bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -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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# === Bioroebe::Taxonomy::Chart
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#
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# The "Taxonomy Chart" keeps tracks of all of our nodes.
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#
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# Unfortunately this is way too slow.
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#
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# Usage example:
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#
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# x = Bioroebe::Taxonomy::Chart.new; x.find_id 55
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#
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# =========================================================================== #
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require 'bioroebe/base/commandline_application/commandline_application.rb'
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module Bioroebe
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module Taxonomy # === Bioroebe::Taxonomy
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# =========================================================================== #
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# === Bioroebe::Taxonomy::Chart
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# =========================================================================== #
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class Chart < ::Bioroebe::CommandlineApplication
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attr_accessor :hash
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# ========================================================================= #
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# === initialize
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# ========================================================================= #
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def initialize(
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dataset = nodes?,
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run_already = true
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) # Initialized with all nodes.
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reset
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@dataset = dataset
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run if run_already
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end
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# ========================================================================= #
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# === reset (reset tag)
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# ========================================================================= #
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def reset
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super()
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# ======================================================================= #
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# === @hash
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# ======================================================================= #
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@hash = {} # Main hash to keep all of our Nodes.
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end
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# ========================================================================= #
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# === find_parent_of
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#
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# Find the parent here.
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# ========================================================================= #
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def find_parent_of(i)
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result = find_id(i)
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cliner {
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pp result
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pp result
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pp result
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}
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return result.parent_taxid
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end; alias find_parent find_parent_of # === find_parent
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# ========================================================================= #
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# === populate_hash_from_the_dataset
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# ========================================================================= #
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def populate_hash_from_the_dataset
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@dataset.each {|entry|
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new_node = Node.parse(entry)
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id = new_node.taxid.to_sym
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@hash[id] = new_node
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}
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end
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# ========================================================================= #
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# === run
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# ========================================================================= #
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def run
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populate_hash_from_the_dataset
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remove_instance_variable :@dataset # Dont need it anymore here.
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return @hash
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end
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# ========================================================================= #
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# === Bioroebe::Taxonomy::Chart[]
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# ========================================================================= #
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def [](i)
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i = i.to_sym unless i.is_a? Fixnum # For now these are symbols.
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return @hash[i]
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end; alias find_id [] # === find_id
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end; end; end
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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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# We bundle class-method related code of the Taxonomy module here.
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# =========================================================================== #
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module Bioroebe
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module Taxonomy # === Bioroebe::Taxonomy
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require 'bioroebe/taxonomy/shared.rb'
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require 'bioroebe/colours/rev.rb'
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require 'bioroebe/toplevel_methods/extract.rb'
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require 'bioroebe/toplevel_methods/time_and_date.rb'
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require 'bioroebe/toplevel_methods/taxonomy.rb'
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require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
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extend Colours::E
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extend Taxonomy::Shared
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# ========================================================================= #
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# === status
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#
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# Invoke this method like that:
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#
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# Taxonomy.status
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#
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# ========================================================================= #
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def self.status
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e "The status for the Taxonomy-related datafiles is as follows:#{N}"
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array = %w(
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names.dmp
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merged.dmp
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delnodes.dmp
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citations.dmp
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nodes.dmp
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taxdump.tar
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)
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sorted_array = array.sort_by {|entry| File.size?(entry) }
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sorted_array.reverse.each {|entry|
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file = base_dir?+entry
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if File.exist? file
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filesize = File.size?(file)
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_ = ('The file `'+file+'` exists.').ljust(65, ' ')
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_ << (' (Filesize: '+filesize.to_s+')').ljust(30, ' ')
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e _
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if entry.include? 'dump.tar'
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e 'Consider extracting this .tar-file if it was not yet '+
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'extracted - it contains the various .dmp files.'
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end
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else
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e 'We could not find any file at '+sfile(file)
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end
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}
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end
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require 'bioroebe/toplevel_methods/download_and_fetch_data.rb' # Needed for wget-like functionality.
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# ========================================================================= #
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# === Bioroebe::Taxonomy.download_directory?
