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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# require 'bioroebe/toplevel_methods/complement.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.complement
|
11
|
-
#
|
12
|
-
# This method will return the complementary DNA strand.
|
13
|
-
#
|
14
|
-
# We will use possibilities though.
|
15
|
-
#
|
16
|
-
# Usage example:
|
17
|
-
#
|
18
|
-
# Bioroebe.complement 'ATGGGTCCC' # => "TACCCAGGG"
|
19
|
-
#
|
20
|
-
# ========================================================================= #
|
21
|
-
def self.complement(
|
22
|
-
i = nil
|
23
|
-
)
|
24
|
-
require 'bioroebe/constants/nucleotides.rb'
|
25
|
-
# ======================================================================= #
|
26
|
-
# Refer to the main Hash.
|
27
|
-
# ======================================================================= #
|
28
|
-
hash = HASH_DNA_NUCLEOTIDES
|
29
|
-
result = ''.dup
|
30
|
-
i = i.first if i.is_a? Array
|
31
|
-
if i
|
32
|
-
if File.exist?(i)
|
33
|
-
i = File.readlines(i).join(' ').strip
|
34
|
-
end
|
35
|
-
i.each_char { |char|
|
36
|
-
char = char.upcase
|
37
|
-
if hash.has_key? char
|
38
|
-
result << hash[char]
|
39
|
-
else
|
40
|
-
case char.downcase # case tag
|
41
|
-
when 'n' # Means any.
|
42
|
-
result << '(A/T/G/C)'
|
43
|
-
when 'r' # Means a purine. (larger)
|
44
|
-
result << '(A/G)'
|
45
|
-
when 'y' # Means a pyrimidine. (smaller)
|
46
|
-
result << '(T/C)'
|
47
|
-
end
|
48
|
-
end
|
49
|
-
}
|
50
|
-
return result
|
51
|
-
end
|
52
|
-
end
|
53
|
-
|
54
|
-
end
|
55
|
-
|
56
|
-
if __FILE__ == $PROGRAM_NAME
|
57
|
-
puts Bioroebe.complement(ARGV) # => "TACCCAGGG"
|
58
|
-
end # bioroebecomplement TACCCAGGG
|
@@ -1,39 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/convert_global_env.rb'
|
6
|
-
# Bioroebe.convert_global_env(ARGV)
|
7
|
-
# =========================================================================== #
|
8
|
-
module Bioroebe
|
9
|
-
|
10
|
-
# ========================================================================= #
|
11
|
-
# === Bioroebe.convert_global_env
|
12
|
-
#
|
13
|
-
# Note that the method will pick only the first argument given to it
|
14
|
-
# if an Array is supplied.
|
15
|
-
# ========================================================================= #
|
16
|
-
def self.convert_global_env(i)
|
17
|
-
if i.is_a? Array
|
18
|
-
i = i.first
|
19
|
-
end
|
20
|
-
unless Object.const_defined? :ConvertGlobalEnv
|
21
|
-
begin # Require an external gem in this case.
|
22
|
-
require 'convert_global_env'
|
23
|
-
rescue LoadError; end
|
24
|
-
end
|
25
|
-
if Object.const_defined? :ConvertGlobalEnv
|
26
|
-
if i and !i.start_with?('$')
|
27
|
-
i = i.dup if i.frozen?
|
28
|
-
i.prepend('$')
|
29
|
-
end
|
30
|
-
return ConvertGlobalEnv.convert(i, :do_not_report_errors) # Handle ENV variables.
