bioroebe 0.12.24 → 0.13.31
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- checksums.yaml +4 -4
- data/LICENSE.md +7 -8
- data/README.md +566 -354
- data/bin/all_positions_of_this_nucleotide +1 -1
- data/bin/aminoacid_frequencies +1 -1
- data/bin/automatically_rename_this_fasta_file +1 -1
- data/bin/base_composition +1 -1
- data/bin/batch_create_windows_executables +1 -1
- data/bin/bioroebe +12 -1
- data/bin/bioroebe_cat +7 -0
- data/bin/calculate_exponential_growth +7 -0
- data/bin/calculate_n50_value +1 -1
- data/bin/calculate_the_frequencies_of_this_species +7 -0
- data/bin/chunked_display +1 -1
- data/bin/codon_frequency +1 -1
- data/bin/codon_to_aminoacid +1 -1
- data/bin/colourize_this_fasta_sequence +1 -1
- data/bin/complementary_dna_strand +1 -1
- data/bin/complementary_rna_strand +1 -1
- data/bin/consensus_sequence +1 -1
- data/bin/dna_to_rna +1 -1
- data/bin/downcase_chunked_display +1 -1
- data/bin/download_this_pdb +1 -1
- data/bin/fasta_index +1 -1
- data/bin/fetch_data_from_uniprot +1 -1
- data/bin/filter_away_invalid_nucleotides +1 -1
- data/bin/find_substring +1 -1
- data/bin/input_as_dna +1 -1
- data/bin/is_palindrome +1 -1
- data/bin/leading_five_prime +1 -1
- data/bin/longest_ORF +1 -1
- data/bin/longest_substring +1 -1
- data/bin/open_reading_frames +1 -1
- data/bin/partner_nucleotide +1 -1
- data/bin/plain_palindrome +1 -1
- data/bin/random_dna_sequence +1 -1
- data/bin/random_sequence +1 -1
- data/bin/raw_hamming_distance +1 -1
- data/bin/return_longest_substring_via_LCS_algorithm +1 -1
- data/bin/reverse_sequence +1 -1
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
- data/bin/show_atomic_composition +1 -1
- data/bin/show_fasta_header +1 -1
- data/bin/show_nucleotide_sequence +1 -1
- data/bin/show_this_dna_sequence +1 -1
- data/bin/show_time_now +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
- data/bin/strict_filter_away_invalid_aminoacids +1 -1
- data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
- data/bin/three_to_one +1 -1
- data/bin/to_rna +1 -1
- data/bin/trailing_three_prime +1 -1
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
- data/bioroebe.gemspec +6 -7
- data/doc/README.gen +534 -322
- data/doc/blosum/blosum.md +4 -0
- data/doc/compatibility/BIO_PHP.md +20 -18
- data/doc/compatibility/README.md +2 -3
- data/doc/compatibility/emboss.md +5 -3
- data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
- data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
- data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
- data/doc/statistics/statistics.md +12 -10
- data/doc/todo/bioroebe_GUI_todo.md +6 -1
- data/doc/todo/bioroebe_java_todo.md +3 -2
- data/doc/todo/bioroebe_todo.md +328 -310
- data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
- data/lib/bioroebe/abstract/features.rb +0 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
- data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
- data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
- data/lib/bioroebe/base/base.rb +101 -6
- data/lib/bioroebe/base/base_module/base_module.rb +9 -1
- data/lib/bioroebe/base/colours.rb +3 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
- data/lib/bioroebe/base/commandline_application/README.md +1 -1
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +661 -22
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
- data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
- data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
- data/lib/bioroebe/base/prototype/prototype.rb +155 -14
- data/lib/bioroebe/biomart/attribute.rb +1 -1
- data/lib/bioroebe/biomart/biomart.rb +8 -9
- data/lib/bioroebe/biomart/server.rb +1 -1
- data/lib/bioroebe/blosum/blosum.rb +2 -2
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
- data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
- data/lib/bioroebe/cell/cell.rb +3 -2
- data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
- data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
- data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
- data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
- data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
- data/lib/bioroebe/codons/codon_table.rb +10 -2
- data/lib/bioroebe/codons/codons.rb +3 -3
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
- data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
- data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
- data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
- data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
- data/lib/bioroebe/codons/start_codons.rb +7 -3
- data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
- data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
- data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
- data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
- data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
- data/lib/bioroebe/colours/colours.rb +172 -15
- data/lib/bioroebe/configuration/configuration.rb +1 -1
- data/lib/bioroebe/constants/GUIs.rb +2 -2
- data/lib/bioroebe/constants/constants.rb +1349 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +9 -3
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
- data/lib/bioroebe/count/count_at.rb +2 -1
- data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
- data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +6 -6
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
- data/lib/bioroebe/ext/main.cpp +0 -1
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +8 -14
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
- data/lib/bioroebe/genome/genome.rb +1 -1
- data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
- data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
- data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
- data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
- data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
- data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
- data/lib/bioroebe/gui/{shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb → universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb} +297 -107
- data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
- data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
- data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
- data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
- data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
- data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
- data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
- data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb} +228 -47
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
- data/lib/bioroebe/images/images.html +953 -1170
- data/lib/bioroebe/images/misc/README.md +6 -0
- data/lib/bioroebe/images/misc/activation.avif +0 -0
- data/lib/bioroebe/images/misc/inhibition.avif +0 -0
- data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
- data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
- data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
- data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
- data/lib/bioroebe/misc/ruler.rb +5 -5
- data/lib/bioroebe/misc/useful_formulas.rb +3 -3
- data/lib/bioroebe/ncbi/efetch.rb +1 -2
- data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
- data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
- data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
- data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
- data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
- data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
- data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
- data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
- data/lib/bioroebe/parsers/gff.rb +9 -9
- data/lib/bioroebe/parsers/parse_embl.rb +2 -6
- data/lib/bioroebe/parsers/stride_parser.rb +4 -12
- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
- data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
- data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
- data/lib/bioroebe/project/project.rb +3 -1
- data/lib/bioroebe/raw_sequence/README.md +8 -8
- data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
- data/lib/bioroebe/regexes/regexes.rb +1 -2
- data/lib/bioroebe/requires/commandline_application.rb +3 -1
- data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
- data/lib/bioroebe/requires/require_colours.rb +1 -1
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
