bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -0
@@ -0,0 +1,416 @@
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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# =========================================================================== #
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# require 'bioroebe/codons/codon_table.rb'
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# Bioroebe.codon_table_in_use?
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# Bioroebe.codon_table_dataset?
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# =========================================================================== #
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module Bioroebe
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require 'bioroebe/requires/require_yaml.rb'
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# ========================================================================= #
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# {"TAA"=>"*", "TGA"=>'*',"CCA"=>"P", ...
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#
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# and so forth.
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# ========================================================================= #
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def self.codon_table_dataset?
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@codon_table_dataset
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end
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#
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# method anyway.
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#
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# Example:
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#
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# ========================================================================= #
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def self.set_codon_table_in_use(
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)
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end
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case be_verbose
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when :be_verbose
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be_verbose = :be_verbose
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end
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if be_verbose
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e 'We will use this codon table next:'
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p use_this_codon_table
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end
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@codon_table_in_use = i
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end; self.instance_eval { alias codon_table= set_codon_table_in_use } # === Bioroebe.codon_table=
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self.instance_eval { alias set_codon_table set_codon_table_in_use } # === Bioroebe.set_codon_table
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# ========================================================================= #
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# === Bioroebe.codon_table_in_use?
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#
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# Query method to return the currently used codon table.
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# ========================================================================= #
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def self.codon_table_in_use?
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@codon_table_in_use
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end; self.instance_eval { alias codon_table? codon_table_in_use? } # === Bioroebe.codon_table?
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self.instance_eval { alias codons codon_table_in_use? } # === Bioroebe.codons
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# ========================================================================= #
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# === Bioroebe.load_the_codon_table_dataset
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#
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# Several aliases can be used as input for this method, such as:
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#
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# Bioroebe.load_the_codon_table_dataset(:codons_of_the_aminoacids)
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#
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# ========================================================================= #
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def self.load_the_codon_table_dataset(
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use_this_codon_table = @codon_table_in_use
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)
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this_file = nil
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# ======================================================================= #
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# We ideally prefer a Symbol here as input, but we won't force it.
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# shall be able to supply a String too, onto which we can then
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# use a regex. Thus, we have to extend the following entries to
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# last position.
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# ======================================================================= #
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case use_this_codon_table # case tag
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# ======================================================================= #
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# === :human
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# ======================================================================= #
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when :human,
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:humans,
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:default,
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:codons_of_the_aminoacids,
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/^Standard(-|_| |,)?\(?Eukaryote\)?$/i,
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/^human?$/i,
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1
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this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/1.yml"
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# ======================================================================= #
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# === :mitochondria
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#
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# This actually refers to "The Vertebrate Mitochondrial Code".
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# ======================================================================= #
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when :mitochondria,
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:vertebrate_mitochondria,
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/^Vertebrate(-|_| |,)?Mitochondrial$/i,
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2
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this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/2.yml"
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# ======================================================================= #
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# === :yeast_mitochondria
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# ======================================================================= #
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when :yeast_mitochondrial_code,
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:yeast_mitochondria,
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:yeast_mt,
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/^Yeast(-|_| |,)?Mitochondrial$/i,
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3
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this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/3.yml"
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# ======================================================================= #
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# === Coelenterate Mitochondrial Code
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# ======================================================================= #
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when 4,
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/^Coelenterate(-|_| |,)?Mitochondrial$/i,
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/^Coelenterate(-|_| |,)?Mitochondrial(-|_| |,)?Code$/i,
|
142
|
+
/^Mold(-|_| |,)?(-|_| |,)?Protozoan(-|_| |,)?(-|_| |,)?Coelenterate(-|_| |,)?Mitochondrial(-|_| |,)?and(-|_| |,)?Mycoplasma\/Spiroplasma$/i
|
143
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/4.yml"
|
144
|
+
# ======================================================================= #
|
145
|
+
# === 5
|
146
|
+
# ======================================================================= #
|
147
|
+
when 5,
|
148
|
+
/^Invertebrate(-|_| |,)?Mitochondrial$/i
|
149
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/5.yml"
|
150
|
+
# ======================================================================= #
|
151
|
+
# === 6
|
152
|
+
# ======================================================================= #
|
153
|
+
when 6,
|
154
|
+
/^Ciliate(-|_| |,)?Macronuclear(-|_| |,)?and(-|_| |,)?Dasycladacean$/i
|
155
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/6.yml"
|
156
|
+
# ======================================================================= #
|
157
|
+
# === 7
|
158
|
+
# ======================================================================= #
|
159
|
+
when 7
|
160
|
+
e 'No codon table 7 exists. Please avoid calling it.'