|
31
|
-
end
|
32
|
-
return i
|
33
|
-
end
|
34
|
-
|
35
|
-
end
|
36
|
-
|
37
|
-
if __FILE__ == $PROGRAM_NAME
|
38
|
-
puts Bioroebe.convert_global_env(ARGV)
|
39
|
-
end # rb convert_global_env.rb MY_DATA
|
@@ -1,73 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/databases.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
require 'bioroebe/constants/database_constants.rb'
|
10
|
-
|
11
|
-
# ========================================================================= #
|
12
|
-
# === Bioroebe.set_pgpassword (password tag)
|
13
|
-
#
|
14
|
-
# Set the password for Postgresql here. As input to this method you
|
15
|
-
# can pass the password for the postgreSQL database.
|
16
|
-
# ========================================================================= #
|
17
|
-
def self.set_pgpassword(
|
18
|
-
new_password = Bioroebe::Postgresql::POSTGRE_PASSWORD
|
19
|
-
)
|
20
|
-
ENV['PGPASSWORD'] = new_password
|
21
|
-
end; self.instance_eval { alias set_password set_pgpassword } # === Bioroebe.set_password
|
22
|
-
|
23
|
-
# ========================================================================= #
|
24
|
-
# === Bioroebe.run_sql_query
|
25
|
-
#
|
26
|
-
# This method will run a SQL query using --command.
|
27
|
-
#
|
28
|
-
# It will return the result as well.
|
29
|
-
#
|
30
|
-
# The second argument determines whether we will be verbose or not.
|
31
|
-
#
|
32
|
-
# The result, however, will always be displayed.
|
33
|
-
# ========================================================================= #
|
34
|
-
def self.run_sql_query(
|
35
|
-
i,
|
36
|
-
be_verbose = true,
|
37
|
-
optional_append_this = ''
|
38
|
-
)
|
39
|
-
set_pgpassword
|
40
|
-
i = i.to_s
|
41
|
-
_ = ''
|
42
|
-
if is_on_roebe?
|
43
|
-
_ << POSTGRE_LOGIN_COMMAND_HOME
|
44
|
-
else
|
45
|
-
_ << POSTGRE_LOGIN_COMMAND
|
46
|
-
end
|
47
|
-
case be_verbose
|
48
|
-
when :silent
|
49
|
-
be_verbose = false
|
50
|
-
end
|
51
|
-
case optional_append_this
|
52
|
-
# ======================================================================= #
|
53
|
-
# === :bare
|
54
|
-
# ======================================================================= #
|
55
|
-
when :bare,
|
56
|
-
:tuples
|
57
|
-
optional_append_this = ' --tuples-only'
|
58
|
-
end
|
59
|
-
_ << optional_append_this.to_s
|
60
|
-
_ << ' --command="'
|
61
|
-
_ << i
|
62
|
-
_ << '"' unless _.end_with? '"'
|
63
|
-
result = `#{_}`.chomp
|
64
|
-
erev _ if be_verbose
|
65
|
-
erev result if be_verbose
|
66
|
-
return result
|
67
|
-
end
|
68
|
-
|
69
|
-
end
|
70
|
-
|
71
|
-
if __FILE__ == $PROGRAM_NAME
|
72
|
-
Bioroebe.run_sql_query 'foo bar'
|
73
|
-
end
|
@@ -1,19 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/delimiter.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.delimiter?
|
11
|
-
#
|
12
|
-
# This is simply the delimiter used for reading "multiline input"
|
13
|
-
# of the Bioroebe::Shell component.
|
14
|
-
# ========================================================================= #
|
15
|
-
def self.delimiter?
