bioroebe 0.10.80 → 0.11.12

data/lib/bioroebe/parsers/genbank_parser.rb

@@ -4,10 +4,29 @@
 # =========================================================================== #
 # === Bioroebe::GenbankParser
 #
-# This class can be used to parse genbank-files. Their file extension is
-# typically ".gbk".
+# This class can be used to parse genbank-files (typically stored as .genbank
+# or .gbk, so their file extension is usually ".gbk").
+#
+# Since as of the rewrite in July 2022 the class can also handle multiple
+# fasta entries now.
+#
+# The class is similar to class FastaParser, but instead it will only
+# select the content between "ORIGIN" and "VERSION" entries.
+#
+# The user can pass the content of a genbank-file to this class, and it
+# can then 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.
+#
+# Usage example:
+#
+#   Bioroebe::GenbankParser.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/parsers/genbank_parser.rb'
+# require 'bioroebe/genbank/genbank_parser.rb'
+# genbank_parser = Bioroebe::GenbankParser.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
 
@@ -20,59 +39,369 @@ class GenbankParser < ::Bioroebe::CommandlineApplication # === Bioroebe::Genbank
   # ========================================================================= #
   NAMESPACE = inspect
 
+  # ========================================================================= #
+  # === UPCASE_THE_SEQUENCE
+  #
+  # Setting this constant to true will cause this class to store the
+  # FASTA sequence in an upcased variant, e. g. "AGCAGCTA" rather
+  # than "acgatcag".
+  # ========================================================================= #
+  UPCASE_THE_SEQUENCE = true
+
+  # ========================================================================= #
+  # === TEST_STRING
+  #
+  # Our example test-string, to see how such a genbank file usually looks
+  # like.
+  #
+  # This will contain two different FASTA sequences.
+  # ========================================================================= #
+  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(
-      commandline_arguments = ARGV,
+      commandline_arguments = nil,
       run_already           = true
     )
     reset
     set_commandline_arguments(
       commandline_arguments
     )
+    menu
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === :do_not_report_anything
+      # ===================================================================== #
+      when :do_not_report_anything
+        @internal_hash[:report_the_dataset] = false
+      end
+    end
     run if run_already
   end
 
   # ========================================================================= #
-  # === reset
+  # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
     super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @internal_hash
+    # ======================================================================= #
+    @internal_hash = {}
+    # ======================================================================= #
+    # === :work_on_this_file
+    # ======================================================================= #
+    @internal_hash[:work_on_this_file] = nil
+    # ======================================================================= #
+    # === :report_the_dataset
+    # ======================================================================= #
+    @internal_hash[:report_the_dataset] = true
+    # ======================================================================= #
+    # === :n_FASTA_entries_in_the_file
+    #
+    # This variable will keep track how many FASTA entries are in
+    # the genbank file at hand.
+    # ======================================================================= #
+    @internal_hash[:n_FASTA_entries_in_the_file] = 0
+    # ======================================================================= #
+    # === :dataset_from_all_FASTA_entries_as_a_hash
+    #
+    # This hash will contain all the FASTA sequences in the given
+    # genbank file at hand. This constitutes the main dataset of
+    # this clas.
+    # ======================================================================= #
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash] = {}
   end
 
   # ========================================================================= #
-  # === run
+  # === menu                                                       (menu tag)
   # ========================================================================= #
-  def run
-    _ = first_argument?
-    if _ and File.exist?(_)
-      dataset = File.readlines(_).select {|line|
-        line.start_with? '     '
-      }.map {|entry|
-        splitted = entry.strip.split(' ')
-        splitted.pop # Remove the last element.
-        splitted.join.strip
-      }
-      if dataset.is_a? Array
-        dataset = dataset.join
+  def menu(
+      i = commandline_arguments_containing_leading_hyphens?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # (case tag)
+      # ===================================================================== #
+      # === gparser --help
+      # ===================================================================== #
+      when /^-?-?help$/i
+        show_help
+        exit
+      # ===================================================================== #
+      # === gparser --test
+      #
+      # This entry point can be used to test the default TEST_STRING.
+      # ===================================================================== #
+      when /^-?-?test$/i,
+           /^-?-?test(-|_)?string$/i
+        analyse_this_dataset(TEST_STRING)
+        exit
       end
-      @sequence = dataset
     end
   end
 