- data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
- data/lib/bioroebe/requires/require_the_constants.rb +2 -14
- data/lib/bioroebe/requires/require_yaml.rb +7 -5
- data/lib/bioroebe/sequence/alignment.rb +1 -1
- data/lib/bioroebe/sequence/dna.rb +4 -2
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
- data/lib/bioroebe/sequence/protein.rb +2 -2
- data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
- data/lib/bioroebe/sequence/rna.rb +9 -8
- data/lib/bioroebe/sequence/sequence.rb +3 -3
- data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
- data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
- data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
- data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
- data/lib/bioroebe/shell/help/class.rb +68 -19
- data/lib/bioroebe/shell/menu.rb +5244 -5322
- data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
- data/lib/bioroebe/shell/shell.rb +11240 -453
- data/lib/bioroebe/siRNA/siRNA.rb +3 -3
- data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
- data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
- data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
- data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
- data/lib/bioroebe/string_matching/hamming_distance.rb +11 -10
- data/lib/bioroebe/string_matching/levensthein.rb +5 -17
- data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
- data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
- data/lib/bioroebe/svg/glyph.rb +4 -1
- data/lib/bioroebe/svg/mini_feature.rb +1 -1
- data/lib/bioroebe/svg/page.rb +18 -7
- data/lib/bioroebe/svg/svgee.rb +22 -13
- data/lib/bioroebe/svg/track.rb +20 -4
- data/lib/bioroebe/taxonomy/chart.rb +2 -2
- data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
- data/lib/bioroebe/taxonomy/constants.rb +1 -1
- data/lib/bioroebe/taxonomy/info/info.rb +1 -1
- data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
- data/lib/bioroebe/taxonomy/interactive.rb +1 -2
- data/lib/bioroebe/taxonomy/menu.rb +1 -1
- data/lib/bioroebe/taxonomy/node.rb +1 -1
- data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
- data/lib/bioroebe/taxonomy/shared.rb +5 -4
- data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
- data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
- data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5568 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
- data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
- data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
- data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
- data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
- data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
- data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
- data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
- data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
- data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
- data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
- data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
- data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
- data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
- data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
- data/lib/bioroebe/virus/virus.rb +76 -0
- data/lib/bioroebe/www/bioroebe.cgi +4 -3
- data/lib/bioroebe/www/embeddable_interface.rb +85 -49
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
- data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
- data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
- data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
- data/spec/testing_toplevel_method_editor.rb +1 -1
- data/spec/testing_toplevel_method_verbose.rb +1 -1
- data/test/testing_dna_to_rna_conversion.rb +1 -1
- metadata +127 -235
- data/doc/blosum.md +0 -5
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
- data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
- data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
- data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
- data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
- data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
- data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
- data/lib/bioroebe/base/initialize.rb +0 -18
- data/lib/bioroebe/base/misc.rb +0 -129
- data/lib/bioroebe/base/namespace.rb +0 -16
- data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
- data/lib/bioroebe/base/prototype/misc.rb +0 -114
- data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
- data/lib/bioroebe/base/prototype/reset.rb +0 -36
- data/lib/bioroebe/colours/misc_colours.rb +0 -80
- data/lib/bioroebe/colours/rev.rb +0 -44
- data/lib/bioroebe/colours/sdir.rb +0 -21
- data/lib/bioroebe/colours/sfancy.rb +0 -21
- data/lib/bioroebe/colours/sfile.rb +0 -21
- data/lib/bioroebe/colours/simp.rb +0 -21
- data/lib/bioroebe/colours/swarn.rb +0 -29
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
- data/lib/bioroebe/constants/carriage_return.rb +0 -14
- data/lib/bioroebe/constants/codon_tables.rb +0 -77
- data/lib/bioroebe/constants/database_constants.rb +0 -107
- data/lib/bioroebe/constants/files_and_directories.rb +0 -606
- data/lib/bioroebe/constants/misc.rb +0 -209
- data/lib/bioroebe/constants/newline.rb +0 -14
- data/lib/bioroebe/constants/nucleotides.rb +0 -121
- data/lib/bioroebe/constants/regex.rb +0 -28
- data/lib/bioroebe/constants/roebe.rb +0 -38
- data/lib/bioroebe/constants/row_terminator.rb +0 -16
- data/lib/bioroebe/constants/tabulator.rb +0 -14
- data/lib/bioroebe/constants/unicode.rb +0 -12
- data/lib/bioroebe/constants/urls.rb +0 -50
- data/lib/bioroebe/gui/gtk +0 -1
- data/lib/bioroebe/gui/gtk3/README.md +0 -2
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
- data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
- data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
- data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
- data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
- data/lib/bioroebe/gui/libui/README.md +0 -4
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
- data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
- data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
- data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
- data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
- data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
- data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
- data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
- data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
- data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
- data/lib/bioroebe/shell/colours/colours.rb +0 -235
- data/lib/bioroebe/shell/help/help.rb +0 -25
- data/lib/bioroebe/shell/misc.rb +0 -10227
- data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
- data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
- data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
- data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
- data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
- data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
- data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
- data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
- data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
- data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
- data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
- data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
- data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
- data/lib/bioroebe/toplevel_methods/e.rb +0 -20
- data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
- data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
- data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
- data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
- data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
- data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
- data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
- data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
- data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
- data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
- data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
- data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
- data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
- data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