|
16
|
-
'___'
|
17
|
-
end
|
18
|
-
|
19
|
-
end
|
@@ -1,81 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/digest.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.digest_this_dna
|
11
|
-
#
|
12
|
-
# Usage examples:
|
13
|
-
#
|
14
|
-
# x = Bioroebe.digest_this_dna(:lambda_genome, with: :EcoRI)
|
15
|
-
# x = Bioroebe.digest_this_dna("/root/Bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta", with: :EcoRI)
|
16
|
-
# x = Bioroebe.digest_this_dna("/Depot/j/foobar.fasta", with: :PvuII)
|
17
|
-
#
|
18
|
-
# ========================================================================= #
|
19
|
-
def self.digest_this_dna(
|
20
|
-
this_DNA_sequence,
|
21
|
-
hash = {}
|
22
|
-
)
|
23
|
-
require 'bioroebe/constants/files_and_directories.rb'
|
24
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
25
|
-
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
26
|
-
restriction_enzymes = Bioroebe.load_and_return_the_restriction_enzymes
|
27
|
-
this_restriction_enzyme = nil
|
28
|
-
nucleotide_sequence = nil
|
29
|
-
if this_DNA_sequence.is_a? Array
|
30
|
-
this_DNA_sequence = this_DNA_sequence.first
|
31
|
-
end
|
32
|
-
if this_DNA_sequence.is_a?(String) and File.exist?(this_DNA_sequence)
|
33
|
-
nucleotide_sequence = ::Bioroebe::ParseFasta.new(this_DNA_sequence).sequence?
|
34
|
-
end
|
35
|
-
# ======================================================================= #
|
36
|
-
# === Handle the hash next (and ensure that it is a Hash)
|
37
|
-
# ======================================================================= #
|
38
|
-
if hash.is_a? Hash
|
39
|
-
# ===================================================================== #
|
40
|
-
# === :with
|
41
|
-
# ===================================================================== #
|
42
|
-
if hash.has_key? :with
|
43
|
-
this_restriction_enzyme = hash.delete(:with).to_s
|
44
|
-
end
|
45
|
-
end
|
46
|
-
target_sequence = restriction_enzymes[this_restriction_enzyme].dup
|
47
|
-
if target_sequence =~ /\d$/ # If it ends with a number.
|
48
|
-
target_sequence.chop!
|
49
|
-
target_sequence.strip!
|
50
|
-
end
|
51
|
-
if nucleotide_sequence and
|
52
|
-
nucleotide_sequence.include?(target_sequence)
|
53
|
-
print rev+'Yes, the restriction-sequence '+
|
54
|
-
lightblue(target_sequence)+
|
55
|
-
rev+
|
56
|
-
' is found in the given sequence. '
|
57
|
-
scanned = nucleotide_sequence.scan(
|
58
|
-
/#{target_sequence}/
|
59
|
-
)
|
60
|
-
erev "It can be found #{steelblue(scanned.size.to_s)}#{rev} "\
|
61
|
-
"times, at these positions:"
|
62
|
-
e
|
63
|
-
sub_sequences = nucleotide_sequence.split(/#{target_sequence}/)
|
64
|
-
sub_sequences.sort_by {|entry| entry.size }.reverse.each {|sequence|
|
65
|
-
erev " #{sequence.size}"
|
66
|
-
}
|
67
|
-
e
|
68
|
-
return sub_sequences
|
69
|
-
else
|
70
|
-
e 'Nothing found.'
|
71
|
-
end
|
72
|
-
end
|
73
|
-
|
74
|
-
end
|
75
|
-
|
76
|
-
if __FILE__ == $PROGRAM_NAME
|
77
|
-
Bioroebe.digest_this_dna(
|
78
|
-
"/home/Temp/bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta",
|
79
|
-
with: :EcoRI
|
80
|
-
)
|
81
|
-
end # rb digest.rb
|
@@ -1,146 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/download_and_fetch_data.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
10
|
-
require 'bioroebe/toplevel_methods/esystem.rb'
|
11
|
-
require 'bioroebe/toplevel_methods/fasta_and_fastq.rb'
|
12
|
-
require 'bioroebe/toplevel_methods/log_directory.rb'
|
13
|
-
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
14
|
-
require 'bioroebe/colours/colours.rb'