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# ========================================================================= #
|
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|
+
def self.download_directory?
|
63
|
+
DOWNLOAD_DIR
|
64
|
+
end
|
65
|
+
|
66
|
+
# ========================================================================= #
|
67
|
+
# === Bioroebe::Taxonomy.status? (status tag)
|
68
|
+
#
|
69
|
+
# Feedback the status to the user.
|
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|
+
# ========================================================================= #
|
71
|
+
def self.status?
|
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|
+
e
|
73
|
+
e 'The localomics URL should be at:'
|
74
|
+
e ' '+sfancy('http://localomics.imp.univie.ac.at:8666/')
|
75
|
+
e 'The shared data of the local mirror can be found at: '
|
76
|
+
e ' '+sdir(LOCAL_MIRROR)
|
77
|
+
e 'The shared folder (where we generate our .sql files '+
|
78
|
+
'to) can be found at: '
|
79
|
+
e ' '+sdir(AUTOGENERATED_SQL_FILES_DIR)
|
80
|
+
e 'The '+File.basename(LOCALOME_DIR)+'/ directory can be found at: '
|
81
|
+
e ' '+sdir(LOCALOME_DIR)
|
82
|
+
e 'The '+File.basename(AA_DIR)+'/ directory can be found at: '
|
83
|
+
e ' '+sdir(AA_DIR)
|
84
|
+
e 'The '+File.basename(NT_DIR)+'/ directory can be found at: '
|
85
|
+
e ' '+sdir(NT_DIR)
|
86
|
+
e 'The '+File.basename(INFO_DIR)+'/ directory can be found at: '
|
87
|
+
e ' '+sdir(INFO_DIR)
|
88
|
+
e 'The '+File.basename(INCOMING_DIR)+'/ directory can be found at: '
|
89
|
+
e ' '+sdir(INCOMING_DIR)
|
90
|
+
e
|
91
|
+
end
|
92
|
+
|
93
|
+
# ========================================================================= #
|
94
|
+
# === Taxonomy.cleanup
|
95
|
+
#
|
96
|
+
# Get rid of some .sql files through this method here.
|
97
|
+
# ========================================================================= #
|
98
|
+
def self.cleanup
|
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|
+
e 'Trying to remove some files now.'
|
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|
+
i = 'names.sql'
|
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|
+
remove_file(i) if File.exist? i
|
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|
+
i = 'nodes.sql'
|
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|
+
remove_file(i) if File.exist? i
|
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|
+
end
|
105
|
+
|
106
|
+
# ========================================================================= #
|
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|
+
# === Taxonomy.load
|
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|
+
#
|
109
|
+
# Load a specific .dmp file via this method.
|
110
|
+
#
|
111
|
+
# The first argument should be the target location of the file that we
|
112
|
+
# wish to load (we assume this to be a local file for now).
|
113
|
+
# ========================================================================= #
|
114
|
+
def self.load(_ = 'taxonomy/citations.dmp')
|
115
|
+
if File.exist? _
|
116
|
+
data = File.readlines(_).map {|line| sanitize(line) } # Needed because File.readlines() may read in an invalid encoding.
|
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|
+
return data
|
118
|
+
else
|
119
|
+
e 'File at location `'+_+'` does not exist.'
|
120
|
+
return nil
|
121
|
+
end
|
122
|
+
end
|
123
|
+
|
124
|
+
# ========================================================================= #
|
125
|
+
# === project_base_dir?
|
126
|
+
# ========================================================================= #
|
127
|
+
def project_base_dir?
|
128
|
+
Taxonomy.base_dir?
|
129
|
+
end; alias base_dir? project_base_dir? # === base_dir?
|
130
|
+
|
131
|
+
# ========================================================================= #
|
132
|
+
# === Taxonomy.base_dir?
|
133
|
+
# ========================================================================= #
|
134
|
+
def self.base_dir?
|
135
|
+
PROJECT_BASE_DIR2
|
136
|
+
end
|
137
|
+
|
138
|
+
# ========================================================================= #
|
139
|
+
# === Taxonomy.be_verbose?
|
140
|
+
# ========================================================================= #
|
141
|
+
def self.be_verbose?
|
142
|
+
Taxonomy::Constants::BE_VERBOSE
|
143
|
+
end
|
144
|
+
|
145
|
+
# ========================================================================= #
|
146
|
+
# === Taxonomy.report_n_species
|
147
|
+
#
|
148
|
+
# This method will report how many species are registered in
|
149
|
+
# the NCBI database.
|
150
|
+
# ========================================================================= #
|
151
|
+
def self.report_n_species
|
152
|
+
remote_url = 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics&unclassified=hide&uncultured=hide&unspecified=hide&period=&from=&to='
|
153
|
+
e 'We will now obtain how many species are registered. This '\
|
154
|
+
'may take a while.'