- data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
- data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
- data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
- data/lib/bioroebe/toplevel_methods/url.rb +0 -36
- data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
- data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
- data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
- data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
- /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
- /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
- /data/doc/{resources.md → resources/resources.md} +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
- /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
- /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
- /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
@@ -11,21 +11,105 @@
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# =========================================================================== #
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# require 'bioroebe/utility_scripts/showorf/showorf.rb'
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# =========================================================================== #
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require 'bioroebe/
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require 'bioroebe/utility_scripts/showorf/constants.rb'
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require 'bioroebe/utility_scripts/showorf/help.rb'
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require 'bioroebe/utility_scripts/showorf/initialize.rb'
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require 'bioroebe/utility_scripts/showorf/menu.rb'
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require 'bioroebe/utility_scripts/showorf/reset.rb'
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require 'bioroebe/utility_scripts/showorf/show.rb'
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require 'bioroebe/utility_scripts/showorf/run.rb'
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require 'bioroebe/requires/commandline_application.rb'
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module Bioroebe
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class ShowOrf < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowOrf
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require 'bioroebe/codons/
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require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
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# ========================================================================= #
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# === COLOURIZE_VERTICAL_TOKEN
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# ========================================================================= #
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COLOURIZE_VERTICAL_TOKEN = true
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# ========================================================================= #
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# === LIMIT_AT_N_NUCLEOTIDES
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#
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# How many nucleotides we will display per given row.
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#
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# This should not be a too high value, because it may otherwise overflow
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# into the next line.
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# ========================================================================= #
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LIMIT_AT_N_NUCLEOTIDES = 100
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# ========================================================================= #
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# === COLOURIZE_STOP_CODONS_IN_RED
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#
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# If true then all '*' will become red.
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# ========================================================================= #
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COLOURIZE_STOP_CODONS_IN_RED = true
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# ========================================================================= #
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# === initialize
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#
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# The first argument to this method should be the DNA nucleotide
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# string whose ORF you wish to show.
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#
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# The second argument to this method determines which frames to show.
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#
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# The class assumes that the first input given is an Array, such as
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# ARGV in particular.
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# ========================================================================= #
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def initialize(
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i = ARGV, # The input should be an Array.
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show_these_frames = [:frame1],
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run_already = true
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)
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reset
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# ======================================================================= #
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# First set up the default frames. This can be overruled lateron,
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# in particular upon the invocation of the method called
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# obtain_commandline_arguments_and_reject_double_separators.
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# ======================================================================= #
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set_show_these_frames(show_these_frames)
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# ======================================================================= #
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# === Handle blocks next
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# ======================================================================= #
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if block_given?
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yielded = yield
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case yielded
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when :show_three_frames
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set_show_these_frames(:show_three_frames)
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else
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set_show_these_frames(yielded)
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end
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end
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# ======================================================================= #
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# Next, set the input sequence.
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# ======================================================================= #
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i = obtain_commandline_arguments_and_reject_double_separators(i)
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set_input_sequence(i)
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run if run_already
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85
|
+
end
|
86
|
+
|
87
|
+
# ========================================================================= #
|
88
|
+
# === reset
|
89
|
+
# ========================================================================= #
|
90
|
+
def reset
|
91
|
+
super()
