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
@@ -7,7 +7,7 @@
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alias return_arguments_with_leading_hyphens select_entries_starting_with_two_hyphens # === return_arguments_with_leading_hyphens
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alias return_commandline_arguments_starting_with_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_hyphens
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alias return_commandline_arguments_starting_with_two_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_two_hyphens
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alias commandline_arguments_with_leading_hyphens? select_entries_starting_with_two_hyphens # === commandline_arguments_with_leading_hyphens?
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end; end
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#
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#
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end # internal_hash_module
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# Bioroebe::Base
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|
# =========================================================================== #
|
8
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-
|
9
|
-
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-
|
11
|
-
|
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-
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-
|
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-
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-
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-
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-
|
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|
-
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-
|
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-
|
21
|
-
require
|
8
|
+
module Bioroebe
|
9
|
+
|
10
|
+
class Base # === Bioroebe::Base
|
11
|
+
|
12
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+
# ========================================================================= #
|
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+
# === Bioroebe::Base::NAMESPACE
|
14
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+
# ========================================================================= #
|
15
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+
NAMESPACE = inspect
|
16
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+
|
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+
require 'bioroebe/requires/require_encoding.rb'
|
18
|
+
require 'bioroebe/constants/constants.rb'
|
19
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+
|
20
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+
# ========================================================================= #
|
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+
# Next, batch-require all toplevel_methods/ from the bioroebe project:
|
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|
+
# ========================================================================= #
|
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|
+
require 'bioroebe/requires/require_the_toplevel_methods.rb'
|
24
|
+
|
25
|
+
# ========================================================================= #
|
26
|
+
# === Add the InternalHashModule next:
|
27
|
+
# ========================================================================= #
|
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|
+
require 'bioroebe/base/internal_hash_module/internal_hash_module.rb'
|
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|
+
include Bioroebe::InternalHashModule
|
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+
|
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|
+
# ========================================================================= #
|
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|
+
# === Add the BaseModule next:
|
33
|
+
# ========================================================================= #
|
34
|
+
require 'bioroebe/base/base_module/base_module.rb'
|
35
|
+
include Bioroebe::BaseModule
|
36
|
+
|
37
|
+
# ========================================================================= #
|
38
|
+
# The following two aliases may have to be changed at some later point,
|
39
|
+
# but for now, let's keep things simple and use a simple alias, too.
|
40
|
+
#
|
41
|
+
# The old code was like this:
|
42
|
+
#
|
43
|
+
# def e(i = ''); ::Bioroebe.e(i)
|
44
|
+
#
|
45
|
+
# ========================================================================= #
|
46
|
+
alias e puts
|
47
|
+
|
48
|
+
alias ee print
|
49
|
+
|
50
|
+
# ========================================================================= #
|
51
|
+
# === mkdir (mkdir tag)
|
52
|
+
# ========================================================================= #
|
53
|
+
def mkdir(i)
|
54
|
+
::Bioroebe.mkdir(i)
|
55
|
+
end; alias create_directory mkdir # === create_directory
|
56
|
+
|
57
|
+
# ========================================================================= #
|
58
|
+
# === reset (reset tag)
|
59
|
+
# ========================================================================= #
|
60
|
+
def reset
|
61
|
+
# ======================================================================= #
|
62
|
+
# === @namespace
|
63
|
+
# ======================================================================= #
|
64
|
+
@namespace = NAMESPACE # We store the namespace here.
|
65
|
+
end
|
66
|
+
|
67
|
+
# ========================================================================= #
|
68
|
+
# === return_the_first_line_of_this_file
|
69
|
+
# ========================================================================= #
|
70
|
+
def return_the_first_line_of_this_file(i)
|
71
|
+
if File.exist? i
|
72
|
+
return File.open(i) {|this_file| this_file.readline.strip }
|
73
|
+
end
|
74
|
+
return i
|
75
|
+
end
|
76
|
+
|
77
|
+
# ========================================================================= #
|
78
|
+
# === is_on_roebe?
|
79
|
+
# ========================================================================= #
|
80
|
+
def is_on_roebe?
