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
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)+
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p(
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"The <b>following actions</b>, as links, can be used to make use "\
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"of the Bioroebe project's www interface (through <b>sinatra</b>).<br>\n<br>\n"
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)+
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return_index_of_hyperlinks
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Cyberweb.html_template(
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title: title?,
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css_rules_to_use: USE_THESE_CSS_RULES_FOR_THE_WHOLE_WEBPAGE,
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body_css_style: BODY_CSS_STYLE,
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body: body
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)
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end; alias return_root_string return_view_string # === return_root_string
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+
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# ========================================================================= #
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# === INPUT_TYPE_TEXT_AND_BR_TAG
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# ========================================================================= #
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# ========================================================================= #
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# === return_sinatra_to_dna
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#
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# This is:
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# This is:
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#
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# http://localhost:4567/to_dna
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#
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# ========================================================================= #
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def return_sinatra_to_dna
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if Object.const_defined?(:Roebe) and Roebe.const_defined?(:Controller)
|
@@ -215,26 +269,20 @@ module EmbeddableInterface
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else
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_ = return_intro_for_to_dna_conversion
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end
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-
Cyberweb
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+
Cyberweb.html_template(
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title: 'Convert to DNA',
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body: _+
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-
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-
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+
p(
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+
"You can \"<b>convert</b>\" a RNA sequence into DNA through "\
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+
"this API.<br>\n"
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)+
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-
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+
p(
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280
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'Simply input the nucleotide String, such as "ATGCT", '\
|
226
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-
'without the "" quotes.'
|
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+
'without the "" quotes.'+"<br>"
|
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)+
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return_form_for_to_dna_action+
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hyperlink_paragraph
|
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-
|
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|
-
end
|
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-
|
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-
# ========================================================================= #
|
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|
-
# === title?
|
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|
-