|
92
|
+
infer_the_namespace
|
93
|
+
# ======================================================================= #
|
94
|
+
# === @show_these_frames
|
95
|
+
#
|
96
|
+
# Specify which frames are to be shown.
|
97
|
+
#
|
98
|
+
# By default, we will show all 3 forward and all 3 reverse frames.
|
99
|
+
#
|
100
|
+
# This can change on the commandline. For example,
|
101
|
+
# showorf ATGCGC --only-frame-1 would keep only :frame1
|
102
|
+
# in this array.
|
103
|
+
# ======================================================================= #
|
104
|
+
@show_these_frames = [
|
105
|
+
:frame1,
|
106
|
+
:frame2,
|
107
|
+
:frame3,
|
108
|
+
:reverse_frame1,
|
109
|
+
:reverse_frame2,
|
110
|
+
:reverse_frame3,
|
111
|
+
]
|
112
|
+
end
|
29
113
|
|
30
114
|
# ========================================================================= #
|
31
115
|
# === set_show_these_frames
|
@@ -80,6 +164,29 @@ class ShowOrf < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowOrf
|
|
80
164
|
]
|
81
165
|
end
|
82
166
|
end
|
167
|
+
# ========================================================================= #
|
168
|
+
# === show_help (help tag)
|
169
|
+
#
|
170
|
+
# Invocation example:
|
171
|
+
#
|
172
|
+
# showorf --help
|
173
|
+
#
|
174
|
+
# ========================================================================= #
|
175
|
+
def show_help
|
176
|
+
e
|
177
|
+
opnerev 'This class is capable of showing the ORF (open '\
|
178
|
+
'reading frame) from the'
|
179
|
+
opnerev 'given input string (which is assumed to be a '\
|
180
|
+
'nucleotide sequence).'
|
181
|
+
e
|
182
|
+
opnerev 'By default, this class will show all 3 reading frames, but'
|
183
|
+
opnerev 'you can also selectively show only one frame. Examples:'
|
184
|
+
e
|
185
|
+
opnerev ' --frame1 # show reading frame1 (forward frame 1)'
|
186
|
+
opnerev ' --frame2 # show reading frame1 (forward frame 2)'
|
187
|
+
opnerev ' --frame3 # show reading frame1 (forward frame 3)'
|
188
|
+
e
|
189
|
+
end
|
83
190
|
|
84
191
|
# ========================================================================= #
|
85
192
|
# === show_frame_1?
|
@@ -469,6 +576,295 @@ class ShowOrf < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowOrf
|
|
469
576
|
def complement(i)
|
470
577
|
::Bioroebe.complement(i)
|
471
578
|
end
|
579
|
+
# ========================================================================= #
|
580
|
+
# === orange_f1
|
581
|
+
# ========================================================================= #
|
582
|
+
def orange_f1
|
583
|
+
orange(' F1 ')+rev
|
584
|
+
end; alias f1 orange_f1 # === f1
|
585
|
+
|
586
|
+
# ========================================================================= #
|
587
|
+
# === orange_f2
|
588
|
+
# ========================================================================= #
|
589
|
+
def orange_f2
|
590
|
+
orange(' F2 ')+rev
|
591
|
+
end; alias f2 orange_f2 # === f2
|
592
|
+
|
593
|
+
# ========================================================================= #
|
594
|
+
# === orange_f3
|
595
|
+
# ========================================================================= #
|
596
|
+
def orange_f3
|
597
|
+
orange(' F3 ')+rev
|
598
|
+
end; alias f3 orange_f3 # === f3
|
599
|
+
|
600
|
+
# ========================================================================= #
|
601
|
+
# === r1
|
602
|
+
# ========================================================================= #
|
603
|
+
def r1
|
604
|
+
orangered(' R1 ')+rev
|
605
|
+
end
|
606
|
+
|
607
|
+
# ========================================================================= #
|
608
|
+
# === r2
|
609
|
+
# ========================================================================= #
|
610
|
+
def r2
|
611
|
+
orangered(' R2 ')+rev
|
612
|
+
end
|
613
|
+
|
614
|
+
# ========================================================================= #
|
615
|
+
# === r3
|
616
|
+
# ========================================================================= #
|
617
|
+
def r3
|
618
|
+
orangered(' R3 ')+rev
|
619
|
+
end
|
620
|
+
|
621
|
+
# ========================================================================= #
|
622
|
+
# === show_this_frame
|
623
|
+
# ========================================================================= #
|
624
|
+
def show_this_frame(
|
625
|
+
i = frame_1,
|
626
|
+
which_frame = :frame1
|
627
|
+
)
|
628
|
+
_ = max_allowed_size_per_line
|
629
|
+
n_aminoacids = i.delete(' ').chars.size.to_s
|
630
|
+
right_padding = ' '.dup
|
631
|
+
case which_frame
|
632
|
+
when :frame1
|
633
|
+
which_frame = orange_f1
|
634
|
+
right_padding << ' '
|
635
|
+
when :frame2
|
636
|
+
which_frame = orange_f2
|
637
|
+
right_padding << ' '
|
638
|
+
when :frame3
|
639
|
+
which_frame = orange_f3
|
640
|
+
end
|
641
|
+
leading_part = which_frame+(' ' * 3)+' '+i
|
642
|
+
# ======================================================================= #
|
643
|
+
# === Colourize stop codons in the colour red
|
644
|
+
# ======================================================================= #
|
645
|
+
if colourize_stop_codons_in_red? and use_colours?
|
646
|
+
leading_part.gsub!(/(\*)/, swarn('\\1')+rev)
|
647
|
+
end
|
648
|
+
leading_part << right_padding
|
649
|
+
# ======================================================================= #
|
650
|
+
# We may have to modify the variable n_aminoacids if there is a stop
|
651
|
+
# codon.
|
652
|
+
# ======================================================================= #
|
653
|
+
if i.include? '*'
|
654
|
+
n_aminoacids = i[(i.rindex('*')+1) .. i.size].delete(' ').size.to_s.