|
155
|
+
e
|
156
|
+
e 'In 26.09.2011, the Taxonomy database included exactly'
|
157
|
+
e '234_991 species with a formal name.'
|
158
|
+
e
|
159
|
+
# ======================================================================= #
|
160
|
+
# See: http://rubular.com/r/awsCk2nF4D
|
161
|
+
# ======================================================================= #
|
162
|
+
regex_to_use = /gov\/taxonomy\/\?term.+">(\d+)<\/A><\/TD>\s+<\/TR>$/
|
163
|
+
dataset = open(remote_url).read.split(N)
|
164
|
+
_ = ''
|
165
|
+
is_open = false
|
166
|
+
dataset.each {|line|
|
167
|
+
if is_open
|
168
|
+
_ << line
|
169
|
+
end
|
170
|
+
if line.include? '<TR><TD><A HREF="/Taxonomy/Browser/wwwtax.cgi?id=1">All taxa</A></TD>'
|
171
|
+
is_open = true
|
172
|
+
elsif line.include? '</TR>'
|
173
|
+
is_open = false
|
174
|
+
end
|
175
|
+
}
|
176
|
+
_ =~ regex_to_use
|
177
|
+
n_species = $1.to_s.dup
|
178
|
+
e 'We found `'+sfancy(n_species)+::Bioroebe.rev+'` registered species.'
|
179
|
+
end; self.instance_eval { alias report_species report_n_species } # === Taxonomy.report_species
|
180
|
+
|
181
|
+
end; end
|
@@ -0,0 +1,26 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
module Bioroebe
|
6
|
+
|
7
|
+
module Taxonomy # === Bioroebe::Taxonomy
|
8
|
+
|
9
|
+
require 'bioroebe/colours/colours.rb'
|
10
|
+
|
11
|
+
# ========================================================================= #
|
12
|
+
# === Bioroebe::Taxonomy.use_colours?
|
13
|
+
# ========================================================================= #
|
14
|
+
def self.use_colours?
|
15
|
+
::Bioroebe.use_colours?
|
16
|
+
end
|
17
|
+
|
18
|
+
# ========================================================================= #
|
19
|
+
# === Bioroebe::Taxonomy.enable_colours
|
20
|
+
# ========================================================================= #
|
21
|
+
def self.enable_colours
|
22
|
+
e 'Enabling colours.'
|
23
|
+
::Bioroebe.enable_colours
|
24
|
+
end
|
25
|
+
|
26
|
+
end; end
|
@@ -0,0 +1,218 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
module Bioroebe
|
6
|
+
|
7
|
+
module Taxonomy
|
8
|
+
|
9
|
+
module Constants # === Bioroebe::Taxonomy::Constants
|
10
|
+
|
11
|
+
require 'bioroebe/toplevel_methods/log_directory.rb'
|
12
|
+
|
13
|
+
# ========================================================================= #
|
14
|
+
# === FILE_USE_THIS_DATABASE
|
15
|
+
# ========================================================================= #
|
16
|
+
FILE_USE_THIS_DATABASE =
|
17
|
+
"#{::Bioroebe::Taxonomy.project_base_dir?}yaml/use_this_database.yml"
|
18
|
+
|
19
|
+
# ========================================================================= #
|
20
|
+
# === BE_VERBOSE
|
21
|
+
# ========================================================================= #
|
22
|
+
BE_VERBOSE = true
|
23
|
+
|
24
|
+
# ========================================================================= #
|
25
|
+
# === POSTGRESQL_QUERY_SIZE
|
26
|
+
#
|
27
|
+
# We want to query the size of the postgresql database -
|
28
|
+
# the following string achieves precisely that.
|
29
|
+
# ========================================================================= #
|
30
|
+
POSTGRESQL_QUERY_SIZE = <<-EOF
|
31
|
+
|
32
|
+
SELECT nspname || '.' || relname AS "relation",
|
33
|
+
pg_size_pretty(pg_total_relation_size(C.oid)) AS "total_size"
|
34
|
+
FROM pg_class C
|
35
|
+
LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
|
36
|
+
WHERE nspname NOT IN ('pg_catalog', 'information_schema')
|
37
|
+
AND C.relkind <> 'i'
|
38
|
+
AND nspname !~ '^pg_toast'
|
39
|
+
ORDER BY pg_total_relation_size(C.oid) DESC
|
40
|
+
LIMIT 20;
