequence?
    first = @hash.values.first.upcase
    total_size   = first.size
    n_adenines   = first.count('A')
    n_thymidines = first.count('T')
    n_cytodines  = first.count('C')
    n_guanines   = first.count('G')
    erev "The nucleotide composition is as follows:"
    e "  "\
      "#{steelblue(n_adenines)}#{rev}x A (#{(n_adenines * 100.0 / total_size).round(2)}%), "\
      "#{steelblue(n_thymidines)}#{rev}x T (#{(n_thymidines * 100.0 / total_size).round(2)}%), "\
      "#{steelblue(n_cytodines)}#{rev}x C (#{(n_cytodines * 100.0 / total_size).round(2)}%), "\
      "#{steelblue(n_guanines)}#{rev}x G (#{(n_guanines * 100.0 / total_size).round(2)}%)"
  elsif is_a_protein?
    # ===================================================================== #
    # Report the composition of the protein:
    # ===================================================================== #
    sequence = @hash.values.first.delete("\n")
    erev "The protein composition (aminoacids) is as follows:"
    # e colourize_this_aminoacid_sequence_for_the_commandline("  #{sequence}")
    e orchid("  #{sequence}")
  end
end

#report_the_sequence? ⇒ Boolean

#

report_the_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 646

def report_the_sequence?
  @internal_hash[:report_the_sequence]
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 141

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @is_a_genbank_file
  # ======================================================================= #
  @is_a_genbank_file = false
  # ======================================================================= #
  # === @input_file
  #
  # This variable denotes which input file is used to read data from.
  #
  # It is nil initially because we may skip reading from an existing
  # file and e. g. only read from a String or some other non-file
  # entity.
  # ======================================================================= #
  @input_file = nil
  # ======================================================================= #
  # === @hash
  #
  # This is the main variable for the class. It will keep entries such
  # as this one here:
  #
  #   {
  #     "ENSMUSG00000020122|ENSMUST08" => "CCCTCC"
  #   }
  #
  # ======================================================================= #
  @hash = {}
  # ======================================================================= #
  # === @internal_hash
  #
  # This Hash exists for internal configuration of the class.
  # ======================================================================= #
  @internal_hash = {}
  # ======================================================================= #
  # === :report_the_sequence
  # ======================================================================= #
  @internal_hash[:report_the_sequence] = false
  # ======================================================================= #
  # === :overwrite_the_original_file
  # ======================================================================= #
  @internal_hash[:overwrite_the_original_file] = false
  # ======================================================================= #
  # === :save_the_file
  # ======================================================================= #
  @internal_hash[:save_the_file] = false
  # ======================================================================= #
  # === :remove_numbers_from_input
  # ======================================================================= #
  @internal_hash[:remove_numbers_from_input] = false
  # ======================================================================= #
  # === :show_the_translated_protein_sequence
  #
  # This setting is false initially. If set to true via the commandline
  # then report() will show the translated protein sequence as well.
  # ======================================================================= #
  @internal_hash[:show_the_translated_protein_sequence] = false
  # ======================================================================= #
  # === :condense_the_sequence_onto_a_single_line
  #
  # By default the output of this class will include newlines for the
  # sequence. If this is not wanted by the user then the following
  # variable keeps track of that behaviour. You can use the flag
  # called --one-line to enable a condensed output, with newlines
  # being removed.
  # ======================================================================= #
  @internal_hash[:condense_the_sequence_onto_a_single_line] = false
  # ======================================================================= #
  # === :limit_the_display_to_n_nucleotides
  #
  # If this variable is a number rather than nil, then it will be used
  # to display only a limited number of nucleotides, e. g. "1000" if
  # the user passes in 1000.
  # ======================================================================= #
  @internal_hash[:limit_the_display_to_n_nucleotides] = nil
  # ======================================================================= #
  # === @may_we_exit
  # ======================================================================= #
  @may_we_exit = false
  # ======================================================================= #
  # === @current_key
  # ======================================================================= #
  @current_key = nil
  # ======================================================================= #
  # === @use_opn
  # ======================================================================= #
  @use_opn = ::Bioroebe.use_opn?
  # ======================================================================= #
  # === @colourize_sequence
  # ======================================================================= #
  @colourize_sequence = false
  # ======================================================================= #
  # === @sort_by_size
  #
  # If the following variable is set to true, then this class will
  # run a sizeseq-comparison, that is, it will compare all sequences
  # and output them in a size-sorted manner, similar to the EMBOSS
  # sizeseq action.
  # ======================================================================= #
  @sort_by_size = false
  # ======================================================================= #
  # === @show_the_header
  #
  # If this variable is true then the header will be shown.
  # ======================================================================= #
  @show_the_header = false
  set_round_to :default
  set_be_verbose
end