|
655
|
+
rjust(i.size.to_s.size)
|
656
|
+
end
|
657
|
+
# ======================================================================= #
|
658
|
+
# Next also append how many aminoacids are part of this squence:
|
659
|
+
# ======================================================================= #
|
660
|
+
string = leading_part+
|
661
|
+
darkolivegreen(
|
662
|
+
n_aminoacids.to_s+' aminoacids'
|
663
|
+
)+rev
|
664
|
+
e string
|
665
|
+
end
|
666
|
+
|
667
|
+
# ========================================================================= #
|
668
|
+
# === menu (menu tag)
|
669
|
+
#
|
670
|
+
# By default, the input to this menu will be solely commandline
|
671
|
+
# arguments that have '--' as part of their name.
|
672
|
+
# ========================================================================= #
|
673
|
+
def menu(
|
674
|
+
i = commandline_arguments?
|
675
|
+
)
|
676
|
+
if i.is_a? Array
|
677
|
+
i.each {|entry| menu(entry) }
|
678
|
+
else
|
679
|
+
case i # case tag
|
680
|
+
# ===================================================================== #
|
681
|
+
# === showorf CACAGCAGCAGGCCCTCGGTCGTCGCTCCACATCAGCCGTCACATAGAGCTGATAG --all
|
682
|
+
# ===================================================================== #
|
683
|
+
when /^-?-?all$/
|
684
|
+
set_show_these_frames(:all_frames)
|
685
|
+
# ===================================================================== #
|
686
|
+
# === showorf CACAGCAGCAGGCCCGTCACATAGAGCTGATAG --frame3
|
687
|
+
# ===================================================================== #
|
688
|
+
when /^-?-?frame3$/,
|
689
|
+
/^-?-?show-?only-?frame-?3$/,
|
690
|
+
/^-?-?f3$/
|
691
|
+
set_show_these_frames(:f3)
|
692
|
+
# ===================================================================== #
|
693
|
+
# === showorf --frame2
|
694
|
+
# ===================================================================== #
|
695
|
+
when /^-?-?frame2$/,
|
696
|
+
/^-?-?show-?only-?frame-?2$/,
|
697
|
+
/^-?-?f2$/
|
698
|
+
set_show_these_frames(:f2)
|
699
|
+
# ===================================================================== #
|
700
|
+
# === showorf --frames_1_2_3
|
701
|
+
# ===================================================================== #
|
702
|
+
when /^-?-?frames_?1_?2_?3/,
|
703
|
+
/^-?-?show-?frame-?1-?2-?3/
|
704
|
+
set_show_these_frames(:f1_and_f2_and_f3)
|
705
|
+
# ===================================================================== #
|
706
|
+
# === showorf --frame1-and-2
|
707
|
+
# ===================================================================== #
|
708
|
+
when /^-?-?frame-?1(_|-)?and(_|-)?2/
|
709
|
+
set_show_these_frames(:f1_and_f2)
|
710
|
+
# ===================================================================== #
|
711
|
+
# === showorf --frame1
|
712
|
+
# ===================================================================== #
|
713
|
+
when /^-?-?frame1$/,
|
714
|
+
/-?-?show-?only-?frame-?1/
|
715
|
+
set_show_these_frames(:f1)
|
716
|
+
# ===================================================================== #
|
717
|
+
# === showorf --help
|
718
|
+
# ===================================================================== #
|
719
|
+
when /help/
|
720
|
+
show_help
|
721
|
+
exit
|
722
|
+
end
|
723
|
+
end
|
724
|
+
end
|
725
|
+
|
726
|
+
# ========================================================================= #
|
727
|
+
# === run (run tag)
|
728
|
+
# ========================================================================= #
|
729
|
+
def run
|
730
|
+
menu
|
731
|
+
_ = input?.dup # Keep a pointer to the input given to us.
|
732
|
+
n_nucleotides = _.size.to_s
|
733
|
+
# ======================================================================= #
|
734
|
+
# Chop the main string up into chunks of 100 each.
|
735
|
+
# ======================================================================= #
|
736
|
+
chopped_input = _.scan(/.{1,100}/m)
|
737
|
+
converted_sequence_for_frame_1 = to_frame1(_)
|
738
|
+
converted_sequence_for_frame_2 = to_frame2(_)
|
739
|
+
converted_sequence_for_frame_3 = to_frame3(_)
|
740
|
+
converted_sequence_for_reverse_frame_1 = to_reverse_frame1(_)
|
741
|
+
converted_sequence_for_reverse_frame_2 = to_reverse_frame2(_)
|
742
|
+
converted_sequence_for_reverse_frame_3 = to_reverse_frame3(_)
|
743
|
+
e
|
744
|
+
e "#{rev}Translation of requested code (5' #{steelblue('→')} #{rev}3') "\
|
745
|
+
"for #{simp(n_nucleotides)}#{rev} nucleotides.#{N}"