|
15
|
-
|
16
|
-
# ========================================================================= #
|
17
|
-
# === Bioroebe.fetch_data_from_uniprot
|
18
|
-
#
|
19
|
-
# The first argument to this method should be the name of the protein
|
20
|
-
# at hand. Alternatively it can also be just the full URL.
|
21
|
-
#
|
22
|
-
# The second argument specifies whether we will automatically try
|
23
|
-
# to rename this FASTA file. By default this is enabled, largely
|
24
|
-
# because it makes it a bit easier to know what a particular
|
25
|
-
# fasta sequence contains.
|
26
|
-
# ========================================================================= #
|
27
|
-
def self.fetch_data_from_uniprot(
|
28
|
-
i = 'B5ZC00',
|
29
|
-
do_perform_rename_action = true
|
30
|
-
)
|
31
|
-
require 'open-uri'
|
32
|
-
# ======================================================================= #
|
33
|
-
# Support Array as input:
|
34
|
-
# ======================================================================= #
|
35
|
-
if i.is_a? Array
|
36
|
-
i.each {|entry|
|
37
|
-
fetch_data_from_uniprot(entry, do_perform_rename_action)
|
38
|
-
}
|
39
|
-
else
|
40
|
-
if i.frozen?
|
41
|
-
i = i.dup
|
42
|
-
end
|
43
|
-
i.strip!
|
44
|
-
if i.start_with? 'http'
|
45
|
-
remote_url = i
|
46
|
-
else
|
47
|
-
remote_url = "https://www.uniprot.org/uniprot/#{i}".dup
|
48
|
-
end
|
49
|
-
# ======================================================================= #
|
50
|
-
# Next, we will append a trailing ".fasta" part for uniprot, if
|
51
|
-
# the very last part does NOT include a '.' character.
|
52
|
-
# ======================================================================= #
|
53
|
-
_ = File.basename(remote_url)
|
54
|
-
unless _.include?('.')
|
55
|
-
remote_url << '.fasta' unless remote_url.end_with? '.fasta'
|
56
|
-
end
|
57
|
-
# ======================================================================= #
|
58
|
-
# Store this protein sequence at an appropriate location:
|
59
|
-
# ======================================================================= #
|
60
|
-
e
|
61
|
-
erev "Trying to obtain remote data from "\
|
62
|
-
"#{sfancy(remote_url)} #{rev}next:"
|
63
|
-
e
|
64
|
-
store_here = LOCAL_DIRECTORY_FOR_UNIPROT+
|
65
|
-
File.basename(remote_url)
|
66
|
-
# ======================================================================= #
|
67
|
-
# Next create the directory unless it already exists.
|
68
|
-
# ======================================================================= #
|
69
|
-
unless File.directory? LOCAL_DIRECTORY_FOR_UNIPROT
|
70
|
-
mkdir LOCAL_DIRECTORY_FOR_UNIPROT
|
71
|
-
end
|
72
|
-
dataset = URI.open(remote_url).read
|
73
|
-
e "The remote dataset will be stored here: "\
|
74
|
-
"#{sfile(store_here)}"
|
75
|
-
e
|
76
|
-
write_what_into(dataset, store_here)
|
77
|
-
# ======================================================================= #
|
78
|
-
# Next comes a rename action - this will make the .fasta file more
|
79
|
-
# verbose, but I think this may still be helpful, in particular if you
|
80
|
-
# have a lot of .fasta files. There is a switch that controls this
|
81
|
-
# setting though.
|
82
|
-
# ======================================================================= #
|
83
|
-
if do_perform_rename_action
|
84
|
-
# ===================================================================== #
|
85
|
-
# The initially assumed filename may be like this:
|
86
|
-
#
|
87
|
-
# /root/Bioroebe/A2Z669_CSPLT_ORYSI_CASP-like_protein_5A2_OS=Oryza_sativa_subsp_indica_OX=39946_GN=OsI_33147_PE=3_SV=1.fasta
|
88
|
-
#
|
89
|
-
# ===================================================================== #
|
90
|
-
assumed_filename = ::Bioroebe.return_new_filename_based_on_fasta_identifier(store_here)
|
91
|
-
new_filename = LOCAL_DIRECTORY_FOR_UNIPROT+
|
92
|
-
File.basename(assumed_filename)
|
93
|
-
erev "Next renaming `#{sfile(store_here)}#{rev}` to"
|
94
|
-
erev " `#{sfile(new_filename)}`."