#return_size_sorted_hash(i = @hash) ⇒ Object

#

return_size_sorted_hash

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 895

def return_size_sorted_hash(i = @hash)
  _ = i.sort_by {|key, value| value.size }
  i = Hash[_]
  return i
end

#round_to? ⇒ Boolean

#

round_to?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 698

def round_to?
  @internal_hash[:round_to]
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 653

def run
  menu
  do_process_the_commandline_arguments_that_are_files
  do_save_the_file if save_the_file?
end

#sanitize_data(i) ⇒ Object

#

sanitize_data

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 662

def sanitize_data(i)
  if i.is_a? Array
    i.flatten!
    i.reject! {|entry| entry.start_with? '#' }
    i.reject! {|entry| entry.strip.empty? }
    if i.first and i.first.include? "\r"
      # =================================================================== #
      # Some FASTA files include "\r" line endings. We will check first
      # for the first entry to contain a \r, and if so, we assume the
      # whole FASTA file may have \r, which then will be removed.
      # =================================================================== #
      i.map! {|entry| entry.delete("\r") }
    end
  end
  # ========================================================================= #
  # === Run through SanitizeNucleotideSequence
  # ========================================================================= #
  if @internal_hash[:remove_numbers_from_input]
    i = Bioroebe::SanitizeNucleotideSequence[i]
  end
  i
end

#sanitize_the_description ⇒ Object

#

sanitize_the_description

This method will iterate over the description entry and sanitize it. In this context sanitizing means to add the “length” entry, and the “type” entry, such as in:

" # length=231; type=dna"
#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 475

def sanitize_the_description
  @data.map! {|line|
    if line.start_with?('>') and !line.include?('length=')
      length = 0
      if @hash.has_key? line.delete('>')
        length = @hash[line.delete('>')].size
      end
      line << " # length=#{length}; type=dna" # Currently hardcoded to DNA.
    end
    line
  }
end

#save ⇒ Object

#

save

This method will save our FASTA file.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1191

def save
  if @input_file.nil?
    erev "The generic file #{sfile('foobar.fasta')}#{rev} "\
         "will be used."
    set_input_file('foobar.fasta')
  end
  into = @input_file
  what = @data.join("\n")
  erev 'Storing into '+sfile(into)+rev+'.'
  write_what_into(what, into)
  return into
end

#save_into_a_fasta_file(be_verbose = be_verbose? ) ⇒ Object Also known as: do_save_the_file

#

save_into_a_fasta_file

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1078

def save_into_a_fasta_file(
    be_verbose = be_verbose?
  )
  case be_verbose
  when :be_verbose
    be_verbose = true
  end
  if @data
    what = @data.join("\n")
    into = 'standard.fasta'
    erev 'Saving into '+sfile(into)+rev+'.' if be_verbose
    write_what_into(what, into)
    return File.absolute_path(into) # And return the file we saved into.
  else
    opnn; erev 'No @data variable exists.'
  end
end

#save_the_file? ⇒ Boolean

#

save_the_file?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1026

def save_the_file?
  @internal_hash[:save_the_file]
end

#sequence ⇒ Object Also known as: fasta_sequence, sequence?, body?, body, naseq, nucleotide_sequence, return_sequence, content?

#

sequence

This method will return the sequence, without any newlines. It is also called the “body” of a FASTA file.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1173

def sequence
  _ = @hash.values.first
  _.chomp! if _ and _.end_with?(N)
  return no_newlines(_)
end

#sequence_object ⇒ Object

#

sequence_object

This method will return a Sequence object.

Usage example:

x = Bioroebe.parse_fasta 'ls_orchid.fasta'
y = x.sequence_object # y is now an instance of Bioroebe::Sequence
#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1311

def sequence_object
  ::Bioroebe::Sequence.new(main_sequence?)
end

#sequences? ⇒ Boolean Also known as: sequences, values

#

sequences?