|
746
|
+
e
|
747
|
+
# ======================================================================= #
|
748
|
+
# Next, we build up the 3 different frames. In order to do so,
|
749
|
+
# we will first insert two ' ' after every position.
|
750
|
+
# ======================================================================= #
|
751
|
+
converted_sequence_for_frame_1 = converted_sequence_for_frame_1.chars.map {|entry|
|
752
|
+
entry+' '
|
753
|
+
}.join
|
754
|
+
converted_sequence_for_frame_2 = ' '+converted_sequence_for_frame_2.chars.map {|entry|
|
755
|
+
entry+' '
|
756
|
+
}.join
|
757
|
+
converted_sequence_for_frame_3 = ' '+converted_sequence_for_frame_3.chars.map {|entry|
|
758
|
+
entry+' '
|
759
|
+
}.join
|
760
|
+
converted_sequence_for_reverse_frame_1 = converted_sequence_for_reverse_frame_1.chars.map {|entry|
|
761
|
+
entry+' '
|
762
|
+
}.join
|
763
|
+
converted_sequence_for_reverse_frame_2 = ' '+converted_sequence_for_reverse_frame_2.chars.map {|entry|
|
764
|
+
entry+' '
|
765
|
+
}.join
|
766
|
+
converted_sequence_for_reverse_frame_3 = ' '+converted_sequence_for_reverse_frame_3.chars.map {|entry|
|
767
|
+
entry+' '
|
768
|
+
}.join
|
769
|
+
# ======================================================================= #
|
770
|
+
# We will chop them up into runs of 100, but only display
|
771
|
+
# for how many we get. The seagreen bar is on the very top,
|
772
|
+
# the "10 20" and so on.
|
773
|
+
# ======================================================================= #
|
774
|
+
e ' '+
|
775
|
+
seagreen(
|
776
|
+
return_numbers_based_on_this_input(_)
|
777
|
+
)+
|
778
|
+
rev
|
779
|
+
# ======================================================================= #
|
780
|
+
# === Get rid of newlines
|
781
|
+
# ======================================================================= #
|
782
|
+
if chopped_input.any? {|entry| entry.include? N }
|
783
|
+
chopped_input = remove_newlines(chopped_input)
|
784
|
+
end
|
785
|
+
chopped_input = strip(chopped_input)
|
786
|
+
chopped_input.each_with_index {|aminoacids_in_this_line, index|
|
787
|
+
|
788
|
+
left_nucleotide_position = ((index * 100)+1).to_s.rjust(3)
|
789
|
+
right_position = ((100 * index)+aminoacids_in_this_line.size).to_s
|
790
|
+
|
791
|
+
# ===================================================================== #
|
792
|
+
# Return the properly formated spacer tokens next. We need to find
|
793
|
+
# out how many tokens we have to display.
|
794
|
+
# ===================================================================== #
|
795
|
+
display_n_tokens = (right_position.to_i+1 - left_nucleotide_position.strip.to_i)
|
796
|
+
|
797
|
+
# ===================================================================== #
|
798
|
+
# Display the first frame next, then the other two frames.
|
799
|
+
# ===================================================================== #
|
800
|
+
set_frame_1(
|
801
|
+
converted_sequence_for_frame_1[(100 * index)..((100 * index)+100-1)]
|
802
|
+
) if show_frame_1?
|
803
|
+
|
804
|
+
set_frame_2(
|
805
|
+
converted_sequence_for_frame_2[(100 * index)..((100 * index)+100-1)]
|
806
|
+
) if show_frame_2?
|
807
|
+
|
808
|
+
set_frame_3(
|
809
|
+
converted_sequence_for_frame_3[(100 * index)..((100 * index)+100-1)]
|
810
|
+
) if show_frame_3?
|
811
|
+
# ===================================================================== #
|
812
|
+
# Next add the '----|' separators.
|
813
|
+
# ===================================================================== #
|
814
|
+
e " #{return_properly_formated_spacer_tokens(display_n_tokens)}"
|
815
|
+
# ===================================================================== #
|
816
|
+
# === Next show the main nucleotide sequence
|
817
|
+
# ===================================================================== #
|
818
|
+
e ' '+
|
819
|
+
mediumspringgreen(left_nucleotide_position)+rev+
|
820
|
+
' '+
|
821
|
+
mediumseagreen(aminoacids_in_this_line.upcase)+rev+' '+
|
822
|
+
mediumspringgreen( # <- This here is the end-part that is colourized.
|
823
|
+
((100 * index)+aminoacids_in_this_line.size).to_s
|
824
|
+
)
|
825
|
+
# ===================================================================== #
|
826
|
+
# The number should be reset after a '*' character.
|
827
|
+
# ===================================================================== #
|
828
|
+
|
829
|
+
# ===================================================================== #
|
830
|
+
# === Handle Frame1 next
|
831
|
+
# ===================================================================== #
|
832
|
+
if show_frame_1?
|
833
|
+
show_this_frame(frame_1, :frame1)
|
834
|
+
end
|
835
|
+
|
836
|
+
# ===================================================================== #
|
837
|
+
# === Handle Frame2
|
838
|
+
# ===================================================================== #
|
839
|
+
if show_frame_2?
|
840
|
+
show_this_frame(frame_2, :frame2)
|
841
|
+
end
|
842
|
+
|
843
|
+
# ===================================================================== #
|
844
|
+
# === Handle Frame3
|
845
|
+
# ===================================================================== #
|
846
|
+
if show_frame_3?
|
847
|
+
show_this_frame(frame_3, :frame3)
|
848
|
+
end
|
849
|
+
|
850
|
+
# ===================================================================== #
|
851
|
+
# Next, consider showing the reverse frames.
|
852
|
+
# ===================================================================== #
|
853
|
+
if show_reverse_frame_1?