|
81
|
+
::Bioroebe.is_on_roebe?
|
82
|
+
end; alias on_roebe? is_on_roebe? # === on_roebe?
|
83
|
+
|
84
|
+
# ========================================================================= #
|
85
|
+
# === main_encoding?
|
86
|
+
#
|
87
|
+
# The main encoding in use. Currently this is hardcoded to UTF-8.
|
88
|
+
# ========================================================================= #
|
89
|
+
def main_encoding?
|
90
|
+
USE_THIS_ENCODING
|
91
|
+
end
|
92
|
+
|
93
|
+
# ========================================================================= #
|
94
|
+
# === move_file
|
95
|
+
#
|
96
|
+
# This method can be used to relocate or rename a file.
|
97
|
+
# ========================================================================= #
|
98
|
+
def move_file(
|
99
|
+
this_file, target
|
100
|
+
)
|
101
|
+
if File.exist? this_file
|
102
|
+
begin
|
103
|
+
FileUtils.mv(this_file, target)
|
104
|
+
rescue Exception => error
|
105
|
+
pp error
|
106
|
+
end
|
107
|
+
else
|
108
|
+
e rev+'No file exists at `'+sfile(this_file)+'`.'
|
109
|
+
end
|
110
|
+
end; alias rename move_file # === rename
|
111
|
+
|
112
|
+
# ========================================================================= #
|
113
|
+
# === rds
|
114
|
+
#
|
115
|
+
# The abbreviation rds stands short for "remove double slashes".
|
116
|
+
# ========================================================================= #
|
117
|
+
def rds(i)
|
118
|
+
::Bioroebe.rds(i)
|
119
|
+
end
|
120
|
+
|
121
|
+
# ========================================================================= #
|
122
|
+
# === return_pwd
|
123
|
+
# ========================================================================= #
|
124
|
+
def return_pwd
|
125
|
+
"#{Dir.pwd}/".squeeze('/')
|
126
|
+
end; alias return_working_directory return_pwd # === return_working_directory
|
127
|
+
|
128
|
+
# ========================================================================= #
|
129
|
+
# === mv
|
130
|
+
#
|
131
|
+
# Move/Rename a file or directory.
|
132
|
+
# ========================================================================= #
|
133
|
+
def mv(old, new)
|
134
|
+
FileUtils.mv(old, new)
|
135
|
+
end
|
136
|
+
|
137
|
+
# ========================================================================= #
|
138
|
+
# === delete_file
|
139
|
+
# ========================================================================= #
|
140
|
+
def delete_file(i)
|
141
|
+
File.delete(i) if File.exist? i
|
142
|
+
end; alias remove_file delete_file # === remove_file
|
143
|
+
alias remove delete_file # === remove
|
144
|
+
|
145
|
+
# ========================================================================= #
|
146
|
+
# === no_newlines
|
147
|
+
#
|
148
|
+
# This method will remove all newlines from a given (input) String.
|
149
|
+
# ========================================================================= #
|
150
|
+
def no_newlines(i)
|
151
|
+
i.delete!(N) if i
|
152
|
+
return i
|
153
|
+
end
|
154
|
+
|
155
|
+
# ========================================================================= #
|
156
|
+
# === no_file_exists_at
|
157
|
+
# ========================================================================= #
|
158
|
+
def no_file_exists_at(i)
|
159
|
+
::Bioroebe.no_file_exists_at(i)