|
161
|
+
# ======================================================================= #
|
162
|
+
# === 8
|
163
|
+
# ======================================================================= #
|
164
|
+
when 8
|
165
|
+
e 'No codon table 8 exists. Please avoid calling it.'
|
166
|
+
# ======================================================================= #
|
167
|
+
# === 9
|
168
|
+
# ======================================================================= #
|
169
|
+
when 9,
|
170
|
+
/^Echinoderm(-|_| |,)?Mitochondrial$/i
|
171
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/9.yml"
|
172
|
+
# ======================================================================= #
|
173
|
+
# === 11
|
174
|
+
# ======================================================================= #
|
175
|
+
when 10,
|
176
|
+
/^Euplotid(-|_| |,)?Nuclear$/i
|
177
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/10.yml"
|
178
|
+
# ======================================================================= #
|
179
|
+
# === :bacteria
|
180
|
+
#
|
181
|
+
# This is the codon-table for bacteria, including E. coli.
|
182
|
+
# ======================================================================= #
|
183
|
+
when :bacteria,
|
184
|
+
:bacterium,
|
185
|
+
:prokaryotes,
|
186
|
+
:ecoli,
|
187
|
+
:e_coli,
|
188
|
+
11,
|
189
|
+
/^Bacteria$/i
|
190
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/11.yml"
|
191
|
+
# ======================================================================= #
|
192
|
+
# === 11
|
193
|
+
# ======================================================================= #
|
194
|
+
when 12,
|
195
|
+
/^Alternative(-|_| |,)?Yeast(-|_| |,)?Nuclear$/i
|
196
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/12.yml"
|
197
|
+
# ======================================================================= #
|
198
|
+
# === 13
|
199
|
+
# ======================================================================= #
|
200
|
+
when 13,
|
201
|
+
/^Ascidian(-|_| |,)?Mitochondrial$/i
|
202
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/13.yml"
|
203
|
+
# ======================================================================= #
|
204
|
+
# === 14
|
205
|
+
# ======================================================================= #
|
206
|
+
when 14,
|
207
|
+
/^Flatworm(-|_| |,)?Mitochondrial$/i
|
208
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/14.yml"
|
209
|
+
# ======================================================================= #
|
210
|
+
# === Blepharisma Macronuclear
|
211
|
+
#
|
212
|
+
# This refers to a unicellular protist. See:
|
213
|
+
#
|
214
|
+
# https://en.wikipedia.org/wiki/Blepharisma
|
215
|
+
#
|
216
|
+
# ======================================================================= #
|
217
|
+
when :blepharisma_macronuclear,
|
218
|
+
15,
|
219
|
+
/^Blepharisma(-|_| |,)?Macronuclear$/i
|
220
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/15.yml"
|
221
|
+
# ======================================================================= #
|
222
|
+
# === Chlorophycean Mitochondrial
|
223
|
+
# ======================================================================= #
|
224
|
+
when :chlorophycean_mitochondrial,
|
225
|
+
16,
|
226
|
+
/^Chlorophycean(-|_| |,)?Mitochondrial$/i
|
227
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/16.yml"
|
228
|
+
# ======================================================================= #
|
229
|
+