|
41
|
+
|
42
|
+
EOF
|
43
|
+
|
44
|
+
# ========================================================================= #
|
45
|
+
# === ARRAY_PROJECT_FILES
|
46
|
+
#
|
47
|
+
# We list, at the least the more important, project files here.
|
48
|
+
# ========================================================================= #
|
49
|
+
ARRAY_PROJECT_FILES = %w(
|
50
|
+
info.rb
|
51
|
+
interactive.rb
|
52
|
+
parse_fasta.rb
|
53
|
+
shared.rb
|
54
|
+
taxonomy.rb
|
55
|
+
INSTRUCTIONS.md
|
56
|
+
)
|
57
|
+
|
58
|
+
# ========================================================================= #
|
59
|
+
# === POSTGRE_LOGIN_COMMAND
|
60
|
+
# ========================================================================= #
|
61
|
+
POSTGRE_LOGIN_COMMAND = '
|
62
|
+
psql --host=bunuel.imp.univie.ac.at --port=5471 --username=dummy --dbname=dummy_db --quiet
|
63
|
+
'.delete("\n").strip
|
64
|
+
|
65
|
+
# ========================================================================= #
|
66
|
+
# === SHARED_HOME
|
67
|
+
# ========================================================================= #
|
68
|
+
SHARED_HOME = ::Bioroebe.log_dir?
|
69
|
+
|
70
|
+
# ========================================================================= #
|
71
|
+
# === TMP_DIR
|
72
|
+
# ========================================================================= #
|
73
|
+
TMP_DIR = ::Bioroebe.log_dir?
|
74
|
+
TEMP_DIR = TMP_DIR
|
75
|
+
|
76
|
+
# ========================================================================= #
|
77
|
+
# The two main .sql files of interest, are NODES_SQL and NAMES_SQL.
|
78
|
+
# Note that for the following constants to work,
|
79
|
+
# AUTOGENERATED_SQL_FILES_DIR must have been defined.
|
80
|
+
# ========================================================================= #
|
81
|
+
|
82
|
+
# ========================================================================= #
|
83
|
+
# === NODES_SQL
|
84
|
+
# ========================================================================= #
|
85
|
+
NODES_SQL = AUTOGENERATED_SQL_FILES_DIR+'nodes.sql'
|
86
|
+
|
87
|
+
# ========================================================================= #
|
88
|
+
# === NAMES_SQL
|
89
|
+
# ========================================================================= #
|
90
|
+
NAMES_SQL = AUTOGENERATED_SQL_FILES_DIR+'names.sql'
|
91
|
+
|
92
|
+
# ========================================================================= #
|
93
|
+
# === DATA_DIR
|
94
|
+
# ========================================================================= #
|
95
|
+
DATA_DIR = '/data/'
|
96
|
+
LOCAL_MIRROR = DATA_DIR+'ncbi/taxonomy/' # Here we have the local nodes.dmp and names.dmp
|
97
|
+
CURATED_DIR = DATA_DIR+'curated/'
|
98
|
+
SEQUENCES_DIR = CURATED_DIR+'sequences/'
|
99
|
+
|
100
|
+
# ========================================================================= #
|
101
|
+
# === INFO_DIR
|
102
|
+
# ========================================================================= #
|
103
|
+
INFO_DIR = SEQUENCES_DIR+'INFO/' # The various .INFO files.
|
104
|
+
AA_DIR = SEQUENCES_DIR+'aa/'
|
105
|
+
NT_DIR = SEQUENCES_DIR+'nt/'
|
106
|
+
LOCALOME_DIR = SEQUENCES_DIR+'localome/'
|
107
|
+
INCOMING_DIR = LOCALOME_DIR+'incoming/'
|
108
|
+
TEST_DIR = LOCALOME_DIR+'test/'