|
160
|
+
end
|
161
|
+
|
162
|
+
end; end
|
@@ -10,19 +10,18 @@
|
|
10
10
|
# Biomart::Server.
|
11
11
|
# =========================================================================== #
|
12
12
|
|
13
|
-
# =========================================================================== #
|
14
|
-
# Next, require the ruby files that are part of biomart.
|
15
|
-
# =========================================================================== #
|
16
|
-
require 'bioroebe/biomart/attribute.rb'
|
17
|
-
require 'bioroebe/biomart/database.rb'
|
18
|
-
require 'bioroebe/biomart/dataset.rb'
|
19
|
-
require 'bioroebe/biomart/filter.rb'
|
20
|
-
require 'bioroebe/biomart/server.rb'
|
21
|
-
|
22
13
|
module Bioroebe
|
23
14
|
|
24
15
|
module Biomart
|
25
16
|
|
17
|
+
# ========================================================================= #
|
18
|
+
# Next, require the ruby files that are part of biomart.
|
19
|
+
# ========================================================================= #
|
20
|
+
require 'bioroebe/biomart/attribute.rb'
|
21
|
+
require 'bioroebe/biomart/database.rb'
|
22
|
+
require 'bioroebe/biomart/dataset.rb'
|
23
|
+
require 'bioroebe/biomart/filter.rb'
|
24
|
+
require 'bioroebe/biomart/server.rb'
|
26
25
|
require 'net/http'
|
27
26
|
require 'rexml/document' # Rexml is a part of ruby stdlib.
|
28
27
|
require 'csv'
|
@@ -11,10 +11,10 @@
|
|
11
11
|
# =========================================================================== #
|
12
12
|
module Bioroebe
|
13
13
|
|
14
|
-
module Blosum
|
14
|
+
module Blosum # === Bioroebe::Blosum
|
15
15
|
|
16
16
|
require 'bioroebe/project/project.rb'
|
17
|
-
require 'bioroebe/constants/
|
17
|
+
require 'bioroebe/constants/constants.rb'
|
18
18
|
|
19
19
|
alias e puts
|
20
20
|
|
@@ -3,7 +3,7 @@
|
|
3
3
|
# frozen_string_literal: true
|
4
4
|
# =========================================================================== #
|
5
5
|
# === Bioroebe::CalculateBlosumScore
|
6
|
-
|
6
|
+
#
|
7
7
|
# This small class will calculate the BLOSUM score.
|
8
8
|
#
|
9
9
|
# Currently we default to a BLOSUM50 substitution matrix.
|
@@ -12,11 +12,11 @@
|
|
12
12
|
# =========================================================================== #
|
13
13
|
# require 'bioroebe/calculate/calculate_blosum_score.rb'
|
14
14
|
# =========================================================================== #
|
15
|
-
require 'bioroebe/
|
15
|
+
require 'bioroebe/requires/commandline_application.rb'
|
16
16
|
|
17
17
|
module Bioroebe
|
18
18
|
|
19
|
-
class CalculateBlosumScore <
|
19
|
+
class CalculateBlosumScore < ::Bioroebe::CommandlineApplication # === Bioroebe::CalculateBlosumScore
|
20
20
|
|
21
21
|
require 'bioroebe/parsers/blosum_parser.rb'
|
22
22
|
|
@@ -43,6 +43,8 @@ class CalculateBlosumScore < Base # === Bioroebe::CalculateBlosumScore
|
|
43
43
|
)
|
44
44
|
reset
|
45
45
|
# ======================================================================= #
|
46
|
+
# === Default to BLOSUM50
|
47
|
+
#
|
46
48
|
# Determine which blosum-dataset to use next:
|
47
49
|
# ======================================================================= #
|
48
50
|
blosum50_dataset = Bioroebe::BlosumParser.new(FILE_BLOSUM50)
|
@@ -14,7 +14,7 @@
|
|
14
14
|
# require 'bioroebe/calculate/calculate_gc_content.rb'
|
15
15
|
# Bioroebe.gc_content('ATCG') # => 50.0
|
16
16
|
# ============================================================================ #
|
17
|
-
require 'bioroebe/
|
17
|
+
require 'bioroebe/requires/commandline_application.rb'
|
18
18
|
|
19
19
|
module Bioroebe
|
20
20
|
|
@@ -7,8 +7,7 @@
|
|
7
7
|
module Bioroebe
|
8
8
|
|
9
9
|
require 'bioroebe/colours/colours.rb'
|
10
|
-
require 'bioroebe/
|
11
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
10
|
+
require 'bioroebe/toplevel_methods/toplevel_methods.rb'
|
12
11
|
|
13
12
|
# ========================================================================= #
|
14
13
|
# === Bioroebe.calculate_levensthein_distance
|
@@ -83,9 +82,12 @@ end
|
|
83
82
|
if __FILE__ == $PROGRAM_NAME
|
84
83
|
if ARGV.empty?