# === Trematode Mitochondrial Code
|
230
|
+
# ======================================================================= #
|
231
|
+
when :trematode_mitochondrial_code,
|
232
|
+
21,
|
233
|
+
/^Trematode(-|_| |,)?Mitochondrial$/i
|
234
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/21.yml"
|
235
|
+
# ======================================================================= #
|
236
|
+
# === Scenedesmus obliquus mitochondrial
|
237
|
+
# ======================================================================= #
|
238
|
+
when :scenedesmus_obliquus_mitochondrial,
|
239
|
+
22,
|
240
|
+
/^Scenedesmus(-|_| |,)?obliquus(-|_| |,)?mitochondrial$/i
|
241
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/22.yml"
|
242
|
+
# ======================================================================= #
|
243
|
+
# === Thraustochytrium Mitochondrial
|
244
|
+
# ======================================================================= #
|
245
|
+
when :thraustochytrium_mitochondrial,
|
246
|
+
23,
|
247
|
+
/^Thraustochytrium(-|_| |,)?Mitochondrial$/i
|
248
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/23.yml"
|
249
|
+
# ======================================================================= #
|
250
|
+
# === Pterobranchia Mitochondrial
|
251
|
+
# ======================================================================= #
|
252
|
+
when :pterobranchia_mitochondrial,
|
253
|
+
24,
|
254
|
+
/^Pterobranchia(-|_| |,)?Mitochondrial(-|_| |,)?Code$/i
|
255
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/24.yml"
|
256
|
+
# ======================================================================= #
|
257
|
+
# === Candidate Division SR1 and Gracilibacteria Code
|
258
|
+
# ======================================================================= #
|
259
|
+
when :candidate_division_sr1_and_gracilibacteria,
|
260
|
+
25,
|
261
|
+
/^Candidate(-|_| |,)?Division(-|_| |,)?SR1(-|_| |,)?and(-|_| |,)?Gracilibacteria(-|_| |,)?Code$/i
|
262
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/25.yml"
|
263
|
+
# ======================================================================= #
|
264
|
+
# === Pachysolen tannophilus Nuclear Code
|
265
|
+
# ======================================================================= #
|
266
|
+
when :pachysolen_tannophilus_nuclear,
|
267
|
+
:pachysolen_tannophilus_nuclear_code,
|
268
|
+
26,
|
269
|
+
/^Pachysolen(-|_| |,)?tannophilus(-|_| |,)?Nuclear(-|_| |,)?Code$/i
|
270
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/26.yml"
|
271
|
+
# ======================================================================= #
|
272
|
+
# === Karyorelict
|
273
|
+
# ======================================================================= #
|
274
|
+
when :karyorelict,
|
275
|
+
:karyorelict_nuclear_code,
|
276
|
+
27,
|
277
|
+
/^Karyorelict(-|_| |,)?Nuclear$/i
|
278
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/27.yml"
|
279
|
+
# ======================================================================= #
|
280
|
+
# === Condylostoma Nuclear Code
|
281
|
+
# ======================================================================= #
|
282
|
+
when :condylostoma,
|
283
|
+
:condylostoma_nuclear_code,
|
284
|
+
28,
|
285
|
+
/^Condylostoma(-|_| |,)?Nuclear$/i
|
286
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/28.yml"
|
287
|
+
# ======================================================================= #
|
288
|
+
# === Mesodinium Nuclear Code
|
289
|
+