|
95
|
-
::Bioroebe.mv(store_here, new_filename)
|
96
|
-
return new_filename
|
97
|
-
end
|
98
|
-
return store_here
|
99
|
-
end
|
100
|
-
end
|
101
|
-
|
102
|
-
# ========================================================================= #
|
103
|
-
# === Bioroebe.wget_download
|
104
|
-
#
|
105
|
-
# This variant will always use "wget" - hence the name.
|
106
|
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# ========================================================================= #
|
107
|
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def self.wget_download(target)
|
108
|
-
esystem "wget #{target}"
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109
|
-
end
|
110
|
-
|
111
|
-
# ========================================================================= #
|
112
|
-
# === Bioroebe.download
|
113
|
-
# ========================================================================= #
|
114
|
-
def self.download(
|
115
|
-
from_these_URLs
|
116
|
-
)
|
117
|
-
require 'open-uri'
|
118
|
-
array_these_urls = [from_these_URLs].flatten.compact
|
119
|
-
array_these_urls.each {|remote_url|
|
120
|
-
# ===================================================================== #
|
121
|
-
# First, we must determine the remote file listing here.
|
122
|
-
# Due to convenience we will simply use curl here.
|
123
|
-
# ===================================================================== #
|
124
|
-
cmd = "curl -s \"#{remote_url}\" --list-only"
|
125
|
-
# e cmd
|
126
|
-
remote_files = `#{cmd}`.split("\n")
|
127
|
-
remote_files.each {|this_remote_file|
|
128
|
-
target = remote_url+this_remote_file
|
129
|
-
e "Downloading `#{this_remote_file}` next. '"\
|
130
|
-
"(Full target: '#{target})"
|
131
|
-
wget_download(target)
|
132
|
-
}
|
133
|
-
}
|
134
|
-
end
|
135
|
-
|
136
|
-
end
|
137
|
-
|
138
|
-
if __FILE__ == $PROGRAM_NAME
|
139
|
-
Bioroebe.download(ARGV)
|
140
|
-
Bioroebe.fetch_data_from_uniprot(ARGV)
|
141
|
-
end # bioroebedownload ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
|
142
|
-
# fetchdatafromuniprot
|
143
|
-
# fetchdatafromuniprot B5ZC00
|
144
|
-
# fetchdatafromuniprot A2Z669
|
145
|
-
# fetchdatafromuniprot P07204_TRBM_HUMAN
|
146
|
-
# fetchdatafromuniprot P20840_SAG1_YEAST
|
@@ -1,20 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/e.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.e
|
11
|
-
# ========================================================================= #
|
12
|
-
def self.e(i = '')
|
13
|
-
puts i
|
14
|
-
end
|
15
|
-
|
16
|
-
end
|
17
|
-
|
18
|
-
if __FILE__ == $PROGRAM_NAME
|
19
|
-
Bioroebe.e('Hello world!')
|
20
|
-
end
|
@@ -1,21 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/editor.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.editor?
|
11
|
-
# ========================================================================= #
|
12
|
-
def self.editor?
|
13
|
-
require 'bioroebe/configuration/constants.rb'
|
14
|
-
::Bioroebe::Configuration::DEFAULT_EDITOR_TO_USE
|
15
|
-
end
|
16
|
-
|
17
|
-
end
|
18
|
-
|
19
|
-
if __FILE__ == $PROGRAM_NAME
|
20
|
-
puts Bioroebe.editor? # Would output "bluefish" on my home setup.