This method will obtain all found sequences.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 808

def sequences?
  @hash.values
end

#set_be_verbose_and_report_the_sequence ⇒ Object

#

set_be_verbose_and_report_the_sequence

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 880

def set_be_verbose_and_report_the_sequence
  set_be_verbose
  @internal_hash[:report_the_sequence] = true
end

#set_data(i = @input_file) ⇒ Object Also known as: set_sequence

#

set_data

This is the setter-method towards @data. It is no longer allowed to invoke set_input_file() since as of 12.06.2020. This means that you have to invoke that method prior to calling this method.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 846

def set_data(i = @input_file)
  # ======================================================================= #
  # The next line attempts to ensure that even an Array can be used
  # as input to that method.
  # ======================================================================= #
  i = [i].flatten.compact.first.to_s.dup
  if File.exist? i.to_s # First try to read in from a file.
    if be_verbose?
      opnn; erev "Will read from the file `#{sfile(i)}#{rev}`."
    end
    i = File.readlines(i)
    if @is_a_genbank_file
      selected = i.select {|line|
        line.start_with?('       ') and # such as: "       61 atggggcctg caatggggcc tgcaatgggg cctgca\n"
        (line.strip =~ /\d+/)
      }.map {|inner_line|
        inner_line.strip.delete(' 0123456789').strip.upcase
      }
      i = ["> genbank file"]+selected
    end
  end
  if i.nil? or i.empty?
    i = DEFAULT_FASTA
    opnn; erev 'No input was provided. Thus a default FASTA '\
               'sequence will be used instead.'
  end
  i = sanitize_data(i)
  i = i.split(N) if i.is_a? String
  @data = i
end

#set_input_file(i = nil) ⇒ Object Also known as: set_input_files

#

set_input_file

This method will be used to keep track of the input-file, from which we will read the dataset.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 985

def set_input_file(i = nil)
  if i.nil?
    # ===================================================================== #
    # First, we try to find a .fasta or .fa file in the current
    # directory. If we can find it, we will use that instead.
    # ===================================================================== #
    unless Dir['*.{fa,fasta}'].empty?
      file = Dir['*.{fa,fasta}'].first
      if be_verbose?
        result = 'A '
        if file.end_with? '.fasta'
          result < 'FASTA '
        end
        result << 'file was found in this directory ('+sfile(file)+').'
        opnn; erev result
        opnn; erev 'We will use it.'
      end
      i = file
    end
    unless Dir['*.{fa,fasta}'].empty?
      file = Dir['*.{fa,fasta}'].first
      if be_verbose?
        opnn; erev "We have found a file in this "\
                   "directory (#{sfile(file)}#{rev})."
        opnn; erev 'We will use it.'
      end
      i = file
    end
  end
  if i and File.exist?(i)
    dataset = File.read(i)
    if dataset[0 .. ('LOCUS'.size - 1)] == 'LOCUS'
      @is_a_genbank_file = true
    end
  end
  @input_file = i
end

#set_round_to(i = :default) ⇒ Object

#

set_round_to

This will set to how many decimal numbers we will round to. This is mostly done for display-purposes, hence why the default is a fairly low value.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 403

def set_round_to(
    i = :default
  )
  case i
  # ======================================================================= #
  # === :default
  #
  # Since as of April 2021, the new default is 2, for rounding.
  # ======================================================================= #
  when :default
    i = DEFAULT_ROUND_TO
  end
  @internal_hash[:round_to] = i.to_i
end

#short_headers? ⇒ Boolean

#

short_headers?

The short-headers are like the headers, but if a ' ' token is found then the line will be truncated towards that first ' '.

An example is:

sp|Q91FT8|234R_IIV6 Uncharacterized protein 234R OS=Invertebrate iridescent virus 6 OX=176652 GN=IIV6-234R PE=4 SV=1

This will be truncated towards

sp|Q91FT8|234R_IIV6

This could then be used to automatically rename FASTA files, for instance.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 830

def short_headers?
  headers?.map {|entry|
    if entry.include? ' '
      entry = entry.split(' ').first
    end
    entry
  }
end

#show_help ⇒ Object

#

show_help (help tag)

This method will inform the user how this class may be used from the commandline.