|
109
|
+
|
110
|
+
# ========================================================================= #
|
111
|
+
# === HOME_DIR
|
112
|
+
#
|
113
|
+
# Define the HOME_DIR here.
|
114
|
+
# ========================================================================= #
|
115
|
+
begin
|
116
|
+
HOME_DIR = File.expand_path('~')+'/'
|
117
|
+
rescue ArgumentError
|
118
|
+
HOME_DIR = '/root/'
|
119
|
+
end
|
120
|
+
|
121
|
+
# ========================================================================= #
|
122
|
+
# === GEM_DIR
|
123
|
+
# ========================================================================= #
|
124
|
+
GEM_DIR = HOME_DIR+'.gem/ruby/2.7.1/gems/'
|
125
|
+
|
126
|
+
# ========================================================================= #
|
127
|
+
# === MODULE_PATH
|
128
|
+
# ========================================================================= #
|
129
|
+
MODULE_PATH = GEM_DIR+'lib/taxonomy/'
|
130
|
+
BASE = BASE_DIR = TAXONOMY_DIR = HOME_DIR+'taxonomy/'
|
131
|
+
|
132
|
+
# ========================================================================= #
|
133
|
+
# === LAST_INTERACTIVE_COMMAND
|
134
|
+
#
|
135
|
+
# The following line must come after Shared was included.
|
136
|
+
#
|
137
|
+
# In order for this to work, PROJECT_BASE_DIR2 must exist.
|
138
|
+
# ========================================================================= #
|
139
|
+
LAST_INTERACTIVE_COMMAND = TEMP_DIR+'LAST_INTERACTIVE_COMMAND.md'
|
140
|
+
|
141
|
+
# ========================================================================= #
|
142
|
+
# === PROJECT_DOC_DIR
|
143
|
+
#
|
144
|
+
# Where we will keep our docs.
|
145
|
+
# ========================================================================= #
|
146
|
+
PROJECT_DOC_DIR = File.absolute_path(
|
147
|
+
::Bioroebe::Taxonomy.project_base_dir?+'../../doc/'
|
148
|
+
)+'/'
|
149
|
+
|
150
|
+
# ========================================================================= #
|
151
|
+
# === NCBI_BASE
|
152
|
+
# ========================================================================= #
|
153
|
+
NCBI_BASE = 'https://www.ncbi.nlm.nih.gov/'
|
154
|
+
|
155
|
+
# ========================================================================= #
|
156
|
+
# === TAXONOMY_BROWSER
|
157
|
+
# ========================================================================= #
|
158
|
+
TAXONOMY_BROWSER = NCBI_BASE+'Taxonomy/Browser/'
|
159
|
+
|
160
|
+
# ========================================================================= #
|
161
|
+
# === BASE_URL
|
162
|
+
# ========================================================================= #
|
163
|
+
BASE_URL = NCBI_CGI_SCRIPT = TAXONOMY_BROWSER+'wwwtax.cgi?'
|
164
|
+
|
165
|
+
# ========================================================================= #
|
166
|
+
# === URL1
|
167
|
+
# ========================================================================= #
|
168
|
+
URL1 = NCBI_CGI_SCRIPT+'mode=Undef&name=Arabidopsis+thaliana&lvl=0&srchmode=1&keep=1&unlock'
|
169
|
+
|
170
|
+
# ========================================================================= #
|
171
|
+
# == Taxonomy entries
|
172
|
+
#
|
173
|
+
# Some hardcoded Taxonomy ID entries come next - these can be used
|
174
|
+
# to find out which entries are Eukarya and which ones are Prokarya.
|
175
|
+
# This will then provide us with the starting point to build a
|
176
|
+
# rooted taxonomic tree.
|
177
|
+
# ========================================================================= #
|
178
|
+
Bacteria_Taxonomy_ID = 2
|
179
|
+
Archaea_Taxonomy_ID = 2157
|
180
|
+
Eukaryota_Taxonomy_ID = 2759
|
181
|
+
|
182
|
+
if File.exist? BASE+'delnodes.dmp'
|
183
|
+
DELNODES = BASE+'delnodes.dmp'
|
184
|
+
MERGED = BASE+'merged.dmp'
|
185
|
+
CITATIONS = BASE+'citations.dmp'
|
186
|
+
DIVISION = BASE+'division.dmp'
|
187
|
+
GENCODE = BASE+'gencode.dmp'
|
188
|
+
NODES = BASE+'nodes.dmp'
|
189
|
+
NAMES = BASE+'names.dmp'
|
190
|
+
else # Else assume _DOWNLOAD_DIR dir.
|
191
|
+
_DOWNLOAD_DIR = ::Bioroebe.download_dir?