# ========================================================================= #
|
236
|
-
def title?
|
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-
'BioRoebe Web-API'
|
285
|
+
)
|
238
286
|
end
|
239
287
|
|
240
288
|
# ========================================================================= #
|
@@ -577,27 +625,6 @@ module EmbeddableInterface
|
|
577
625
|
alias hyperlink_paragraph return_paragraph_of_hyperlinks # === hyperlink_paragraph
|
578
626
|
alias hyperlinks_paragraph return_paragraph_of_hyperlinks # === hyperlinks_paragraph
|
579
627
|
|
580
|
-
# ========================================================================= #
|
581
|
-
# === return_view_string
|
582
|
-
# ========================================================================= #
|
583
|
-
def return_view_string
|
584
|
-
body = HtmlTags.h1(
|
585
|
-
HtmlTags.image('https://i.imgur.com/Ufb3XW3.png')+'<br>'+
|
586
|
-
TITLE,
|
587
|
-
css_style: 'margin-left: 0.40em;'
|
588
|
-
)+
|
589
|
-
HtmlTags.p(
|
590
|
-
"The <b>following actions</b>, as links, can be used to make use "\
|
591
|
-
"of the Bioroebe project's www interface (through <b>sinatra</b>)."
|
592
|
-
)+
|
593
|
-
return_index_of_hyperlinks
|
594
|
-
Cyberweb.template(
|
595
|
-
title: title?,
|
596
|
-
body_css_style: BODY_CSS_STYLE,
|
597
|
-
body: body
|
598
|
-
).to_s
|
599
|
-
end; alias return_root_string return_view_string # === return_root_string
|
600
|
-
|
601
628
|
# ========================================================================= #
|
602
629
|
# === return_header_to_aminoacid_conversion
|
603
630
|
# ========================================================================= #
|
@@ -636,15 +663,20 @@ module EmbeddableInterface
|
|
636
663
|
|
637
664
|
# ========================================================================= #
|
638
665
|
# === method_reverse_complement
|
666
|
+
#
|
667
|
+
# API:
|
668
|
+
#
|
669
|
+
# http://localhost:4568/reverse_complement
|
670
|
+
#
|
639
671
|
# ========================================================================= #
|
640
672
|
def method_reverse_complement
|
641
673
|
return_intro_for_reverse_complement_conversion+
|
642
|
-
|
643
|
-
|
674
|
+
p(
|
675
|
+
"You can <b>reverse complement</b> a DNA sequence through this API.<br>\n<br>\n"
|
644
676
|
)+
|
645
|
-
|
646
|
-
|
647
|
-
|
677
|
+
p(
|
678
|
+
"Simply input the nucleotide String, such as \"ATGCT\", "\
|
679
|
+
"without the \"\" quotes.<br><br>\n\n"
|
648
680
|
)+
|
649
681
|
return_form_for_reverse_complement_action+
|
650
682
|
hyperlink_paragraph
|
@@ -746,4 +778,8 @@ def self.embeddable_interface
|
|
746
778
|
return object
|
747
779
|
end
|
748
780
|
|
781
|
+
end
|
782
|
+
|
783
|
+
if __FILE__ == $PROGRAM_NAME
|
784
|
+
include Bioroebe::EmbeddableInterface
|
749
785
|
end
|
@@ -12,10 +12,10 @@
|
|
12
12
|
# agarose concentration in [% w/v] : DNA-length in kb
|
13
13
|
# =========================================================================== #
|
14
14
|
|
15
|
-
0.3: 5 - 50
|
16
|
-
0.6: 1 - 20
|
17
|
-
0.7: 0.8 - 10
|
18
|
-
0.9: 0.5 - 7
|
19
|
-
1.2: 0.4 - 6
|
20
|
-
1.5: 0.2 - 3
|
15
|
+
0.3: 5 - 50
|
16
|
+
0.6: 1 - 20
|
17
|
+
0.7: 0.8 - 10
|
18
|
+
0.9: 0.5 - 7
|
19
|
+
1.2: 0.4 - 6
|
20
|
+
1.5: 0.2 - 3
|
21
21
|
2.0: 0.1 - 2
|
@@ -1,5 +1,11 @@
|
|
1
|
+
# =========================================================================== #
|
1
2
|
# === blosum50.yml
|
2
3
|
#
|
4
|
+
# Note that some blosum50 matrices, on the world wide web, are a bit
|
5
|
+
# truncated compared to the file here. The difference can often be
|
6
|
+
# found in the last parts, e. g. B, J, Z, X and * are not evaluated
|
7
|
+
# by these smaller matrices.
|
8
|
+
#
|
3
9
|
# A reference implementation can be seen here:
|
4
10
|
#
|
5
11
|
# https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM50
|
@@ -8,6 +8,7 @@
|
|
8
8
|
# https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM90
|
9
9
|
#
|
10
10
|
# =========================================================================== #
|
11
|
+
|
11
12
|
A R N D C Q E G H I L K M F P S T W Y V B J Z X *
|
12
13
|
A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -2 -1 -1 -6
|
13
14
|
R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 -3 0 -1 -6
|
@@ -33,4 +34,4 @@ B -2 -2 5 5 -4 -1 1 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 5 -5 0 -1 -6
|
|
33
34
|
J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 4 -3 2 0 -4 -3 -2 -3 -2 1 -5 4 -4 -1 -6
|
34
35
|
Z -1 0 -1 1 -5 5 5 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 -4 5 -1 -6