Invocation example:

pfasta --help
#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 371

def show_help
  e
  eparse '  --size'
  eparse '  --also-show-the-sequence'
  eparse '  --header     # show the header as well (normally the '\
         'header is not shown)'
  eparse '  --limit=1000 # limit to show only the first 1000 '\
         'nucleotides; use'
  eparse '               # any number that you need here'
  eparse '  --one-line   # show the sequence on one line only, '\
         'e. g. all newlines'
  eparse '               # were removed'
  eparse '  --toprotein  # show the protein sequence as well '\
         '(assumes DNA or RNA'
  eparse '               # .fasta file)'
  e
end

#show_the_translated_protein_sequence? ⇒ Boolean

#

show_the_translated_protein_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 392

def show_the_translated_protein_sequence?
  @internal_hash[:show_the_translated_protein_sequence]
end

#simplify_header ⇒ Object

#

simplify_header

This method can be called to simplify the header. It will save into a .fasta file at once.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1124

def simplify_header
  _ = header?
  # ======================================================================= #
  # Next, simplify the header. We must start with checking for [] first,
  # because if there are any [] in the FASTA header then we can simplify
  # stuff at once.
  # ======================================================================= #
  if _.include?('[') and _.include?(']')
    _ = '> '+_.strip.scan(/\[.+\]/).flatten.first.delete('[]')+"\n"
  elsif _.include? ','
    _ = _[0 .. (_.index(',') - 1) ].strip
  end
  what = nil
  # ======================================================================= #
  # Next, designate where to store this file.
  # ======================================================================= #
  into = 'new_fasta_file.fasta'
  if overwrite_the_original_file?
    into = @input_file
  end
  if _.start_with? '>'
    what = _
  elsif _.include?('[') and _.include?(']') # For example: [Pan troglodytes]
    # ===================================================================== #
    # See rubular at:
    #
    #   https://rubular.com/r/aDjI0JwMOUlZzP
    #
    # ===================================================================== #
    what = "> "+_.scan(/\[(.+)\]/).flatten.first.to_s+"\n".dup 
  elsif _.include? 'Human'
    _scanned_result = _.scan(/(Human)/)
    what = "> "+$1.to_s.dup+"\n".dup
  else
    erev "Unsure what to do: #{steelblue(_)}"
  end
  if what and into
    what << raw_body?
    erev 'Storing into `'+sfile(into)+rev+'`.'
    write_what_into(what, into)
  end
end

#split_into_proper_sections ⇒ Object

#

split_into_proper_sections

Split up into the fasta identifier, and the content.

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1042

def split_into_proper_sections
  unless @data.to_s.include? '>'
    erev 'No ">" character was found in this dataset.'
    erev 'It is recommended to always have a > identifier '\
         'for the'
    erev 'FASTA format (such as in a .fasta or a .fa file).'
  end if be_verbose? # Ok, the input data includes >. We can proceed.
  @data.each { |line|
    # ===================================================================== #
    # === Handle the leading > FASTA identifier first
    # ===================================================================== #
    if line.start_with? '>' # leading identifier.
      @current_key = line[1..-1].chomp # Select all but the first character.
      @hash[@current_key] = ''.dup
    else
      line.delete!('_')
      unless @current_key
        @current_key = 'standard'
        @hash[@current_key] = ''.dup
      end
      # =================================================================== #
      # === Retain the newlines
      #
      # Here we may decide to get rid of newlines, but it is better to
      # NOT remove the newlines - that way we can simply save the
      # dataset again.
      # @hash[@current_key] << no_newlines(line)
      # =================================================================== #
      @hash[@current_key] << line
    end
  }
end

#type? ⇒ Boolean

#

type?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 1230

def type?
  if is_the_sequence_a_polypeptide?
    :protein
  elsif is_this_sequence_a_polynucleotide_sequence?
    :dna_or_rna
  else
    :unknown
  end
end

#use_opn? ⇒ Boolean

#

use_opn?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 712

def use_opn?
  @use_opn
end

#we_may_exit ⇒ Object

#

we_may_exit

#

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# File 'lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb', line 498

def we_may_exit
  @may_we_exit = true
end