|
192
|
+
DELNODES = _DOWNLOAD_DIR+'delnodes.dmp'
|
193
|
+
MERGED = _DOWNLOAD_DIR+'merged.dmp'
|
194
|
+
CITATIONS = _DOWNLOAD_DIR+'citations.dmp'
|
195
|
+
DIVISION = _DOWNLOAD_DIR+'division.dmp'
|
196
|
+
GENCODE = _DOWNLOAD_DIR+'gencode.dmp'
|
197
|
+
NODES = _DOWNLOAD_DIR+'nodes.dmp'
|
198
|
+
NAMES = _DOWNLOAD_DIR+'names.dmp'
|
199
|
+
end
|
200
|
+
|
201
|
+
# ========================================================================= #
|
202
|
+
# === info_dir?
|
203
|
+
# ========================================================================= #
|
204
|
+
def info_dir?
|
205
|
+
INFO_DIR
|
206
|
+
end
|
207
|
+
|
208
|
+
# ========================================================================= #
|
209
|
+
# === work_directory?
|
210
|
+
#
|
211
|
+
# For now, the work-directory defaults to the TEMP_DIR value.
|
212
|
+
# ========================================================================= #
|
213
|
+
def work_directory?
|
214
|
+
TEMP_DIR
|
215
|
+
end; alias working_directory? work_directory? # === working_directory?
|
216
|
+
alias working_dir? work_directory? # === working_dir?
|
217
|
+
|
218
|
+
end; end; end
|
@@ -0,0 +1,97 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/taxonomy/edit.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
module Taxonomy # === Bioroebe::Taxonomy
|
10
|
+
|
11
|
+
require 'bioroebe/configuration/configuration.rb'
|
12
|
+
|
13
|
+
# ========================================================================= #
|
14
|
+
# === edit_instructions
|
15
|
+
# ========================================================================= #
|
16
|
+
def edit_instructions
|
17
|
+
esystem "#{Bioroebe.editor?} #{return_instructions}"
|
18
|
+
end
|
19
|
+
|
20
|
+
# ========================================================================= #
|
21
|
+
# === edit (edit tag, ed tag)
|
22
|
+
#
|
23
|
+
# This method allows us to quickly open the internal files.
|
24
|
+
#
|
25
|
+
# We can typically use vim for this.
|
26
|
+
# ========================================================================= #
|
27
|
+
def edit(i = '')
|
28
|
+
i = i.to_s
|
29
|
+
i.gsub!(/edit_/,'') if i.include? 'edit_'
|
30
|
+
case i
|
31
|
+
# ======================================================================= #
|
32
|
+
# === taxonomy
|
33
|
+
# ======================================================================= #
|
34
|
+
when /taxonomy/ # Edit the taxonomy "binary".
|
35
|
+
edit_taxonomy
|
36
|
+
# ======================================================================= #
|
37
|
+
# === shared
|
38
|
+
# ======================================================================= #
|
39
|
+
when 'shared',
|
40
|
+
'shared_code'
|
41
|
+
edit_shared_code_file
|
42
|
+
# ======================================================================= #
|
43
|
+
# === gem
|
44
|
+
# ======================================================================= #
|
45
|
+
when 'gem',
|
46
|
+
'gemspec'
|
47
|
+
edit_gemspec
|
48
|
+
# ======================================================================= #
|
49
|
+
# === password
|
50
|
+
# ======================================================================= #
|
51
|
+
when /^password$/,
|
52
|
+
'passwd'
|
53
|
+
edit_password
|
54
|
+
# ======================================================================= #
|
55
|
+
# === login
|
56
|
+
# ======================================================================= #
|
57
|
+
when 'login','main'
|
58
|
+
edit_login_file
|
59
|
+
# ======================================================================= #
|
60
|
+
# === instructions
|
61
|
+
# ======================================================================= #
|
62
|
+
when '','instructions' # '' is default.