+  # ========================================================================= #
+  # === work_on_which_file?
+  # ========================================================================= #
+  def work_on_which_file?
+    @internal_hash[:work_on_this_file]
+  end
+
+  # ========================================================================= #
+  # === report_the_dataset?
+  # ========================================================================= #
+  def report_the_dataset?
+    @internal_hash[:report_the_dataset]
+  end
+
+  # ========================================================================= #
+  # === set_work_on_this_file
+  # ========================================================================= #
+  def set_work_on_this_file(
+      i = first_argument?
+    )
+    @internal_hash[:work_on_this_file] = i
+  end
+
+  # ========================================================================= #
+  # === analyse_this_dataset
+  # ========================================================================= #
+  def analyse_this_dataset(dataset)
+    use_this_regex =
+      /ORIGIN[\/\-\.\s0-9a-zA-Z]+VERSION\s*[\.0-9A-Z]+/ # See: https://rubular.com/r/0q7rFIUflX7yzw
+    scanned = dataset.scan(use_this_regex)
+    @internal_hash[:n_FASTA_entries_in_the_file] = scanned
+    discover_the_corresponding_FASTA_entries_from_this_dataset(scanned)
+    consider_reporting_our_findings_to_the_user
+  end; alias determine_dataset analyse_this_dataset # === determine_dataset
+
+  # ========================================================================= #
+  # === dataset?
+  # ========================================================================= #
+  def dataset?
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash]
+  end; alias main_dataset? dataset? # === main_dataset?
+
+  # ========================================================================= #
+  # === sequences?
+  # ========================================================================= #
+  def sequences?
+    dataset?.values
+  end
+
   # ========================================================================= #
   # === sequence?
   # ========================================================================= #
   def sequence?
-    @sequence
+    sequences?.first
   end; alias coding_sequence? sequence? # === coding_sequence?
        alias cds              sequence? # === cds
 
+  # ========================================================================= #
+  # === discover_the_corresponding_FASTA_entries_from_this_dataset
+  # ========================================================================= #
+  def discover_the_corresponding_FASTA_entries_from_this_dataset(i)
+    regex_to_use_for_the_id = /VERSION\s*([\.A-Za-z0-9]+)/
+    if i.is_a? Array
+      i.each {|this_dataset|
+        this_dataset =~ regex_to_use_for_the_id
+        use_this_id = $1.to_s.dup
+        use_this_FASTA_sequence = this_dataset.scan(
+          /^\s*\d{1,100}([\sa-zA-Z]+)/
+        ).flatten.join(' ').delete(" \n")
+        use_this_FASTA_sequence.upcase! if UPCASE_THE_SEQUENCE
+        @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash][use_this_id] = use_this_FASTA_sequence
+      }
+    end
+  end
+
+  # ========================================================================= #
+  # === verbose_check_whether_the_file_exists
+  # ========================================================================= #
+  def verbose_check_whether_the_file_exists
+    _ = @internal_hash[:work_on_this_file]
+    if _ and File.exist?(_)
+      true
+    else
+      opnn; e 'No file exists at '+sfile(_)
+      false
+    end
+  end
+
+  # ========================================================================= #
+  # === consider_reporting_our_findings_to_the_user              (report tag)
+  # ========================================================================= #
+  def consider_reporting_our_findings_to_the_user
+    if report_the_dataset? and dataset? and !dataset?.empty?
+      main_dataset?.each_pair {|key, value|
+        e steelblue("#{key}:")
+        e lightblue(value)
+        e
+      }
+    end
+  end; alias report             consider_reporting_our_findings_to_the_user # === report
+       alias report_the_dataset consider_reporting_our_findings_to_the_user # === report_the_dataset
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    set_work_on_this_file(first_argument?)
+    # ======================================================================= #
+    # First check whether the given file exists or not:
+    # ======================================================================= #
+    if verbose_check_whether_the_file_exists
+      original_dataset = File.read(@internal_hash[:work_on_this_file]) # Just store it completely.
+      if original_dataset.include?('ORIGIN') and original_dataset.include?('VERSION ')
+        analyse_this_dataset(original_dataset)
+      else
+        opnn; e 'No keywords ORIGIN and VERSION were found in this file.'
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GenbankParser[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME
-  _ = Bioroebe::GenbankParser.new(ARGV)
-  pp _.id
-  pp _.sequence?
-end # genbankparser *genbank
+  alias e puts
+  genbank_parser = Bioroebe::GenbankParser.new(ARGV)
+  # genbank_parser = Bioroebe::GenbankParser.new('/home/Temp/bioroebe/ls_orchid.gbk')
+  e genbank_parser.sequence?
+  # e _.id
+end # genbankparser *genbank
+    # genbankparser
+    # genbankparser sample_file.genbank
+    # genbankparser --test

data/lib/bioroebe/python/README.md

@@ -0,0 +1 @@
+This directory will contain some python-specific code.

