bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb

@@ -1,156 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/fasta_and_fastq/parse_fasta/report.rb'
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
-
-  require 'bioroebe/sequence/dna.rb'
-
-  # ========================================================================= #
-  # === do_report_the_sequence                                   (report tag)
-  #
-  # This method is used to display the main sequence at hand.
-  # ========================================================================= #
-  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; alias display do_report_the_sequence # === display
-       alias report  do_report_the_sequence # === report
-
-  # ========================================================================= #
-  # === report_the_nucleotide_composition
-  # ========================================================================= #
-  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; alias report_the_protein_composition report_the_nucleotide_composition # === report_the_protein_composition 
-
-  # ========================================================================= #
-  # === report_how_many_elements_we_have_found
-  # ========================================================================= #
-  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
-  # ========================================================================= #
-  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
-  # ========================================================================= #
-  def report_the_FASTA_header
-    e "#{rev}The header is: #{steelblue(header?)}"
-  end
-
-  # ========================================================================= #
-  # === report_the_sequence?
-  # ========================================================================= #
-  def report_the_sequence?
-    @internal_hash[:report_the_sequence]
-  end
-
-end; end

data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb

@@ -1,128 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/fasta_and_fastq/parse_fasta/reset.rb' 
-# =========================================================================== #
-module Bioroebe
-
-class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-    super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = 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
-
-end; end