|
63
|
+
edit_instructions
|
64
|
+
end
|
65
|
+
end
|
66
|
+
|
67
|
+
# ========================================================================= #
|
68
|
+
# === edit_gemspec
|
69
|
+
# ========================================================================= #
|
70
|
+
def edit_gemspec
|
71
|
+
esystem Bioroebe.editor?+' '+return_gemspec_file
|
72
|
+
end
|
73
|
+
|
74
|
+
# ========================================================================= #
|
75
|
+
# === edit_taxonomy
|
76
|
+
# ========================================================================= #
|
77
|
+
def edit_taxonomy
|
78
|
+
esystem Bioroebe.editor?+' '+return_taxonomy_file
|
79
|
+
end
|
80
|
+
|
81
|
+
# ========================================================================= #
|
82
|
+
# === edit_shared_code_file
|
83
|
+
# ========================================================================= #
|
84
|
+
def edit_shared_code_file
|
85
|
+
esystem Bioroebe.editor?+' '+return_shared_code
|
86
|
+
end
|
87
|
+
|
88
|
+
# ========================================================================= #
|
89
|
+
# === edit_password
|
90
|
+
#
|
91
|
+
# We can use this method to edit the login-file.
|
92
|
+
# ========================================================================= #
|
93
|
+
def edit_password
|
94
|
+
edit_login_file ' +27'
|
95
|
+
end
|
96
|
+
|
97
|
+
end; end
|
@@ -0,0 +1,65 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
module Bioroebe
|
6
|
+
|
7
|
+
module Taxonomy
|
8
|
+
|
9
|
+
require 'bioroebe/taxonomy/help/helpline.rb'
|
10
|
+
require 'bioroebe/taxonomy/constants.rb' # ← This file also pulls in the file taxonomy_constants.rb
|
11
|
+
|
12
|
+
include Taxonomy::Constants
|
13
|
+
|
14
|
+
# ========================================================================= #
|
15
|
+
# === show_help (help tag)
|
16
|
+
#
|
17
|
+
# Shows the options available in the interactive taxonomy 'shell'.
|
18
|
+
# ========================================================================= #
|
19
|
+
def show_help
|
20
|
+
cliner {
|
21
|
+
e N+'The following options are available (pwd: '+sdir(return_pwd)+'):'+
|
22
|
+
N+N
|
23
|
+
Helpline[:sql,'# Use this to generate the SQL that can be '+
|
24
|
+
'used to populate a SQL database with INSERT statements.']
|
25
|
+
e ' '*(Helpline::LJUST+3)+'# You can pass values such as 1 '+
|
26
|
+
'or 2 (node or name) to this method.'
|
27
|
+
Helpline[:info, '# Show some info about where we store data.']
|
28
|
+
Helpline[:instructions?, '# Show instructions.']
|
29
|
+
Helpline[:fasta, '# Use this to populate the fasta table.']
|
30
|
+
Helpline[:names, '# Use this to populate the names table.']
|
31
|
+
Helpline[:nodes, '# Use this to populate the nodes table.']
|
32
|
+
# ===================================================================== #
|
33
|
+
# Only display the following line when colours are enabled still.
|
34
|
+
# ===================================================================== #
|
35
|
+
if use_colours?
|
36
|
+
Helpline[:nocolours,'# Use this to disable the '+
|
37
|
+
'colours. (Use "yescolours" to enable them again)']
|
38
|
+
end
|
39
|
+
Helpline[:taxid,'# Find out the name of the organism through the '+
|
40
|
+
'input ID from the NCBI dataset. For example: "taxid 33"']
|
41
|
+
Helpline[:table_names?,'# Use this to show the SQL command '+
|
42
|
+
'that was used to generate the SQL Tables.']
|
43
|
+
Helpline[:verify,'# Use this to verify that the '+
|
44
|
+
'.sql files (nodes and names) are valid.']
|
45
|
+
Helpline[:verbose,'# be verbose, in other words provide '+
|
46
|
+
'extra information to us whenever feasible']
|
47
|
+
Helpline[:ll, '# Show the content of the current working '+
|
48
|
+
'directory.']
|
49
|
+
Helpline[:id,'# Query the postgre database to get the ID of '+
|
50
|
+
'a given species.']
|
51
|
+
Helpline[:download,'# Download the remote NCBI database '+
|
52
|
+
'(at '+simp(URL_TO_TAXONOMY_ARCHIVE)+')']
|
53
|
+
if SHALL_WE_LOG_LAST_UPDATE
|
54
|
+
Helpline[:last_update?,'# When did we last update the database']
|
55
|
+
end
|
56
|
+
Helpline[:update_database, '# download the remote NCBI database, '+
|
57
|
+
'extract it, generate nodes.sql and names.sql,']
|
58
|
+
_ = ' ' * Helpline::LJUST
|
59
|
+
e _+Helpline::PADDING+' # and then populate the postgresql-database '+
|
60
|
+
'with this information'
|
61
|
+
e # This here to keep a trailing newline.
|
62
|
+
}
|
63
|
+
end
|
64
|
+
|
65
|
+
end; end
|