# ======================================================================= #
|
290
|
+
when :mesodinium,
|
291
|
+
:mesodinium_nuclear_code,
|
292
|
+
29,
|
293
|
+
/^Mesodinium(-|_| |,)?Nuclear$/i
|
294
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/29.yml"
|
295
|
+
# ======================================================================= #
|
296
|
+
# === Peritrich Nuclear Code
|
297
|
+
# ======================================================================= #
|
298
|
+
when :peritrich,
|
299
|
+
:peritrich_nuclear_code,
|
300
|
+
30,
|
301
|
+
/^Peritrich(-|_| |,)?Nuclear$/i
|
302
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/30.yml"
|
303
|
+
# ======================================================================= #
|
304
|
+
# === Blastocrithidia Nuclear Code
|
305
|
+
# ======================================================================= #
|
306
|
+
when :blastocrithidia,
|
307
|
+
:blastocrithidia_nuclear_code,
|
308
|
+
31,
|
309
|
+
/^Blastocrithidia(-|_| |,)?Nuclear$/i
|
310
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/31.yml"
|
311
|
+
# ======================================================================= #
|
312
|
+
# === Cephalodiscidae Mitochondrial UAA-Tyr Code
|
313
|
+
# ======================================================================= #
|
314
|
+
when :cephalodiscidae,
|
315
|
+
:cephalodiscidae_nuclear_code,
|
316
|
+
33,
|
317
|
+
/^Cephalodiscidae(-|_| |,)?Mitochondrial(-|_| |,)?UAA-Tyr(-|_| |,)?Code$/i
|
318
|
+
this_file = "#{::Bioroebe.project_yaml_directory?}codon_tables/33.yml"
|
319
|
+
else
|
320
|
+
e "(Line: #{__LINE__}) Unknown input was given "\
|
321
|
+
"to file bioroebe/codons/codon_table.rb: `#{use_this_codon_table}`"
|
322
|
+
end
|
323
|
+
@codon_table_dataset = YAML.load_file(this_file)
|
324
|
+
end
|
325
|
+
|
326
|
+
# ========================================================================= #
|
327
|
+
# === Bioroebe.use_this_codon_table
|
328
|
+
#
|
329
|
+
# This method combines setting a specific codon-table in use, and
|
330
|
+
# it will also load the dataset of that codon table.
|
331
|
+
#
|
332
|
+
# Usage example:
|
333
|
+
#
|
334
|
+
# Bioroebe.use_this_codon_table(:yeast_mitochondria)
|
335
|
+
#
|
336
|
+
# ========================================================================= #
|
337
|
+
def self.use_this_codon_table(i)
|
338
|
+
set_codon_table_in_use(i)
|
339
|
+
load_the_codon_table_dataset
|
340
|
+
end
|
341
|
+
|
342
|
+
# ========================================================================= #
|
343
|
+
# === Bioroebe.set_use_this_codon_table
|
344
|
+
#
|
345
|
+
# This method combines three other methods - it will first set the
|
346
|
+
# codon table in use, and then load the codon table dataset
|
347
|
+
# at once and additionally determine the stop codons from the
|
348
|
+
# codon table.
|
349
|
+
#
|
350
|
+
# It is the most complete method for properly using the correct
|
351
|
+
# codon table. I recommend that you use this method - it is
|
352
|
+
# more convenient than the other methods.
|
353
|
+
# ========================================================================= #
|
354
|
+
def self.set_use_this_codon_table(i = :humans)
|
355
|
+
set_codon_table_in_use(i)
|
356
|
+
load_the_codon_table_dataset(i)
|
357
|
+
determine_stop_codons_from_the_codon_table
|
358
|
+
end
|
359
|
+
|
360
|
+
load_the_codon_table_dataset # ← Initialize it at once.
