bioroebe 0.10.80 → 0.11.12
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- checksums.yaml +4 -4
- data/README.md +507 -310
- data/bioroebe.gemspec +3 -3
- data/doc/README.gen +506 -309
- data/doc/todo/bioroebe_todo.md +29 -40
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
- data/lib/bioroebe/base/commandline_application/misc.rb +18 -8
- data/lib/bioroebe/base/prototype/misc.rb +1 -1
- data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
- data/lib/bioroebe/constants/files_and_directories.rb +8 -1
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
- data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
- data/lib/bioroebe/python/README.md +1 -0
- data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
- data/lib/bioroebe/python/gui/gtk3/widget1.py +22 -0
- data/lib/bioroebe/python/mymodule.py +8 -0
- data/lib/bioroebe/python/protein_to_dna.py +30 -0
- data/lib/bioroebe/python/shell/shell.py +19 -0
- data/lib/bioroebe/python/to_rna.py +14 -0
- data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
- data/lib/bioroebe/sequence/sequence.rb +54 -2
- data/lib/bioroebe/shell/menu.rb +3336 -3304
- data/lib/bioroebe/shell/readline/readline.rb +1 -1
- data/lib/bioroebe/shell/shell.rb +11233 -28
- data/lib/bioroebe/siRNA/siRNA.rb +81 -1
- data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
- metadata +17 -36
- data/doc/setup.rb +0 -1655
- data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
- data/lib/bioroebe/shell/add.rb +0 -108
- data/lib/bioroebe/shell/assign.rb +0 -360
- data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
- data/lib/bioroebe/shell/constants.rb +0 -166
- data/lib/bioroebe/shell/download.rb +0 -335
- data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
- data/lib/bioroebe/shell/enzymes.rb +0 -310
- data/lib/bioroebe/shell/fasta.rb +0 -345
- data/lib/bioroebe/shell/gtk.rb +0 -76
- data/lib/bioroebe/shell/history.rb +0 -132
- data/lib/bioroebe/shell/initialize.rb +0 -217
- data/lib/bioroebe/shell/loop.rb +0 -74
- data/lib/bioroebe/shell/misc.rb +0 -4341
- data/lib/bioroebe/shell/prompt.rb +0 -107
- data/lib/bioroebe/shell/random.rb +0 -289
- data/lib/bioroebe/shell/reset.rb +0 -335
- data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
- data/lib/bioroebe/shell/search.rb +0 -337
- data/lib/bioroebe/shell/sequences.rb +0 -200
- data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
- data/lib/bioroebe/shell/startup.rb +0 -127
- data/lib/bioroebe/shell/taxonomy.rb +0 -14
- data/lib/bioroebe/shell/tk.rb +0 -23
- data/lib/bioroebe/shell/user_input.rb +0 -88
- data/lib/bioroebe/shell/xorg.rb +0 -45
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@@ -188,6 +188,20 @@ class Sequence < ::Bioroebe::RawSequence
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@internal_hash[:type]
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end; alias type type? # === type
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# ========================================================================= #
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# === index
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# ========================================================================= #
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def index(i)
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@sequence.index(i)
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end
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# ========================================================================= #
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# === size?
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# ========================================================================= #
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def size?
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@sequence.size
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end
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# ========================================================================= #
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# === to_regexp
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#
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@@ -334,7 +348,7 @@ class Sequence < ::Bioroebe::RawSequence
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# ===================================================================== #
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sequence?.tr!('T','U') if sequence?
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end
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-
end
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end; alias normalize sanitize_dataset # === normalize
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# ========================================================================= #
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# === set_type
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@@ -484,7 +498,8 @@ class Sequence < ::Bioroebe::RawSequence
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# ===================================================================== #
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# === :do_not_downcase
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# ===================================================================== #
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when :do_not_downcase
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when :do_not_downcase,
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:make_no_modification
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# Make no modification in this case.
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# ===================================================================== #
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# === :do_upcase
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@@ -526,6 +541,16 @@ class Sequence < ::Bioroebe::RawSequence
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end; alias set_rna_type set_rna # === set_rna_type
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alias convert_to_rna set_rna # === convert_to_rna
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# ========================================================================= #
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# === automatic_support_for_nucleotides
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#
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# This adds automatic support for RNA and DNA to this sequence object.
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# ========================================================================= #
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def automatic_support_for_nucleotides
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require 'bioroebe/sequence/nucleotide_module/nucleotide_module.rb'
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extend(Bioroebe::NucleotideModule)
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end
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# ========================================================================= #
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# === set_dna
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# ========================================================================= #
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@@ -544,6 +569,33 @@ class Sequence < ::Bioroebe::RawSequence
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}.join
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end
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# ========================================================================= #
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# === remove_invalid_entries_from_the_dna_sequence!
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# ========================================================================= #
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def remove_invalid_entries_from_the_dna_sequence!(i = sequence?)
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result = i.chars.select {|character|
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DNA_NUCLEOTIDES.include? character.upcase
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}.join
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set_sequence(result)
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end
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# ========================================================================= #
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# === randomize
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#
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# Usage example:
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#
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# x = Bioroebe::Sequence.new; x.randomize
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#
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# ========================================================================= #
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def randomize(
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i = { 'A'=>1,'C'=>2,'G'=>3,'T'=>4 }
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)
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if i.is_a? Hash
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i = i.map{|key, value| "#{key * value}" }.join
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end
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::Bioroebe.random_dna(size?, i) # => "GGTAGGGGGGGGTAGGGGGG"
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end
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# ========================================================================= #
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# === Bioroebe::Sequence.sequence_from_file
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#
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