|
85
84
|
alias e puts
|
85
|
+
begin; require 'colours'; rescue LoadError; end
|
86
86
|
e
|
87
87
|
e ::Bioroebe.rev+'Running in testing-mode '\
|
88
|
-
'for the method
|
88
|
+
'for the method '+
|
89
|
+
Colours.tomato('Bioroebe.calculate_levensthein_distance()')+
|
90
|
+
::Bioroebe.rev+':'
|
89
91
|
e
|
90
92
|
# Bioroebe.calculate_levensthein_distance(['saturday','sunday'])
|
91
93
|
Bioroebe.calculate_levensthein_distance('CGTCAGCGTACTT','ATTC--CGTACTT') # 1
|
@@ -19,7 +19,7 @@
|
|
19
19
|
# =========================================================================== #
|
20
20
|
# require 'bioroebe/calculate/calculate_melting_temperature.rb'
|
21
21
|
# =========================================================================== #
|
22
|
-
require 'bioroebe/
|
22
|
+
require 'bioroebe/requires/commandline_application.rb'
|
23
23
|
|
24
24
|
module Bioroebe
|
25
25
|
|
@@ -31,11 +31,6 @@ class CalculateMeltingTemperature < ::Bioroebe::CommandlineApplication # === Bio
|
|
31
31
|
require 'bioroebe/count/count_at.rb'
|
32
32
|
require 'bioroebe/count/count_gc.rb'
|
33
33
|
|
34
|
-
# ========================================================================= #
|
35
|
-
# === NAMESPACE
|
36
|
-
# ========================================================================= #
|
37
|
-
NAMESPACE = inspect
|
38
|
-
|
39
34
|
# ========================================================================= #
|
40
35
|
# === DEFAULT_SEQUENCE
|
41
36
|
# ========================================================================= #
|
@@ -68,10 +63,7 @@ class CalculateMeltingTemperature < ::Bioroebe::CommandlineApplication # === Bio
|
|
68
63
|
# ========================================================================= #
|
69
64
|
def reset
|
70
65
|
super()
|
71
|
-
|
72
|
-
# === @namespace
|
73
|
-
# ======================================================================= #
|
74
|
-
@namespace = NAMESPACE
|
66
|
+
infer_the_namespace
|
75
67
|
end
|
76
68
|
|
77
69
|
# ========================================================================= #
|
data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb
CHANGED
@@ -33,16 +33,11 @@
|
|
33
33
|
# =========================================================================== #
|
34
34
|
# require 'bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb'
|
35
35
|
# =========================================================================== #
|
36
|
-
require 'bioroebe/
|
36
|
+
require 'bioroebe/requires/commandline_application.rb'
|
37
37
|
|
38
38
|
module Bioroebe
|
39
39
|
|
40
|
-
class CalculateMeltingTemperatureForMoreThanThirteenNucleotides <
|
41
|
-
|
42
|
-
# ========================================================================= #
|
43
|
-
# === NAMESPACE
|
44
|
-
# ========================================================================= #
|
45
|
-
NAMESPACE = inspect
|
40
|
+
class CalculateMeltingTemperatureForMoreThanThirteenNucleotides < ::Bioroebe::CommandlineApplication # === Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides
|
46
41
|
|
47
42
|
# ========================================================================= #
|
48
43
|
# === BASE_VALUE
|
@@ -76,10 +71,7 @@ class CalculateMeltingTemperatureForMoreThanThirteenNucleotides < Base # === Bio
|
|
76
71
|
# ========================================================================= #
|
77
72
|
def reset
|
78
73
|
super()
|
79
|
-
|
80
|
-
# === @namespace
|
81
|
-
# ======================================================================= #
|
82
|
-
@namespace = NAMESPACE
|
74
|
+
infer_the_namespace
|
83
75
|
# ======================================================================= #
|
84
76
|
# === @nucleotide_sequence
|
85
77
|
# ======================================================================= #
|
@@ -129,10 +121,9 @@ class CalculateMeltingTemperatureForMoreThanThirteenNucleotides < Base # === Bio
|
|
129
121
|
# ========================================================================= #
|
130
122
|
def report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
|
131
123
|
if @do_report
|
132
|
-
erev
|
133
|
-
sfancy(@nucleotide_sequence.size.to_s)
|
134
|
-
rev
|
135
|
-
' nucleotides. ('+orange(input_sequence?)+rev+')'
|
124
|
+
erev "This nucleotide sequence contains "\
|
125
|
+
"#{sfancy(@nucleotide_sequence.size.to_s)}"\
|
126
|
+
"#{rev} nucleotides. (#{orange(input_sequence?)}#{rev})"
|
136
127
|
erev "The nucleotide-frequencies are: "\
|
137
128
|
"#{simp(n_A?.to_s+'xA')}#{rev}, "\
|
138
129
|
"#{simp(n_T?.to_s+'xT')}#{rev}, "\
|
@@ -10,7 +10,7 @@
|
|
10
10
|
# =========================================================================== #
|
11
11
|
# require 'bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb'
|
12
12
|
# =========================================================================== #
|
13
|
-
require 'bioroebe/
|
13
|
+
require 'bioroebe/requires/commandline_application.rb'
|
14
14
|
|
15
15
|
module Bioroebe
|
16
16
|
|
@@ -99,7 +99,9 @@ class CalculateThePositionSpecificScoringMatrix < ::Bioroebe::CommandlineApplica
|
|
99
99
|
# ========================================================================= #
|
100
100
|
# === menu (menu tag)
|
101
101
|
# ========================================================================= #
|
102
|
-
def menu(
|
102
|
+
def menu(
|
103
|
+
i = commandline_arguments?
|
104
|
+
)
|
103
105
|
if i.is_a? Array
|
104
106
|
i.each {|entry| menu(entry) }
|
105
107
|
else
|
data/lib/bioroebe/cell/cell.rb
CHANGED
@@ -11,12 +11,13 @@
|
|
11
11
|
#
|
12
12
|
# Usage example:
|
13
13
|
#
|
14
|
-
# Cell.new
|
14
|
+
# Bioroebe::Cell.new
|
15
15
|
#
|
16
16
|
# =========================================================================== #
|
17
17
|
# require 'bioroebe/cell/cell.rb'
|
18
|
+
# < Bioroebe::Cell
|
18
19
|
# =========================================================================== #
|
19
|
-
require 'bioroebe/
|
20
|
+
require 'bioroebe/requires/commandline_application.rb'