|
361
|
+
|
362
|
+
module CodonTable
|
363
|
+
|
364
|
+
# ========================================================================= #
|
365
|
+
# === Bioroebe::CodonTable[]
|
366
|
+
#
|
367
|
+
# This method will return a Hash containing the codon table for the
|
368
|
+
# given organism/species at hand. It will NOT modify the main codon
|
369
|
+
# table in use.
|
370
|
+
#
|
371
|
+
# For a list of these codons, see this page:
|
372
|
+
#
|
373
|
+
# https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
|
374
|
+
#
|
375
|
+
# To obtain the human codon table, do either of the following:
|
376
|
+
#
|
377
|
+
# human_codon_table = Bioroebe::CodonTable[:human]
|
378
|
+
# human_codon_table = Bioroebe::CodonTable[1]
|
379
|
+
#
|
380
|
+
# Usage example:
|
381
|
+
#
|
382
|
+
# Bioroebe::CodonTable[2]
|
383
|
+
#
|
384
|
+
# ========================================================================= #
|
385
|
+
def self.[](i)
|
386
|
+
::Bioroebe.load_the_codon_table_dataset(i)
|
387
|
+
end
|
388
|
+
|
389
|
+
# ========================================================================= #
|
390
|
+
# === Bioroebe::CodonTable.by_name
|
391
|
+
#
|
392
|
+
# This method can be used to return the proper codon-table dataset. It
|
393
|
+
# will additionally change the main codon table in use for the
|
394
|
+
# Bioroebe "namespace". If you wish to avoid this, consider using
|
395
|
+
# Bioroebe::CodonTable[] instead.
|
396
|
+
#
|
397
|
+
# Usage example:
|
398
|
+
#
|
399
|
+
# x = Bioroebe::CodonTable.by_name("Vertebrate Mitochondrial")
|
400
|
+
#
|
401
|
+
# ========================================================================= #
|
402
|
+
def self.by_name(i = 'Vertebrate Mitochondrial')
|
403
|
+
::Bioroebe.set_use_this_codon_table(i)
|
404
|
+
return ::Bioroebe.codon_table_dataset?
|
405
|
+
end; self.instance_eval { alias by_id by_name } # === Bioroebe::CodonTable.by_id
|
406
|
+
|
407
|
+
end
|
408
|
+
|
409
|
+
end
|
410
|
+
|
411
|
+
if __FILE__ == $PROGRAM_NAME
|
412
|
+
Bioroebe.set_use_this_codon_table(:human)
|
413
|
+
pp Bioroebe.stop_codons?
|
414
|
+
Bioroebe.set_use_this_codon_table(:bacteria)
|
415
|
+
pp Bioroebe.stop_codons?
|
416
|
+
end
|
@@ -0,0 +1,123 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe.codon_tables
|
6
|
+
#
|
7
|
+
# The dataset for the codon tables is stored in several different
|
8
|
+
# yaml files.
|
9
|
+
# =========================================================================== #
|
10
|
+
# require 'bioroebe/codons/codon_tables.rb'
|
11
|
+
# =========================================================================== #
|
12
|
+
module Bioroebe
|
13
|
+
|
14
|
+
require 'bioroebe/project/project.rb'
|
15
|
+
|
16
|
+
# ========================================================================= #
|
17
|
+
# === Bioroebe.codon_tables
|
18
|
+
#
|
19
|
+
# This method will return all codon tables that we have registered.
|
20
|
+
#
|
21
|
+
# This is probably not so terribly useful for most projects, but
|
22
|
+
# in the event that you do need all codon tables, you can use
|
23
|
+
# this method.
|
24
|
+
#
|
25
|
+
# The result will be a Hash having key->value pairs such as:
|
26
|
+
#
|
27
|
+
# "9" => {"TAA"=>"*", "TAG"=>"*"
|
28
|
+
#
|
29
|
+
# ========================================================================= #
|
30
|
+
def self.codon_tables
|
31
|
+
require 'bioroebe/requires/require_yaml.rb'
|
32
|
+
hash = {}
|
33
|
+
_ = "#{yaml_directory?}codon_tables/*.yml"
|
34
|
+
all_files = Dir[_].sort
|
35
|
+
all_files.each {|yaml_file|
|
36
|
+
next if yaml_file.end_with? 'overview.yml' # We reject this one here.