data/lib/bioroebe/genbank/genbank_parser.rb

@@ -1,291 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GenbankParser
-#
-# This is similar to the FastaParser, but instead it will only select the
-# content between "ORIGIN" and "//" entries.
-#
-# You can pass the content of a genbank-file to this class, and it can
-# report the nucleotide sequence, e. g. the part starting after the
-# ORIGIN string.
-#
-# The reason why this class has been created was because it is sometimes
-# necessary to parse a genebank file.
-# =========================================================================== #
-# require 'bioroebe/genbank/genbank_parser.rb'
-# Bioroebe::GenbankParser.new(ARGV)
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class GenbankParser < ::Bioroebe::CommandlineApplication # === Bioroebe::GenbankParser
- 
-  # ========================================================================= #
-  # === UPCASE_SEQUENCE
-  # ========================================================================= #
-  UPCASE_SEQUENCE = true
-
-  # ========================================================================= #
-  # === TEST_STRING
-  #
-  # Our example test-string, to see how such a genbank file usually looks
-  # like.
-  # ========================================================================= #
-  TEST_STRING = '                   /note="internal transcribed spacer 2"
-ORIGIN      
-        1 cgtaacaagg tttccgtagg tgaaccttcg gaaggatcat tgttgagacc cccaaaaaaa
-       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt ggctactgtg
-      121 gtggccgtga atttccgtcg aacctccttg ggagaattct tgatggcaat tgaacccttg
-      181 gcccggcgca gtttcgcccc aagtcaaatg agatggaacc ggcggagggc atcgtcctcc
-      241 atggaaccgg ggagggccgg cgttcttccg ttccccccat gaattttttt ttgacaactc
-      301 tcggcaacgg atatctcggc tctttgcatc cgatgaaaga acccagcgaa atgtgataag
-      361 tggtgtgaat tgcagaatcc cgtgaaccat cgagtctttg aacgcaagtt gcgcccgagg
-      421 ccatcaggct aagggcacgc ctgcctgggc gttgcgtgct gcatctctct cccattgcta
-      481 aggctgaaca ggcatactgt tcggccggcg cggatgagtg tttggcccct tgttcttcgg
-      541 tgcgatgggt ccaagacctg ggcttttgac ggccggaaat ccggcaagag gtggacggac
-      601 ggtggctgcg acgaagctgt cgtgcgaatg ccctacgctg tcgtatttga tgggccggaa
-      661 taaatccctt ttgagcccca ttggaggcac gtcaacccgt gggcggtcga cggccatttg
-      721 gatgcaaccc caggtcaggt gagga
-//
-LOCUS       Z78510                   750 bp    DNA     linear   PLN 30-NOV-2006
-DEFINITION  P.caricinum 5.8S rRNA gene and ITS1 and ITS2 DNA.
-ACCESSION   Z78510
-VERSION     Z78510.1  GI:2765635
-KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
-            ITS1; ITS2.
-SOURCE      Phragmipedium caricinum
-  ORGANISM  Phragmipedium caricinum
-            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
-            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
-            Cypripedioideae; Phragmipedium.
-REFERENCE   1
-  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
-  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
-            Orchidaceae): nuclear rDNA ITS sequences
-  JOURNAL   Unpublished
-REFERENCE   2  (bases 1 to 750)
-  AUTHORS   Cox,A.V.
-  TITLE     Direct Submission
-  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
-            Richmond, Surrey TW9 3AB, UK
-FEATURES             Location/Qualifiers
-     source          1..750
-                     /organism="Phragmipedium caricinum"
-                     /mol_type="genomic DNA"
-                     /db_xref="taxon:53127"
-     misc_feature    1..380
-                     /note="internal transcribed spacer 1"
-     gene            381..550
-                     /gene="5.8S rRNA"
-     rRNA            381..550
-                     /gene="5.8S rRNA"
-                     /product="5.8S ribosomal RNA"
-     misc_feature    551..750
-                     /note="internal transcribed spacer 2"
-ORIGIN      
-        1 ctaaccaggg ttccgaggtg accttcggga ggattccttt ttaagccccc gaaaaaacga
-       61 tcgaattaaa ccggaggacc ggtttaattt ggtctcccca ggggctttcc ccccttggtg
-      121 gccgtgaatt tccatcgaac ccccctggga gaattcttgg tggccaatgg acccttggcc
-      181 cggcgcaatt tcccccccaa tcaaatgaga taggaccggc agggggcgtc cccccccatg
-      241 gaaccgggga gggccggcat tcttccgttc ccccctcgga ttttttgaca actctcgcaa
-      301 cggatatctc gcctctttgc atcggatgga agaacgcagc gaaatgtgat aagtggtgtg
-      361 aattgcagaa tcccgtgaac catcgagtct ttgaacgcaa gttgcgcccg aggccatcag
-      421 gctaagggca cgcctgcctg ggcgttgcgt gctgcatctc tcccattgct aaggttgaac
-      481 gggcatactg ttcggccggc gcggatgaga gattggcccc ttgttcttcg gtgcgatggg
-      541 tccaagacct gggcttttga cggtccaaaa tccggcaaga ggtggacgga cggtggctgc
-      601 gacaaagctg tcgtgcgaat gccctgcgtt gtcgtttttg atgggccgga ataaatccct
-      661 tttgaacccc attggaggca cgtcaaccca tgggcggttg acggccattt ggatgcaacc
-      721 ccaggtcagg tgagccaccc gctgagttta
-//
-LOCUS       Z78509                   731 bp    DNA     linear   PLN 30-NOV-2006
-DEFINITION  P.pearcei 5.8S rRNA gene and ITS1 and ITS2 DNA.
-ACCESSION   Z78509
-VERSION     Z78509.1  GI:2765634
-KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
-            ITS1; ITS2.
-SOURCE      Phragmipedium pearcei
-  ORGANISM  Phragmipedium pearcei
-            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
-            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
-            Cypripedioideae; Phragmipedium.
-REFERENCE   1
-  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
-  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
-            Orchidaceae): nuclear rDNA ITS sequences
-  JOURNAL   Unpublished
-REFERENCE   2  (bases 1 to 731)
-  AUTHORS   Cox,A.V.
-  TITLE     Direct Submission
-  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
-            Richmond, Surrey TW9 3AB, UK
-FEATURES             Location/Qualifiers
-     source          1..731
-                     /organism="Phragmipedium pearcei"
-                     /mol_type="genomic DNA"
-                     /db_xref="taxon:53135"
-     misc_feature    1..380
-                     /note="internal transcribed spacer 1"
-     gene            381..550
-                     /gene="5.8S rRNA"
-     rRNA            381..550
-                     /gene="5.8S rRNA"
-                     /product="5.8S ribosomal RNA"
-     misc_feature    551..731
-                     /note="internal transcribed spacer 2"