|
35
36
|
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
|
36
|
-
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
|
37
|
+
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
|
@@ -5,7 +5,7 @@
|
|
5
5
|
# =========================================================================== #
|
6
6
|
|
7
7
|
# =========================================================================== #
|
8
|
-
# Species:
|
8
|
+
# Species: 2n
|
9
9
|
# =========================================================================== #
|
10
10
|
Yellow fever mosquito 6
|
11
11
|
Fruit fly: 8
|
@@ -27,4 +27,4 @@ Donkey: 62
|
|
27
27
|
Dog: 78
|
28
28
|
Chicken: 78
|
29
29
|
Carp: 104
|
30
|
-
Butterflies: 380
|
30
|
+
Butterflies: 380
|
@@ -1 +1 @@
|
|
1
|
-
/home/x/Temp/bioroebe
|
1
|
+
/home/x/Temp/bioroebe/
|
@@ -6,10 +6,11 @@
|
|
6
6
|
# =========================================================================== #
|
7
7
|
# OTHLy-ILT
|
8
8
|
# =========================================================================== #
|
9
|
-
|
10
|
-
EC
|
11
|
-
EC
|
12
|
-
EC
|
13
|
-
EC
|
9
|
+
|
10
|
+
EC 1: Oxidoreductases
|
11
|
+
EC 2: Transferases
|
12
|
+
EC 3: Hydrolases
|
13
|
+
EC 4: Lyases
|
14
|
+
EC 5: Isomerases
|
14
15
|
EC 6: Ligases
|
15
|
-
EC 7: Translocases
|
16
|
+
EC 7: Translocases
|
@@ -8,11 +8,11 @@
|
|
8
8
|
# To then get the average:
|
9
9
|
#
|
10
10
|
# sum=[]; x.each_value {|y| sum << y.to_i }; avg(sum)
|
11
|
-
#
|
11
|
+
#
|
12
12
|
# should be a hash. All values in bp.
|
13
13
|
#
|
14
14
|
# The chromsome data was taken from ensembl i.e. from
|
15
|
-
#
|
15
|
+
#
|
16
16
|
# https://www.ensembl.org/Homo_sapiens/mapview?chr=3
|
17
17
|
#
|
18
18
|
# I do not know why this dataset is different from the one mentioned
|
@@ -41,7 +41,7 @@ chromosomes:
|
|
41
41
|
12: 132_349_534
|
42
42
|
13: 114_142_980
|
43
43
|
14: 106_368_585
|
44
|
-
15: 100_338_915
|
44
|
+
15: 100_338_915
|
45
45
|
16: 88_827_254
|
46
46
|
17: 78_774_742
|
47
47
|
18: 76_117_153
|
@@ -6,11 +6,7 @@
|
|
6
6
|
# be part of the bioroebe project.
|
7
7
|
# =========================================================================== #
|
8
8
|
|
9
|
-
|
10
|
-
|
9
|
+
# -----------------------------------------------|-------------------------|-------------------
|
11
10
|
# Name of the mRNA at hand | NCBI reference sequence | Remote URL
|
12
11
|
# -----------------------------------------------|-------------------------|-------------------
|
13
12
|
Homo sapiens erythropoietin (EPO), mRNA | NM_000799.4 | https://www.ncbi.nlm.nih.gov/nuccore/NM_000799.4
|
14
|
-
|
15
|
-
|
16
|
-
|
@@ -1,7 +1,9 @@
|
|
1
1
|
# =========================================================================== #
|
2
|
+
# === 35S.yml
|
3
|
+
#
|
2
4
|
# Taken from:
|
3
5
|
#
|
4
|
-
#
|
6
|
+
# https://www.bios.net/daisy/promoters/242/g1/250.html
|
5
7
|
#
|
6
8
|
# The sequence has one TATA box and two CAAT boxes.
|
7
9
|
# =========================================================================== #
|
@@ -1,4 +1,7 @@
|
|
1
1
|
# =========================================================================== #
|
2
|
-
#
|
2
|
+
# === ubiquitin.yml
|
3
|
+
#
|
4
|
+
# Note that this sequence stored here refers to the human protein; other
|
5
|
+
# species may have a slightly different sequence.
|
3
6
|
# =========================================================================== #
|
4
7
|
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
|
@@ -12,7 +12,7 @@
|
|
12
12
|
#
|
13
13
|
# If you see an entry such as AGGCCT, then this is actually a shorter
|
14
14
|
# variant representing 5' AGGCCT.
|
15
|
-
#
|
15
|
+
#
|
16
16
|
# To update to the latest, one should use the latest enzyme list from REBASE:
|
17
17
|
#
|
18
18
|
# http://rebase.neb.com/rebase/
|
@@ -608,13 +608,13 @@ VpaK11AI: GGWCC 0
|
|
608
608
|
VpaK11BI: GGWCC 1
|
609
609
|
VspI: ATTAAT 2
|
610
610
|
XagI: CCTNNNNNAGG 5
|
611
|
-
XapI: RAATTY
|
612
|
-
XbaI: TCTAGA
|
613
|
-
XceI: RCATGY
|
611
|
+
XapI: RAATTY 1
|
612
|
+
XbaI: TCTAGA 1
|
613
|
+
XceI: RCATGY 5
|
614
614
|
XcmI: CCANNNNNNNNNTGG 8
|
615
|
-
XhoI: CTCGAG
|
616
|
-
XhoII: RGATCY
|
617
|
-
XmaI: CCCGGG
|
615
|
+
XhoI: CTCGAG 1
|
616
|
+
XhoII: RGATCY 1
|
617
|
+
XmaI: CCCGGG 1
|
618
618
|
XmaIII: CGGCCG 1
|
619
619
|
XmaCI: CCCGGG 1
|
620
620
|
XmaJI: CCTAGG 1
|
@@ -5,7 +5,7 @@
|
|
5
5
|
# The code here simply tests whether the DNA→RNA conversion works,
|
6
6
|
# through the toplevel API Bioroebe.to_rna().
|
7
7
|
# =========================================================================== #
|
8
|
-
require 'bioroebe/toplevel_methods/
|
8
|
+
require 'bioroebe/toplevel_methods/toplevel_methods.rb'
|
9
9
|
|
10
10
|
input = 'GATGGAACTTGACTACGTAAATT'
|
11
11
|
|