|
854
|
+
e r1+' '+converted_sequence_for_reverse_frame_1
|
855
|
+
end
|
856
|
+
|
857
|
+
if show_reverse_frame_2?
|
858
|
+
e r2+' '+converted_sequence_for_reverse_frame_2
|
859
|
+
end
|
860
|
+
|
861
|
+
if show_reverse_frame_3?
|
862
|
+
e r3+' '+converted_sequence_for_reverse_frame_3
|
863
|
+
end
|
864
|
+
|
865
|
+
e
|
866
|
+
}
|
867
|
+
end
|
472
868
|
|
473
869
|
end
|
474
870
|
|
@@ -9,7 +9,7 @@ module Bioroebe
|
|
9
9
|
# ========================================================================= #
|
10
10
|
# === VERSION
|
11
11
|
# ========================================================================= #
|
12
|
-
VERSION = '0.
|
12
|
+
VERSION = '0.13.31'
|
13
13
|
|
14
14
|
# ========================================================================= #
|
15
15
|
# === LAST_UPDATE
|
@@ -17,7 +17,7 @@ module Bioroebe
|
|
17
17
|
# This variable keeps track as to when the bioroebe project was last
|
18
18
|
# updated. The notation is: DD.MM.YYYY
|
19
19
|
# ========================================================================= #
|
20
|
-
LAST_UPDATE = '
|
20
|
+
LAST_UPDATE = '22.02.2024'
|
21
21
|
|
22
22
|
# ========================================================================= #
|
23
23
|
# === URL_TO_THE_DOCUMENTATION
|
@@ -9,17 +9,12 @@
|
|
9
9
|
#
|
10
10
|
# It's usefulness will be very limited though.
|
11
11
|
# =========================================================================== #
|
12
|
-
require 'bioroebe/
|
12
|
+
require 'bioroebe/requires/commandline_application.rb'
|
13
13
|
|
14
14
|
module Bioroebe
|
15
15
|
|
16
16
|
class RNALfoldWrapper < ::Bioroebe::CommandlineApplication # === Bioroebe::RNALfoldWrapper
|
17
17
|
|
18
|
-
# ========================================================================= #
|
19
|
-
# === NAMESPACE
|
20
|
-
# ========================================================================= #
|
21
|
-
NAMESPACE = inspect
|
22
|
-
|
23
18
|
# ========================================================================= #
|
24
19
|
# === START_VALUE
|
25
20
|
#
|
@@ -51,10 +46,7 @@ class RNALfoldWrapper < ::Bioroebe::CommandlineApplication # === Bioroebe::RNALf
|
|
51
46
|
# ========================================================================= #
|
52
47
|
def reset
|
53
48
|
super()
|
54
|
-
|
55
|
-
# === @namespace
|
56
|
-
# ======================================================================= #
|
57
|
-
@namespace = NAMESPACE
|
49
|
+
infer_the_namespace
|
58
50
|
# ======================================================================= #
|
59
51
|
# === @target_directory
|
60
52
|
#
|
@@ -102,7 +94,7 @@ class RNALfoldWrapper < ::Bioroebe::CommandlineApplication # === Bioroebe::RNALf
|
|
102
94
|
# === menu
|
103
95
|
# ========================================================================= #
|
104
96
|
def menu(
|
105
|
-
i =
|
97
|
+
i = commandline_arguments?
|
106
98
|
)
|
107
99
|
if i.is_a? Array
|
108
100
|
i.each {|entry| menu(entry) }
|
@@ -136,7 +128,7 @@ class RNALfoldWrapper < ::Bioroebe::CommandlineApplication # === Bioroebe::RNALf
|
|
136
128
|
# ========================================================================= #
|
137
129
|
def report_where_the_commands_will_be_stored_and_store_them
|
138
130
|
_ = determine_log_filename
|
139
|
-
|
131
|
+
opnerev "These commands will be stored in the file `#{sfile(_)}`."
|
140
132
|
what = main_array?.join(N)
|
141
133
|
write_what_into(what, _)
|
142
134
|
end
|
@@ -184,7 +176,7 @@ class RNALfoldWrapper < ::Bioroebe::CommandlineApplication # === Bioroebe::RNALf
|
|
184
176
|
}
|
185
177
|
report_where_the_commands_will_be_stored_and_store_them
|
186
178
|
if @also_run_these_commands
|
187
|
-
|
179
|
+
opnerev 'These commands will also be run next.'
|
188
180
|
@array_cmds.each {|entry| esystem entry }
|
189
181
|
end
|
190
182
|
end
|
@@ -0,0 +1,15 @@
|
|
1
|
+
Note that this directory may contain specialized classes
|
2
|
+
that represent known viruses.
|
3
|
+
|
4
|
+
However had, as there may be thousand of different
|
5
|
+
viruses, we will probably transition to something
|
6
|
+
else, such as a single .yml file containing the
|
7
|
+
dataset for all viruses, or some other way. We can
|
8
|
+
still subclass these, but we then won't do so via
|
9
|
+
individual .rb files.
|
10
|
+
|
11
|
+
For the time being, though, we will retain the "one
|
12
|
+
subclass per virus" approach - just keep in mind
|
13
|
+
that this may be subject to change in the future
|
14
|
+
(written this notice in January of 2024).