data/lib/bioroebe/python/gui/gtk3/widget1.py

@@ -0,0 +1,22 @@
+import gi
+
+gi.require_version("Gtk", "3.0")
+from gi.repository import Gtk
+
+
+class MyWindow(Gtk.Window):
+    def __init__(self):
+        super().__init__(title="Hello World")
+
+        self.button = Gtk.Button(label="Click Here")
+        self.button.connect("clicked", self.on_button_clicked)
+        self.add(self.button)
+
+    def on_button_clicked(self, widget):
+        print("Hello World")
+
+
+win = MyWindow()
+win.connect("destroy", Gtk.main_quit)
+win.show_all()
+Gtk.main()

data/lib/bioroebe/python/mymodule.py

@@ -0,0 +1,8 @@
+def greeting(name):
+  print("Hello, " + name)
+
+person1 = {
+  "name": "John",
+  "age": 36,
+  "country": "Norway"
+}

data/lib/bioroebe/python/protein_to_dna.py

@@ -0,0 +1,30 @@
+import sys
+import yaml
+
+# =========================================================================== #
+# === protein_to_dna
+# =========================================================================== #
+def protein_to_dna(i):
+  output_string = ''
+  yaml_dataset = None
+  aminoacid_sequence = list(i)
+
+  with open(r'/home/x/programming/ruby/src/bioroebe/lib/bioroebe/yaml/codon_tables/1.yml') as file:
+    # The FullLoader parameter handles the conversion from YAML
+    # scalar values to Python the dictionary format
+    yaml_dataset = yaml.load(file, Loader=yaml.FullLoader)
+    yaml_dataset = { v: k for k, v in yaml_dataset.items() }
+
+  for this_aminoacid in aminoacid_sequence:
+    # Now we must obtain the DNA sequence.
+    # print(yaml_dataset[this_aminoacid])
+    output_string += yaml_dataset[this_aminoacid]
+    output_string += '-'
+
+  # print(yaml_dataset)
+  print(output_string[0: -1]) # Remove the last character.
+
+if __name__ == '__main__':
+  i = sys.argv[1]
+  protein_to_dna(i)
+# py protein_to_dna.py KKKLLL

data/lib/bioroebe/python/shell/shell.py

@@ -0,0 +1,19 @@
+#!/usr/bin/python 
+import sys
+
+# =========================================================================== #
+# === obtain_user_input
+# =========================================================================== #
+def obtain_user_input():
+  user_input = input("> ")
+  return user_input
+
+shall_we_continue = True
+
+while (shall_we_continue):
+  result = obtain_user_input
+  if result == "q":
+    shall_we_continue = False
+    # exit
+  else:
+    print(result)

data/lib/bioroebe/python/to_rna.py

@@ -0,0 +1,14 @@
+import sys
+    
+# =========================================================================== #
+# === to_rna
+#
+# This method will simply convert the given input, such as a 
+# nucleotide sequence, to RNA.
+# =========================================================================== #
+def to_rna(i):
+  converted = i.replace('T','U')
+  print(converted)
+
+to_rna(sys.argv[1])
+# py to_rna.py ATG

data/lib/bioroebe/python/toplevel_methods/to_camelcase.py

@@ -0,0 +1,11 @@
+from re import sub
+
+# =========================================================================== #
+# === camel_case
+# =========================================================================== #
+def camel_case(i):
+  i = sub(r"(_|-)+", " ", i).title().replace(" ", "")
+  return ''.join([i[0].upper(), i[1:]])
+
+if __name__ == "__main__":
+  print(camel_case('foo_bar'))

data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb

@@ -72,13 +72,6 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     i.tr('U','T')
   end
 
-  # ========================================================================= #
-  # === to_dna
-  # ========================================================================= #
-  def to_dna
-    seq?.tr('U','T')
-  end; alias dna to_dna # === dna
-
   # ========================================================================= #
   # === n_random_dna
   #
@@ -258,24 +251,6 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     ::Bioroebe.codon_to_aminoacid(codon)
   end; alias translate_aminoacid_into_dna codon_to_aminoacid # === translate_aminoacid_into_dna
 
-  # ========================================================================= #
-  # === to_dna
-  #
-  # This method will convert a RNA sequence into a DNA sequence.
-  #
-  # It will return the translation.
-  #
-  # bio; puts Bioroebe.new.to_dna('actgggcgagagklklklklk')
-  # ========================================================================= #
-  def to_dna(
-      i = sequence?, upcase_me = true
-    )
-    if is_RNA?
-      i = sequence? if i.nil?
-      ::Bioroebe.to_dna(i, upcase_me)
-    end
-  end; alias dna to_dna # === dna
-
   # ========================================================================= #
   # === random
   #
@@ -397,6 +372,34 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     end
   end; alias gc_percent gc_percentage # === gc_percent
 
+  # ========================================================================= #
+  # === to_dna
+  #
+  # This method will convert a RNA sequence into a DNA sequence.
+  #
+  # It will return the translation.
+  #
+  # Usage example:
+  #
+  #   require 'bioroebe'; puts Bioroebe::DNA.new('actgggcgagaguuuuUUUUUU').to_dna
+  #
+  # ========================================================================= #
+  def to_dna(
+      i         = sequence?,
+      upcase_me = true
+    )
+    i = sequence? if i.nil?
+    i = ::Bioroebe.to_dna(i, upcase_me)
+    return i
+  end; alias dna to_dna # === dna
+
+  # ========================================================================= #
+  # === to_dna
+  # ========================================================================= #
+  # def to_dna
+  #   seq?.tr('U','T')
+  # end; alias dna to_dna # === dna
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME