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/requires/require_yaml.rb'
|
13
|
-
require 'bioroebe/constants/files_and_directories.rb'
|
14
|
-
|
15
|
-
# ========================================================================= #
|
16
|
-
# === USE_THIS_BROWSER
|
17
|
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#
|
18
|
-
# This constant specifies the default browser to use for the
|
19
|
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# bioroebe-project.
|
20
|
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# ========================================================================= #
|
21
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# /home/x/programming/ruby/src/bioroebe/lib/bioroebe/yaml/configuration/browser.yml
|
22
|
-
# ========================================================================= #
|
23
|
-
if File.exist? "#{project_yaml_directory?}browser.yml"
|
24
|
-
USE_THIS_BROWSER = YAML.load_file(FILE_BROWSER)
|
25
|
-
elsif ENV['BROWSER']
|
26
|
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USE_THIS_BROWSER = ENV['BROWSER'].to_s.dup
|
27
|
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else
|
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|
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USE_THIS_BROWSER = 'firefox' # opera # Hardcoded value in this case..
|
29
|
-
end
|
30
|
-
|
31
|
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# ========================================================================= #
|
32
|
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# === Bioroebe.open_in_browser
|
33
|
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#
|
34
|
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# This method will try to open a remote URL in the specified browser -
|
35
|
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# the one that has been noted down in 'browser.yml'. It is accessed
|
36
|
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# via the Symbol :use_the_default_browser (as second argument to
|
37
|
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# this method).
|
38
|
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#
|
39
|
-
# If you wish to make use of another browser then you can also
|
40
|
-
# pass in the location to the browser as the second argument tp
|
41
|
-
# this method.
|
42
|
-
#
|
43
|
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# Usage example:
|
44
|
-
#
|
45
|
-
# Bioroebe.open_in_browser('derstandard.at')
|
46
|
-
#
|
47
|
-
# ========================================================================= #
|
48
|
-
def self.open_in_browser(
|
49
|
-
this_url,
|
50
|
-
use_this_browser = :use_the_default_browser
|
51
|
-
)
|
52
|
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if this_url.is_a? Array
|
53
|
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this_url.each {|entry|
|
54
|
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open_in_browser(entry, use_this_browser)
|
55
|
-
}
|
56
|
-
else
|
57
|
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case use_this_browser # case tag
|
58
|
-
# ===================================================================== #
|
59
|
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# === :default
|
60
|
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# ===================================================================== #
|
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|
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when :default,
|
62
|
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:use_the_default_browser
|
63
|
-
# =================================================================== #
|
64
|
-
# Sanitize the default setting here, by loading up the content of
|
65
|
-
# the proper yaml file.
|
66
|
-
# =================================================================== #
|
67
|
-
use_this_browser =
|
68
|
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YAML.load_file(FILE_BROWSER)
|
69
|
-
end
|
70
|
-
this_url = ::Bioroebe.try_to_pass_through_beautiful_url(this_url)
|
71
|
-
esystem "#{use_this_browser.strip} -new-tab #{this_url}"
|
72
|
-
end
|
73
|
-
end
|
74
|
-
|
75
|
-
end
|
76
|
-
|
77
|
-
if __FILE__ == $PROGRAM_NAME
|
78
|
-
Bioroebe.open_in_browser 'https://www.youtube.com/'
|
79
|
-
end # rb open_in_browser.rb
|
@@ -1,236 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/open_reading_frames.rb'
|
6
|
-
# Bioroebe.return_longest_ORF_from_this_sequence(ARGV)
|
7
|
-
# Bioroebe.return_all_open_reading_frames_from_this_sequence
|
8
|
-
# Bioroebe.return_n_ORFs_in_this_sequence
|
9
|
-
# Bioroebe.open_reading_frames_to_aminoacid_sequence
|
10
|
-
# =========================================================================== #
|
11
|
-
module Bioroebe
|
12
|
-
|
13
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
14
|
-
require 'bioroebe/codons/codons.rb'
|
15
|
-
|
16
|
-
# ========================================================================= #
|
17
|
-
# === Bioroebe.return_longest_ORF_from_this_sequence
|
18
|
-
#
|
19
|
-
# This method will return the longest ORF from the given input
|
20
|
-
# sequence. By default it will assume that the input sequence
|
21
|
-
# is meant to have derived from a dsDNA sequence, so the
|
22
|
-
# reverse complement is evaluated as well. If you do not need
|
23
|
-
# or want that behaviour then simply pass "false" as the
|
24
|
-
# second argument to this method.
|
25
|
-
#
|
26
|
-
# Usage example:
|
27
|
-
#
|
28
|
-
# x = Bioroebe.return_longest_ORF_from_this_sequence; puts x
|
29
|
-
#
|
30
|
-
# ========================================================================= #
|
31
|
-
def self.return_longest_ORF_from_this_sequence(
|
32
|
-
i =
|
33
|
-
'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGC'\
|
34
|
-
'GACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATC'\
|
35
|
-
'CGAGTAGCATCTCAG',
|
36
|
-
check_reverse_complement_as_well = true,
|
37
|
-
start_codon = ::Bioroebe.start_codon?,
|
38
|
-
stop_codons = ::Bioroebe.stop_codons? # ← This method will yield an Array.
|
39
|
-
)
|
40
|
-
results = Bioroebe.return_all_open_reading_frames_from_this_sequence(
|
41
|
-
i, check_reverse_complement_as_well, start_codon, stop_codons
|
42
|
-
).sort_by {|entry| entry.size }.reverse
|
43
|
-
longest_result = results.first
|
44
|
-
return longest_result
|
45
|
-
end; self.instance_eval { alias return_longest_open_reading_frame_from_this_sequence return_longest_ORF_from_this_sequence } # === Bioroebe.return_longest_open_reading_frame_from_this_sequence
|
46
|
-
self.instance_eval { alias longest_ORF? return_longest_ORF_from_this_sequence } # === Bioroebe.longest_ORF?
|
47
|
-
|
48
|
-
# ========================================================================= #
|
49
|
-
# === Bioroebe.return_all_open_reading_frames_from_this_sequence
|
50
|
-
#
|
51
|
-
# This method will return an Array of all open reading frames from the
|
52
|
-
# given input-sequence.
|
53
|
-
#
|
54
|
-
# The second argument to this method, called `check_reverse_complement_as_well`,
|
55
|
-
# can be used to find the reverse complement.
|
56
|
-
#
|
57
|
-
# Usage examples:
|
58
|
-
#
|
59
|
-
#
|
60
|
-
# x = Bioroebe.return_all_open_reading_frames_from_this_sequence('AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG', true)
|
61
|
-
#
|
62
|
-
# Bioroebe.return_all_open_reading_frames_from_this_sequence # =>
|
63
|
-
#
|
64
|
-
# ["ATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAG", "ATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGA", "ATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGA", "ATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAG", "ATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGA", "ATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAA", "ATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAA", "ATGTAGCTAACTCAGGTTACATGGGGATGA", "ATGTAG"]
|
65
|
-
#
|
66
|
-
# ========================================================================= #
|
67
|
-
def self.return_all_open_reading_frames_from_this_sequence(
|
68
|
-
i =
|
69
|
-
'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG',
|
70
|
-
check_reverse_complement_as_well = true,
|
71
|
-
start_codon = ::Bioroebe.start_codon?,
|
72
|
-
stop_codons = ::Bioroebe.stop_codons? # ← This method will yield an Array.
|
73
|
-
)
|
74
|
-
if i.is_a? Array
|
75
|
-
# ===================================================================== #
|
76
|
-
# Only handle the first entry in the event that an Array was given.
|
77
|
-
# ===================================================================== #
|
78
|
-
i = i.first
|
79
|
-
end
|
80
|
-
array = [] # ← We will return this Array.
|
81
|
-
if stop_codons.empty?
|
82
|
-
# ===================================================================== #
|
83
|
-
# In this case we will use a hardcoded approach and define all
|
84
|
-
# valid stop codons, referring to the eukaryotic genome.
|
85
|
-
# ===================================================================== #
|
86
|
-
stop_codons = %w(
|
87
|
-
TAG TGA TAA
|
88
|
-
)
|
89
|
-
end
|
90
|
-
# ======================================================================= #
|
91
|
-
# Find all positions for start codons next; it will be stored in
|
92
|
-
# an Array that contains all indices thereof.
|
93
|
-
# ======================================================================= #
|
94
|
-
all_start_codons = (0 ... i.length).find_all { |entry|
|
95
|
-
i[entry, 3] == start_codon # First three must equal the start_codon.
|
96
|
-
}
|
97
|
-
array_all_subsequences = []
|
98
|
-
all_start_codons.each {|start_index|
|
99
|
-
subsequence = i[start_index .. -1]
|
100
|
-
array_all_subsequences << subsequence
|
101
|
-
}
|
102
|
-
# ======================================================================= #
|
103
|
-
# Now that we have all subsequences (stored in array_all_subsequences)
|
104
|
-
# we can now match all subsequences that end with a stop codon.
|
105
|
-
# ======================================================================= #
|
106
|
-
array_all_subsequences.each {|sequence|
|
107
|
-
# ===================================================================== #
|
108
|
-
# We know that these sequences must begin with 'ATG'. Now we must
|
109
|
-
# determine all remaining sequences with a stop-sequence here,
|
110
|
-
# but only if they are in-frame (aka can be divided by 3).
|
111
|
-
#
|
112
|
-
# In order to simplify this, we will group these sequences
|
113
|
-
# in pairs of three.
|
114
|
-
# ===================================================================== #
|
115
|
-
scanned = sequence.scan(/.../)
|
116
|
-
scanned.each_with_index {|codon, index| index += 1
|
117
|
-
if stop_codons.include? codon # In this case it is a valid stop-codon.
|
118
|
-
array << sequence[0 .. ((index * 3)-1)]
|
119
|
-
end
|
120
|
-
}
|
121
|
-
}
|
122
|
-
# ======================================================================= #
|
123
|
-
# The next check will also include the reverse complement as well.
|
124
|
-
# ======================================================================= #
|
125
|
-
if check_reverse_complement_as_well
|
126
|
-
array << return_all_open_reading_frames_from_this_sequence(i.reverse, false)
|
127
|
-
end
|
128
|
-
array.flatten!
|
129
|
-
# ======================================================================= #
|
130
|
-
# Sort by size next - longest substring is returned first.
|
131
|
-
# ======================================================================= #
|
132
|
-
array = array.sort_by {|entry| entry.size }.reverse
|
133
|
-
return array
|
134
|
-
end; self.instance_eval { alias open_reading_frames return_all_open_reading_frames_from_this_sequence } # === Bioroebe.open_reading_frames
|
135
|
-
|
136
|
-
# ========================================================================= #
|
137
|
-
# === Bioroebe.return_n_ORFs_in_this_sequence
|
138
|
-
#
|
139
|
-
# Return how many ORFs are in a given sequence.
|
140
|
-
# ========================================================================= #
|
141
|
-
def self.return_n_ORFs_in_this_sequence(
|
142
|
-
i =
|
143
|
-
'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG',
|
144
|
-
start_codon = Bioroebe.to_aa(::Bioroebe.start_codon?)
|
145
|
-
)
|
146
|
-
if i.is_a? Array
|
147
|
-
i = i.join
|
148
|
-
end
|
149
|
-
if i.is_a? String
|
150
|
-
i = i.chars
|
151
|
-
end
|
152
|
-
n_ORFs_in_this_sequence = 0
|
153
|
-
all_start_codons = (0 ... i.length).find_all {|index|
|
154
|
-
i[index] == start_codon
|
155
|
-
}
|
156
|
-
stop_codons_are_at_that_position = (0 ... i.length).find_all {|index|
|
157
|
-
i[index] == '*'
|
158
|
-
}
|
159
|
-
all_start_codons.each {|this_start_codon_position|
|
160
|
-
stop_codons_are_at_that_position.each {|this_stop_codon_position|
|
161
|
-
if this_start_codon_position < this_stop_codon_position
|
162
|
-
n_ORFs_in_this_sequence += 1
|
163
|
-
break
|
164
|
-
end
|
165
|
-
}
|
166
|
-
}
|
167
|
-
return n_ORFs_in_this_sequence
|
168
|
-
end
|
169
|
-
|
170
|
-
# ========================================================================= #
|
171
|
-
# === Bioroebe.display_all_open_reading_frames_from_this_sequence
|
172
|
-
# ========================================================================= #
|
173
|
-
def self.display_all_open_reading_frames_from_this_sequence(i = ARGV)
|
174
|
-
require 'bioroebe/colours/colours.rb'
|
175
|
-
if i.empty?
|
176
|
-
array = Bioroebe.return_all_open_reading_frames_from_this_sequence
|
177
|
-
pp array
|
178
|
-
pp Bioroebe.to_aa(array)
|
179
|
-
else
|
180
|
-
this_sequence = i
|
181
|
-
array = return_all_open_reading_frames_from_this_sequence(this_sequence)
|
182
|
-
this_sequence = this_sequence.join
|
183
|
-
if array.empty?
|
184
|
-
e "No open reading from has been found from "\
|
185
|
-
"this sequence: #{this_sequence}"
|
186
|
-
else
|
187
|
-
e rev+
|
188
|
-
'The following ORFs have been found in this sequence: '
|
189
|
-
e
|
190
|
-
e " #{Colours.lightgreen(this_sequence)}"
|
191
|
-
e
|
192
|
-
array.each_with_index {|sequence, index| index += 1
|
193
|
-
name_for_the_ORF = "ORF number #{index}"
|
194
|
-
e " #{Colours.steelblue(sequence.ljust(50))} "\
|
195
|
-
"#{Colours.lightslategrey('#')} "\
|
196
|
-
"#{Colours.mediumseagreen(name_for_the_ORF)}"
|
197
|
-
}
|
198
|
-
e
|
199
|
-
end
|
200
|
-
end
|
201
|
-
end
|
202
|
-
|
203
|
-
# ========================================================================= #
|
204
|
-
# === Bioroebe.open_reading_frames_to_aminoacid_sequence
|
205
|
-
#
|
206
|
-
# This method is similar to Bioroebe.open_reading_frames(), but it
|
207
|
-
# will additionally convert to the corresponding aminoacids at once.
|
208
|
-
#
|
209
|
-
# This method will return a String as a result.
|
210
|
-
#
|
211
|
-
# Usage example:
|
212
|
-
#
|
213
|
-
# x = Bioroebe.open_reading_frames_to_aminoacid_sequence('AAAATGGGCCCATGA') # => ["MGP"]
|
214
|
-
#
|
215
|
-
# ========================================================================= #
|
216
|
-
def self.open_reading_frames_to_aminoacid_sequence(
|
217
|
-
i = 'AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGA'\
|
218
|
-
'TTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG'
|
219
|
-
)
|
220
|
-
all_aminoacids = ::Bioroebe.open_reading_frames(i).map {|nucleotide_sequence|
|
221
|
-
::Bioroebe.to_aa(nucleotide_sequence)
|
222
|
-
}
|
223
|
-
if all_aminoacids
|
224
|
-
all_aminoacids = all_aminoacids.first
|
225
|
-
end
|
226
|
-
return all_aminoacids
|
227
|
-
end
|
228
|
-
|
229
|
-
end
|
230
|
-
|
231
|
-
if __FILE__ == $PROGRAM_NAME
|
232
|
-
require 'colours/autoinclude.rb'
|
233
|
-
Bioroebe.display_all_open_reading_frames_from_this_sequence(ARGV)
|
234
|
-
end # openreadingframes AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG
|
235
|
-
# openreadingframes AGTATGGGGATGTAGGTA
|
236
|
-
# openreadingframes ATGATGTGA
|
@@ -1,34 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/opn.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.permanently_disable_opn
|
11
|
-
#
|
12
|
-
# The purpose of this method is to permanently disable opn for the
|
13
|
-
# whole Bioroebe-project.
|
14
|
-
# ========================================================================= #
|
15
|
-
def self.permanently_disable_opn
|
16
|
-
require 'bioroebe/project/project.rb'
|
17
|
-
require 'bioroebe/colours/colours.rb'
|
18
|
-
require 'bioroebe/toplevel_methods/e.rb'
|
19
|
-
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
20
|
-
erev 'Permanently disabling the use of opn for the Bioroebe project next.'
|
21
|
-
target_dir = CONFIGURATION_DIRECTORY
|
22
|
-
target_file = "#{target_dir}use_opn.yml"
|
23
|
-
if File.exist? target_file
|
24
|
-
erev 'Modifying the file `'+
|
25
|
-
sfile(target_file)+rev+'` next.'
|
26
|
-
write_what_into('false', target_file)
|
27
|
-
end
|
28
|
-
end
|
29
|
-
|
30
|
-
end
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-
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if __FILE__ == $PROGRAM_NAME
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Bioroebe.permanently_disable_opn
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end # bioroebepermanentlydisableopn
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@@ -1,155 +0,0 @@
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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/toplevel_methods/palindromes.rb'
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# Bioroebe.plain_palindrome(ARGV)
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# puts Bioroebe.is_palindrome? ARGV
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# =========================================================================== #
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module Bioroebe
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require 'bioroebe/toplevel_methods/e.rb'
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-
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# ========================================================================= #
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# === Bioroebe.plain_palindrome
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#
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# This method is simply than Bioroebe.is_palindrome?. It will simply
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# check for the current sequence.
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#
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# Usage example:
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#
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# Bioroebe.plain_palindrome('OTTO') # => true
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# Bioroebe.plain_palindrome('Saippuakivikauppias') # => true
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#
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# ========================================================================= #
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def self.plain_palindrome(i)
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if i.is_a? Array
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i = i.join(' ').strip
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end
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i = i.dup.downcase
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if i.size.even?
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first_half = i[0 .. (i.size / 2 - 1)]
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second_half = i[(i.size / 2) .. -1]
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return (first_half == second_half.reverse)
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else # This is for odd numbers.
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first_half = i[0 .. (i.size / 2 - 1)]
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second_half = i[(i.size / 2 + 1) .. -1]
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return (first_half == second_half.reverse)
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end
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end
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# ========================================================================= #
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# === Bioroebe.is_palindrome?
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#
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# This method will return true if the target sequence is a palindrome,
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# and false otherwise.
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#
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# When will a sequence be considered to be a "palindrome"?
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#
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# Firstly, it must have an even number of components. If it has an odd
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# number then it can never be a Palindrome, by definition alone.
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#
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# So, "GATC" is a palindrome, but "GATCC" can never be. (GATC is a
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# palindrome because the reverse of GATC will bind to itself again.)
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#
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# Usage examples:
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#
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# Bioroebe.is_palindrome? 'GAATTC' # => true
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# Bioroebe.is_palindrome? 'GAATTCCC' # => false
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#
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# ========================================================================= #
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def self.is_palindrome?(i)
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require 'bioroebe/toplevel_methods/nucleotides.rb'
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if i.is_a? Array
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i = i.first
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end
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hash = ::Bioroebe.partner_nucleotide_hash
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return_value = false
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if i
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if i.to_s.size.odd? # Then it can never be a Palindrome.
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else # Ok, it may be a palindrome here.
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first_half = i[0 .. (i.size / 2)-1]
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_ = ''.dup
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first_half.chars.reverse.each {|char|
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_ << hash[char] if hash.has_key? char
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}
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if (first_half + _) == i # Compare it to the original input.
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return_value = true
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end
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end
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return return_value
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else
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:invalid_input
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end
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end; self.instance_eval { alias is_this_sequence_a_palindrome? is_palindrome? } # === Bioroebe.is_this_sequence_a_palindrome?
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# ========================================================================= #
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# === Bioroebe.return_every_substring_from_this_sequence
|
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# ========================================================================= #
|
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def self.return_every_substring_from_this_sequence(i)
|
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result = []
|
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i.chars.each_with_index {|entry, index|
|
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result << i[0, (index+1)]
|
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}
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return result
|
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end
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|
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# ========================================================================= #
|
98
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# === Bioroebe.every_reverse_palindrome_in_this_string
|
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#
|
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# This method can return every reverse palindrome in the given input
|
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# String.
|
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#
|
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# The output will be an Array such as this:
|
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#
|
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# [[4, 6], [5, 4], [6, 6], [7, 4], [17, 4], [18, 4], [4, 6], [5, 4]]
|
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|
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#
|
107
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# ========================================================================= #
|
108
|
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def self.every_reverse_palindrome_in_this_string(
|
109
|
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i = 'TCAATGCATGCGGGTCTATATGCAT',
|
110
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min_length = 4,
|
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max_length = 12
|
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)
|
113
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require 'bioroebe/sequence/reverse_complement.rb'
|
114
|
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if i.is_a? Array # Arrays will become Strings - or rather, whatever is the first argument.
|
115
|
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i = i.first
|
116
|
-
end
|
117
|
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if i and File.exist?(i)
|
118
|
-
i = File.readlines(i).reject {|entry|
|
119
|
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entry.start_with?('>')
|
120
|
-
}.map {|inner_entry| inner_entry.strip }.join
|
121
|
-
end
|
122
|
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# ======================================================================= #
|
123
|
-
# How do we find all subsequences that are relevant? Well - we
|
124
|
-
# need to find all the sequences between min_length and
|
125
|
-
# max_length, e. g. 4 and 12.
|
126
|
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# ======================================================================= #
|
127
|
-
string = i.dup
|
128
|
-
array_containing_starting_index_and_length_of_reverse_palindromes = []
|
129
|
-
i.size.times {
|
130
|
-
substrings = return_every_substring_from_this_sequence(string)
|
131
|
-
substrings.each {|entry|
|
132
|
-
next if entry.size > max_length
|
133
|
-
if (entry.size >= min_length) and
|
134
|
-
(Bioroebe.reverse_complement(entry) == entry)
|
135
|
-
array_containing_starting_index_and_length_of_reverse_palindromes <<
|
136
|
-
[i.index(entry)+1, entry.size]
|
137
|
-
end
|
138
|
-
}
|
139
|
-
string[0,1] = ''
|
140
|
-
}
|
141
|
-
return array_containing_starting_index_and_length_of_reverse_palindromes
|
142
|
-
end
|
143
|
-
|
144
|
-
end
|
145
|
-
|
146
|
-
if __FILE__ == $PROGRAM_NAME
|
147
|
-
pp Bioroebe.every_reverse_palindrome_in_this_string(ARGV)
|
148
|
-
if ARGV.empty?
|
149
|
-
p 'GAATTC: '+Bioroebe.is_palindrome?('GAATTC').to_s # => true
|
150
|
-
p 'GAATTCCC: '+Bioroebe.is_palindrome?('GAATTCCC').to_s # => false
|
151
|
-
else
|
152
|
-
p Bioroebe.is_palindrome? ARGV
|
153
|
-
end
|
154
|
-
end # ispalindrome GATC # true
|
155
|
-
# ispalindrome GAAG # false
|
@@ -1,59 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# require 'bioroebe/toplevel_methods/parse.rb'
|
6
|
-
# =========================================================================== #
|
7
|
-
module Bioroebe
|
8
|
-
|
9
|
-
# ========================================================================= #
|
10
|
-
# === Bioroebe.parse
|
11
|
-
#
|
12
|
-
# This is a general parse-related method.
|
13
|
-
#
|
14
|
-
# The main ideafor this method is to parse files in particular, in a
|
15
|
-
# simplified manner. That means, for example, if the input to this
|
16
|
-
# method is a genbank file, then this method will simply return the
|
17
|
-
# sequence. If it is a .pdb file, same thing. A .fasta file, same
|
18
|
-
# result - the content will be returned. Thus, this method attempts
|
19
|
-
# to make it simpler to parse a wide array of different file
|
20
|
-
# formats - simply feed it what you want and you get the
|
21
|
-
# "most logical" output.
|
22
|
-
# ========================================================================= #
|
23
|
-
def self.parse(
|
24
|
-
i = ARGV
|
25
|
-
)
|
26
|
-
if i.is_a? Array
|
27
|
-
i = i.first
|
28
|
-
end
|
29
|
-
if i
|
30
|
-
case i
|
31
|
-
# ===================================================================== #
|
32
|
-
# === .genbank
|
33
|
-
# ===================================================================== #
|
34
|
-
when /\.genbank$/i
|
35
|
-
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
36
|
-
i = Bioroebe.genbank_to_fasta(i, :be_quiet)
|
37
|
-
# ===================================================================== #
|
38
|
-
# === .pdb
|
39
|
-
# ===================================================================== #
|
40
|
-
when /\.pdb$/i
|
41
|
-
require 'bioroebe/pdb/parse_pdb_file.rb'
|
42
|
-
i = Bioroebe.return_aminoacid_sequence_from_this_pdb_file(i)
|
43
|
-
# ===================================================================== #
|
44
|
-
# === .fasta
|
45
|
-
# ===================================================================== #
|
46
|
-
when /\.fasta$/i,
|
47
|
-
/\.fa$/i
|
48
|
-
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
49
|
-
i = Bioroebe::ParseFasta.new(i) { :be_quiet }.sequence?
|
50
|
-
end
|
51
|
-
return i
|
52
|
-
end
|
53
|
-
end
|
54
|
-
|
55
|
-
end
|
56
|
-
|
57
|
-
if __FILE__ == $PROGRAM_NAME
|
58
|
-
puts Bioroebe.parse(ARGV)
|
59
|
-
end # bioroebeparse
|