|
21
|
-
end
|
@@ -1,22 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/esystem.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.esystem
|
11
|
-
# ========================================================================= #
|
12
|
-
def self.esystem(i)
|
13
|
-
puts i.to_s
|
14
|
-
system i.to_s
|
15
|
-
end
|
16
|
-
|
17
|
-
end
|
18
|
-
|
19
|
-
if __FILE__ == $PROGRAM_NAME
|
20
|
-
puts 'Running `ls` next:'
|
21
|
-
Bioroebe.esystem 'ls'
|
22
|
-
end
|
@@ -1,74 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/exponential_growth.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.calculate_exponential_growth
|
11
|
-
#
|
12
|
-
# This method can be used to calculate how many bacteria will exist after
|
13
|
-
# n cell divisions (provided that we know, and supply to this method,
|
14
|
-
# how many bacteria existed when we started our calculation).
|
15
|
-
# ========================================================================= #
|
16
|
-
def self.calculate_exponential_growth(
|
17
|
-
number_of_cells = 10,
|
18
|
-
number_of_divisions = 10
|
19
|
-
)
|
20
|
-
if number_of_cells.nil?
|
21
|
-
number_of_cells = 10 # Default value.
|
22
|
-
end
|
23
|
-
if number_of_divisions.nil?
|
24
|
-
number_of_divisions = 10 # Default value.
|
25
|
-
end
|
26
|
-
# ======================================================================= #
|
27
|
-
# === Hashes
|
28
|
-
#
|
29
|
-
# Handle Hash as input given.
|
30
|
-
# ======================================================================= #
|
31
|
-
if number_of_cells.is_a? Hash
|
32
|
-
if number_of_cells.has_key? :n_divisions
|
33
|
-
number_of_divisions = number_of_cells.delete(:n_divisions)
|
34
|
-
end
|
35
|
-
if number_of_cells.has_key? :number_of_cells
|
36
|
-
number_of_cells = number_of_cells.delete(:number_of_cells)
|
37
|
-
elsif number_of_cells.has_key? :n_cells
|
38
|
-
number_of_cells = number_of_cells.delete(:n_cells)
|
39
|
-
end
|
40
|
-
end
|
41
|
-
# ======================================================================= #
|
42
|
-
# We need numbers, aka integers - there are no "1.3" cells.
|
43
|
-
# ======================================================================= #
|
44
|
-
number_of_cells = number_of_cells.to_i
|
45
|
-
number_of_divisions = number_of_divisions.to_i
|
46
|
-
total_amount_of_cells = 0
|
47
|
-
total_amount_of_cells = number_of_cells * (2 ** number_of_divisions)
|
48
|
-
return total_amount_of_cells
|
49
|
-
end
|
50
|
-
|
51
|
-
# ========================================================================= #
|
52
|
-
# === Bioroebe.calculate_original_amount_of_cells_of_exponential_growth
|
53
|
-
#
|
54
|
-
# The first argument, number_of_cells, means "how many cells do we have
|
55
|
-
# now/currently". This is necessary, in order to calculate how many
|
56
|
-
# cells we used to have initially.
|
57
|
-
# ========================================================================= #
|
58
|
-
def self.calculate_original_amount_of_cells_of_exponential_growth(
|
59
|
-
number_of_cells = 1600, # 1600 cells to start with.
|
60
|
-
number_of_divisions = 5 # 5 generations by default.
|
61
|
-
)
|
62
|
-
number_of_cells = number_of_cells.to_i
|
63
|
-
number_of_divisions = number_of_divisions.to_i
|
64
|
-
initial_amount_of_cells_was = 0
|
65
|
-
initial_amount_of_cells_was = number_of_cells / ( 2 ** number_of_divisions )
|
66
|
-
return initial_amount_of_cells_was
|
67
|
-
end
|
68
|
-
|
69
|
-
end
|
70
|
-
|
71
|
-
if __FILE__ == $PROGRAM_NAME
|
72
|
-
puts Bioroebe.calculate_exponential_growth(ARGV[0], ARGV[1])
|
73
|
-
# puts Bioroebe.calculate_original_amount_of_cells_of_exponential_growth()
|
74
|
-
end # calculateexponentialgrowth 10 10
|