-ORIGIN      
-        1 cgtaacaagg tttccgtagg tgaacctgcg gaaggatcat tgttgagacc gccaaatata
-       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt cgccgctgtg
-      121 gtgaccgtga tttgccatcg agcctccttg ggagatttct tgatggcaat tgaacccttg
-      181 gcccggcgca gtttcgcgcc aagtcatatg agatagaacc ggcggagggc gtcgtcctcc
-      241 atggagcggg gagggccggc atgctccgtg cccccccatg aatttttctg acaactctcg
-      301 gcaacggacg taacaaggtt taaatgtgat aagcaggtgt gaattgcaga atcccgtgaa
-      361 ccatcgagtc tttgaacgca agttgcgccc gaggccatca ggttaagggc acgcctgcct
-      421 gggcgttgcg tgctgcatct ctcccattgc taaggttgaa cgggcatact gttcggccgg
-      481 cgcggatgag agtttggccc cttgttcttc ggtgcgatgg gtccaagacc tgggcttttg
-      541 acggtccaaa atccggcaag aggtggacgg acggtggctg cgacagagct gtcgtgcgaa
-      601 tgccctacgt tgtcgttttt gatgggccag aataaatccc ttttgaaccc cattggaggc
-      661 acgtcaaccc aatggggggt gacgggcatt tggttaaccc cggcaagtta aggcacccgt
-      721 taattttagg a
-//
-LOCUS       Z78508                   741 bp    DNA     linear   PLN 30-NOV-2006'
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      dataset     = ARGV,
-      run_already = true
-    )
-    reset
-    determine_dataset(
-      dataset
-    )
-    if block_given?
-      yielded = yield
-      case yielded
-      # ===================================================================== #
-      # === :do_not_report_anything
-      # ===================================================================== #
-      when :do_not_report_anything
-        @report_dataset = false
-      end
-    end
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset
-  # ========================================================================= #
-  def reset
-    super()
-    # ======================================================================= #
-    # === @dataset
-    # ======================================================================= #
-    @dataset = nil
-    # ======================================================================= #
-    # === @report_dataset
-    # ======================================================================= #
-    @report_dataset = true
-  end
-
-  # ========================================================================= #
-  # === determine_dataset
-  # ========================================================================= #
-  def determine_dataset(i = nil)
-    if i.is_a? Array
-      i = i.first
-    end
-    if i.nil?
-      e 'Please provide some input to this class.'
-      return
-    end
-    # ======================================================================= #
-    # === Handle existing .gb files here
-    # ======================================================================= #
-    if File.exist?(i) and File.file?(i)
-      i = File.read(i)
-    end
-    case i # case tag
-    # ======================================================================= #
-    # === --test
-    #
-    # This entry point can be used to test the default TEST_STRING.
-    # ======================================================================= #
-    when nil,
-         /^-?-?test$/i,
-         /^-?-?test(-|_)?string$/i
-      i = TEST_STRING
-    end
-    # ======================================================================= #
-    # Store the results in the following array.
-    # ======================================================================= #
-    array = []
-    open = false
-    splitted = i.split(N)
-    splitted.each {|line|
-      if line.start_with? '//'
-        open = false
-      end
-      if open
-        array.last << line.strip.delete(' ').gsub(/\d/,'')
-        array.flatten!
-      end
-      if line.start_with? 'ORIGIN'
-        open = true
-        array << [] # Append a new Array.
-      end
-    }
-    string = array.first
-    string.upcase! if UPCASE_SEQUENCE
-    @dataset = string # Assign to the main @dataset here.
-  end
-
-  # ========================================================================= #
-  # === report_dataset?
-  # ========================================================================= #
-  def report_dataset?
-    @report_dataset
-  end
-
-  # ========================================================================= #
-  # === dataset?
-  # ========================================================================= #
-  def dataset?
-    @dataset
-  end; alias sequence? dataset? # === sequence?
-
-  # ========================================================================= #
-  # === report_dataset                                           (report tag)
-  #
-  # Simply output the dataset without any further processing to be done.
-  # ========================================================================= #
-  def report_dataset
-    if @dataset
-      e @dataset if report_dataset?
-    end
-  end; alias report report_dataset # === report
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    report_dataset
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GenbankParser[]
-  # ========================================================================= #
-  def self.[](i)
-    new(i)
-  end
-
-end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GenbankParser.new(ARGV) # Report the dataset as well.
-end # genbankparser
-    # genbankparser sample_file.genbank
-    # genbankparser --test

data/lib/bioroebe/java/bioroebe/Codons.java

@@ -1,22 +0,0 @@
-package bioroebe;
-
-/*
- * class Codons
- *
- * This class will include codon-related code.
- *
- */
-class Codons extends Base {
-
-  /* Designate the main start codon to use. */
-  public static String start_codon = "ATG";
-
-  /* new Codons.display_start_codons() */
-  public static void display_start_codons() {
-    e(start_codon);
-  }
-  public static String return_start_codon() {
-    return start_codon;
-  }
-
-}

data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java

@@ -1,19 +0,0 @@
-package bioroebe;
-
-/*
- * PartnerNucleotide.partner_nucleotide("A");
- *
- * This class will simply yield the corresponding nucleotide.
- *
- */
-class PartnerNucleotide extends Base {
-  public static void partner_nucleotide(String i) {
-    switch(i) {
-      case "A": e("T"); break;
-      case "T": e("A"); break;
-      case "C": e("G"); break;
-      case "G": e("C"); break;
-      default: e("Unhandled input "+i); break;
-    }
-  }
-}