|
20
21
|
|
21
22
|
module Bioroebe
|
22
23
|
|
@@ -0,0 +1,60 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::B_cell
|
6
|
+
#
|
7
|
+
# This class describes a B cell (B lymphocyte).
|
8
|
+
#
|
9
|
+
# Usage example:
|
10
|
+
#
|
11
|
+
# Bioroebe::B_cell.new
|
12
|
+
#
|
13
|
+
# =========================================================================== #
|
14
|
+
# require 'bioroebe/cell/specialized_cells/B_cell.rb'
|
15
|
+
# =========================================================================== #
|
16
|
+
require 'bioroebe/cell/cell.rb'
|
17
|
+
|
18
|
+
module Bioroebe
|
19
|
+
|
20
|
+
class B_cell < ::Bioroebe::Cell # === Bioroebe::B_cell
|
21
|
+
|
22
|
+
# ========================================================================= #
|
23
|
+
# === initialize
|
24
|
+
# ========================================================================= #
|
25
|
+
def initialize(
|
26
|
+
commandline_arguments = nil,
|
27
|
+
run_already = true
|
28
|
+
)
|
29
|
+
reset
|
30
|
+
set_commandline_arguments(
|
31
|
+
commandline_arguments
|
32
|
+
)
|
33
|
+
run if run_already
|
34
|
+
end
|
35
|
+
|
36
|
+
# ========================================================================= #
|
37
|
+
# === reset (reset tag)
|
38
|
+
# ========================================================================= #
|
39
|
+
def reset
|
40
|
+
super()
|
41
|
+
end
|
42
|
+
|
43
|
+
# ========================================================================= #
|
44
|
+
# === run (run tag)
|
45
|
+
# ========================================================================= #
|
46
|
+
def run
|
47
|
+
end
|
48
|
+
|
49
|
+
# ========================================================================= #
|
50
|
+
# === Bioroebe::B_cell[]
|
51
|
+
# ========================================================================= #
|
52
|
+
def self.[](i = ARGV)
|
53
|
+
new(i)
|
54
|
+
end
|
55
|
+
|
56
|
+
end; end
|
57
|
+
|
58
|
+
if __FILE__ == $PROGRAM_NAME
|
59
|
+
Bioroebe::B_cell.new(ARGV)
|
60
|
+
end # bioroebecell
|
@@ -0,0 +1,60 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::Macrophage
|
6
|
+
#
|
7
|
+
# This class describes a macrophage.
|
8
|
+
#
|
9
|
+
# Usage example:
|
10
|
+
#
|
11
|
+
# Bioroebe::Macrophage.new
|
12
|
+
#
|
13
|
+
# =========================================================================== #
|
14
|
+
# require 'bioroebe/cell/specialized_cells/macrophage.rb'
|
15
|
+
# =========================================================================== #
|
16
|
+
require 'bioroebe/cell/cell.rb'
|
17
|
+
|
18
|
+
module Bioroebe
|
19
|
+
|
20
|
+
class Macrophage < ::Bioroebe::Cell # === Bioroebe::Macrophage
|
21
|
+
|
22
|
+
# ========================================================================= #
|
23
|
+
# === initialize
|
24
|
+
# ========================================================================= #
|
25
|
+
def initialize(
|
26
|
+
commandline_arguments = nil,
|
27
|
+
run_already = true
|
28
|
+
)
|
29
|
+
reset
|
30
|
+
set_commandline_arguments(
|
31
|
+
commandline_arguments
|
32
|
+
)
|
33
|
+
run if run_already
|
34
|
+
end
|
35
|
+
|
36
|
+
# ========================================================================= #
|
37
|
+
# === reset (reset tag)
|
38
|
+
# ========================================================================= #
|
39
|
+
def reset
|
40
|
+
super()
|
41
|
+
end
|
42
|
+
|
43
|
+
# ========================================================================= #
|
44
|
+
# === run (run tag)
|
45
|
+
# ========================================================================= #
|
46
|
+
def run
|
47
|
+
end
|
48
|
+
|
49
|
+
# ========================================================================= #
|
50
|
+
# === Bioroebe::Macrophage[]
|
51
|
+
# ========================================================================= #
|
52
|
+
def self.[](i = ARGV)
|
53
|
+
new(i)
|
54
|
+
end
|
55
|
+
|
56
|
+
end; end
|
57
|
+
|
58
|
+
if __FILE__ == $PROGRAM_NAME
|
59
|
+
Bioroebe::Macrophage.new(ARGV)
|
60
|
+
end # bioroebecell
|