|
15
|
+
|
@@ -0,0 +1,40 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::TobaccoMosaicVirus
|
6
|
+
#
|
7
|
+
# Tobacco mosaic virus (TMV) is a positive-sense single-stranded RNA virus
|
8
|
+
# species in the genus
|
9
|
+
#
|
10
|
+
# Usage example:
|
11
|
+
#
|
12
|
+
# Bioroebe::TobaccoMosaicVirus.new
|
13
|
+
#
|
14
|
+
# =========================================================================== #
|
15
|
+
# require 'bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb'
|
16
|
+
# =========================================================================== #
|
17
|
+
require 'bioroebe/virus/virus.rb'
|
18
|
+
|
19
|
+
module Bioroebe
|
20
|
+
|
21
|
+
class TobaccoMosaicVirus < ::Bioroebe::Virus # === Bioroebe::TobaccoMosaicVirus
|
22
|
+
|
23
|
+
# ========================================================================= #
|
24
|
+
# === initialize
|
25
|
+
# ========================================================================= #
|
26
|
+
def initialize(
|
27
|
+
commandline_arguments = ARGV,
|
28
|
+
run_already = true
|
29
|
+
)
|
30
|
+
reset
|
31
|
+
super(commandline_arguments, false)
|
32
|
+
genome_type '+ssRNA'
|
33
|
+
run if run_already
|
34
|
+
end
|
35
|
+
|
36
|
+
end; end
|
37
|
+
|
38
|
+
if __FILE__ == $PROGRAM_NAME
|
39
|
+
pp Bioroebe::TobaccoMosaicVirus.new(ARGV)
|
40
|
+
end # bioroebevirus
|
@@ -0,0 +1,76 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::Virus
|
6
|
+
#
|
7
|
+
# This class describes a virus.
|
8
|
+
#
|
9
|
+
# Usage example:
|
10
|
+
#
|
11
|
+
# Bioroebe::Virus.new
|
12
|
+
#
|
13
|
+
# =========================================================================== #
|
14
|
+
# require 'bioroebe/virus/virus.rb'
|
15
|
+
# < Bioroebe::Virus
|
16
|
+
# =========================================================================== #
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
18
|
+
|
19
|
+
module Bioroebe
|
20
|
+
|
21
|
+
class Virus < ::Bioroebe::CommandlineApplication # === Bioroebe::Virus
|
22
|
+
|
23
|
+
# ========================================================================= #
|
24
|
+
# === initialize
|
25
|
+
# ========================================================================= #
|
26
|
+
def initialize(
|
27
|
+
commandline_arguments = nil,
|
28
|
+
run_already = true
|
29
|
+
)
|
30
|
+
reset
|
31
|
+
set_commandline_arguments(
|
32
|
+
commandline_arguments
|
33
|
+
)
|
34
|
+
run if run_already
|
35
|
+
end
|
36
|
+
|
37
|
+
# ========================================================================= #
|
38
|
+
# === reset (reset tag)
|
39
|
+
# ========================================================================= #
|
40
|
+
def reset
|
41
|
+
super()
|
42
|
+
@internal_hash[:genome_type] = nil
|
43
|
+
end
|
44
|
+
|
45
|
+
# ========================================================================= #
|
46
|
+
# === genome_type?
|
47
|
+
# ========================================================================= #
|
48
|
+
def genome_type?
|
49
|
+
@internal_hash[:genome_type]
|
50
|
+
end
|
51
|
+
|
52
|
+
# ========================================================================= #
|
53
|
+
# === set_genome_type
|
54
|
+
# ========================================================================= #
|
55
|
+
def set_genome_type(i)
|
56
|
+
@internal_hash[:genome_type] = i
|
57
|
+
end; alias genome_type set_genome_type # === genome_type
|
58
|
+
|
59
|
+
# ========================================================================= #
|
60
|
+
# === run (run tag)
|
61
|
+
# ========================================================================= #
|
62
|
+
def run
|
63
|
+
end
|
64
|
+
|
65
|
+
# ========================================================================= #
|
66
|
+
# === Bioroebe::Virus[]
|
67
|
+
# ========================================================================= #
|
68
|
+
def self.[](i = ARGV)
|
69
|
+
new(i)
|
70
|
+
end
|
71
|
+
|
72
|
+
end; end
|
73
|
+
|
74
|
+
if __FILE__ == $PROGRAM_NAME
|
75
|
+
Bioroebe::Virus.new(ARGV)
|
76
|
+
end # bioroebevirus
|
@@ -8,11 +8,12 @@ require 'cyberweb/autoinclude'
|
|
8
8
|
require 'bioroebe'
|
9
9
|
|
10
10
|
english('WWW-Bioroebe') {
|
11
|
-
|
11
|
+
default_template 's0_5em'
|
12
12
|
body 'BG_Black White'
|
13
13
|
|
14
|
-
|
15
|
-
h2 'Welcome to WWW-Bioroebe',
|
14
|
+
default_width('mar0px') {
|
15
|
+
h2 'Welcome to WWW-Bioroebe',
|
16
|
+
'yellow'
|
16
17
|
div('mars1em'){
|
17
18
|
# ======================================================================= #
|
18
19
|
# === Available Codon Tables
|