|
37
|
+
dataset = YAML.load_file(yaml_file)
|
38
|
+
entry_number = File.basename(yaml_file).delete_suffix('.yml')
|
39
|
+
dataset = { entry_number => dataset}
|
40
|
+
hash.merge!(dataset)
|
41
|
+
}
|
42
|
+
hash
|
43
|
+
end
|
44
|
+
|
45
|
+
module CodonTables # CodonTables::CODON_TABLES
|
46
|
+
|
47
|
+
# ========================================================================= #
|
48
|
+
# === Bioroebe::CodonTables::DEFINITIONS
|
49
|
+
#
|
50
|
+
# Some of the basic definitions are stored here.
|
51
|
+
#
|
52
|
+
# The table in this .rb file was last updated manually in August 2021.
|
53
|
+
#
|
54
|
+
# They can be found here:
|
55
|
+
#
|
56
|
+
# https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t
|
57
|
+
#
|
58
|
+
# The numbers here are taken from the above URL.
|
59
|
+
# ========================================================================= #
|
60
|
+
DEFINITIONS = {
|
61
|
+
1 => 'Standard (Eukaryote)',
|
62
|
+
2 => 'Vertebrate Mitochondrial',
|
63
|
+
3 => 'Yeast Mitochondrial',
|
64
|
+
4 => 'Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma',
|
65
|
+
5 => 'Invertebrate Mitochondrial',
|
66
|
+
6 => 'Ciliate Macronuclear and Dasycladacean',
|
67
|
+
9 => 'Echinoderm Mitochondrial',
|
68
|
+
10 => 'Euplotid Nuclear',
|
69
|
+
11 => 'Bacteria',
|
70
|
+
12 => 'Alternative Yeast Nuclear',
|
71
|
+
13 => 'Ascidian Mitochondrial',
|
72
|
+
14 => 'Flatworm Mitochondrial',
|
73
|
+
15 => 'Blepharisma Macronuclear',
|
74
|
+
16 => 'Chlorophycean Mitochondrial',
|
75
|
+
21 => 'Trematode Mitochondrial',
|
76
|
+
22 => 'Scenedesmus obliquus mitochondrial',
|
77
|
+
23 => 'Thraustochytrium Mitochondrial',
|
78
|
+
24 => 'Pterobranchia Mitochondrial Code',
|
79
|
+
25 => 'Candidate Division SR1 and Gracilibacteria Code',
|
80
|
+
26 => 'Pachysolen tannophilus Nuclear Code',
|
81
|
+
27 => 'Karyorelict Nuclear',
|
82
|
+
28 => 'Condylostoma Nuclear',
|
83
|
+
29 => 'Mesodinium Nuclear',
|
84
|
+
30 => 'Peritrich Nuclear',
|
85
|
+
31 => 'Blastocrithidia Nuclear',
|
86
|
+
33 => 'Cephalodiscidae Mitochondrial UAA-Tyr Code'
|
87
|
+
}
|
88
|
+
|
89
|
+
# ========================================================================= #
|
90
|
+
# === Bioroebe::CodonTables.human_codon_table?
|
91
|
+
# ========================================================================= #
|
92
|
+
def self.human_codon_table?
|
93
|
+
1
|
94
|
+
end
|
95
|
+
|
96
|
+
# ========================================================================= #
|
97
|
+
# === Bioroebe::CodonTables.definitions?
|
98
|
+
# ========================================================================= #
|
99
|
+
def self.definitions?
|
100
|
+
DEFINITIONS
|
101
|
+
end
|
102
|
+
|
103
|
+
# ========================================================================= #
|
104
|
+
# === Bioroebe::CodonTables.title_for_entry_number?
|
105
|
+
# ========================================================================= #
|
106
|
+
def self.title_for_entry_number?(i = 1)
|
107
|
+
DEFINITIONS[i.to_i]
|
108
|
+
end
|
109
|
+
|
110
|
+
end
|
111
|
+
|
112
|
+
# =========================================================================== #
|
113
|
+
# === Bioroebe.hash_codon_tables?
|
114
|
+
# =========================================================================== #
|
115
|
+
def self.hash_codon_tables?
|
116
|
+
::Bioroebe::CodonTables.definitions?
|
117
|
+
end
|
118
|
+
|
119
|
+
end
|
120
|
+
|
121
|
+
if __FILE__ == $PROGRAM_NAME
|
122
|
+
pp Bioroebe.codon_tables
|
123
|
+
end # rb codon_tables.rb
|