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
@@ -0,0 +1,81 @@
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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/cliner.rb'
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# =========================================================================== #
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module Bioroebe
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# ========================================================================= #
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# === Bioroebe.cliner
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#
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# The first character denotes which token we will use, such as '#',
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# for the line that is to be displayed.
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# ========================================================================= #
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def self.cliner(
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how_many_times = 80,
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use_this_colour = nil
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)
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require 'bioroebe/colours/colours.rb'
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# ===================================================================== #
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# === :length
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# ===================================================================== #
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if use_this_token.has_key? :length
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how_many_times = use_this_token.delete(:length)
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end
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if use_this_token.is_a? Hash
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# =================================================================== #
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# === :token
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# =================================================================== #
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if use_this_token.has_key? :token
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use_this_token = use_this_token.delete(:token)
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end
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end
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use_this_token = :default if use_this_token.is_a? Hash
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end
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# ======================================================================= #
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# The following case-when menu must come after the check for Hashes
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# above.
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# ======================================================================= #
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case use_this_token
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when :default_token, :default
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use_this_token = '='
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end
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# ======================================================================= #
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# === handle blocks next
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# ======================================================================= #
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if block_given?
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yielded = yield
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if yielded.is_a?(Hash)
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# === :colour
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if yielded.has_key? :colour
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use_this_colour = yielded[:colour]
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# === :colours
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elsif yielded.has_key? :colours
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use_this_colour = yielded[:colours]
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end
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#else
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# cliner(use_this_token, how_many_times)
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end
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end
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if use_this_colour
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puts ::Colours.send(use_this_colour, use_this_token * how_many_times)
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else
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puts use_this_token * how_many_times
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end
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end
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end
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if __FILE__ == $PROGRAM_NAME
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# Bioroebe.cliner { puts 'hi there' }
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# puts
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# Bioroebe.cliner('*')
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# Bioroebe.cliner('*', 30)
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# Bioroebe.cliner length: 88
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# Bioroebe.cliner token: 'x'
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Bioroebe.cliner('*') {{ colour: 'steelblue' }}
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Bioroebe.cliner('=') {{ colour: 'dodgerblue' }}
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end
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#!/usr/bin/ruby -w
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/toplevel_methods/complement.rb'
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# =========================================================================== #
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module Bioroebe
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# ========================================================================= #
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# === Bioroebe.complement
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#
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# This method will return the complementary DNA strand.
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#
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# We will use possibilities though.
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#
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# Usage example:
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#
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# Bioroebe.complement 'ATGGGTCCC' # => "TACCCAGGG"
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#
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# ========================================================================= #
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def self.complement(
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i = nil
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)
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require 'bioroebe/constants/nucleotides.rb'
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# ======================================================================= #
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# Refer to the main Hash.
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# ======================================================================= #
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hash = HASH_DNA_NUCLEOTIDES
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result = ''.dup
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i = i.first if i.is_a? Array
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if i
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if File.exist?(i)
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i = File.readlines(i).join(' ').strip
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end
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i.each_char { |char|
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char = char.upcase
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if hash.has_key? char
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result << hash[char]
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else
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case char.downcase # case tag
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when 'n' # Means any.
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result << '(A/T/G/C)'
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when 'r' # Means a purine. (larger)
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result << '(A/G)'
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when 'y' # Means a pyrimidine. (smaller)
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result << '(T/C)'
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end
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end
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}
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return result
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end
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end
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end
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if __FILE__ == $PROGRAM_NAME
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puts Bioroebe.complement(ARGV) # => "TACCCAGGG"
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end # bioroebecomplement TACCCAGGG
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/toplevel_methods/convert_global_env.rb'
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# Bioroebe.convert_global_env(ARGV)
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# =========================================================================== #
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module Bioroebe
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# ========================================================================= #
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|
+
# === Bioroebe.convert_global_env
|
12
|
+
#
|
13
|
+
# Note that the method will pick only the first argument given to it
|
14
|
+
# if an Array is supplied.
|
15
|
+
# ========================================================================= #
|
16
|
+
def self.convert_global_env(i)
|
17
|
+
if i.is_a? Array
|
18
|
+
i = i.first
|
19
|
+
end
|
20
|
+
unless Object.const_defined? :ConvertGlobalEnv
|
21
|
+
begin # Require an external gem in this case.
|
22
|
+
require 'convert_global_env'
|
23
|
+
rescue LoadError; end
|
24
|
+
end
|
25
|
+
if Object.const_defined? :ConvertGlobalEnv
|
26
|
+
if i and !i.start_with?('$')
|
27
|
+
i = i.dup if i.frozen?
|
28
|
+
i.prepend('$')
|
29
|
+
end
|
30
|
+
return ConvertGlobalEnv.convert(i, :do_not_report_errors) # Handle ENV variables.
|
31
|
+
end
|
32
|
+
return i
|
33
|
+
end
|
34
|
+
|
35
|
+
end
|
36
|
+
|
37
|
+
if __FILE__ == $PROGRAM_NAME
|
38
|
+
puts Bioroebe.convert_global_env(ARGV)
|
39
|
+
end # rb convert_global_env.rb MY_DATA
|
@@ -0,0 +1,73 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/databases.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'bioroebe/constants/database_constants.rb'
|
10
|
+
|
11
|
+
# ========================================================================= #
|
12
|
+
# === Bioroebe.set_pgpassword (password tag)
|
13
|
+
#
|
14
|
+
# Set the password for Postgresql here. As input to this method you
|
15
|
+
# can pass the password for the postgreSQL database.
|
16
|
+
# ========================================================================= #
|
17
|
+
def self.set_pgpassword(
|
18
|
+
new_password = POSTGRE_PASSWORD
|
19
|
+
)
|
20
|
+
ENV['PGPASSWORD'] = new_password
|
21
|
+
end; self.instance_eval { alias set_password set_pgpassword } # === Bioroebe.set_password
|
22
|
+
|
23
|
+
# ========================================================================= #
|
24
|
+
# === Bioroebe.run_sql_query
|
25
|
+
#
|
26
|
+
# This method will run a SQL query using --command.
|
27
|
+
#
|
28
|
+
# It will return the result as well.
|
29
|
+
#
|
30
|
+
# The second argument determines whether we will be verbose or not.
|
31
|
+
#
|
32
|
+
# The result, however, will always be displayed.
|
33
|
+
# ========================================================================= #
|
34
|
+
def self.run_sql_query(
|
35
|
+
i,
|
36
|
+
be_verbose = true,
|
37
|
+
optional_append_this = ''
|
38
|
+
)
|
39
|
+
set_pgpassword
|
40
|
+
i = i.to_s
|
41
|
+
_ = ''
|
42
|
+
if is_on_roebe?
|
43
|
+
_ << POSTGRE_LOGIN_COMMAND_HOME
|
44
|
+
else
|
45
|
+
_ << POSTGRE_LOGIN_COMMAND
|
46
|
+
end
|
47
|
+
case be_verbose
|
48
|
+
when :silent
|
49
|
+
be_verbose = false
|
50
|
+
end
|
51
|
+
case optional_append_this
|
52
|
+
# ======================================================================= #
|
53
|
+
# === :bare
|
54
|
+
# ======================================================================= #
|
55
|
+
when :bare,
|
56
|
+
:tuples
|
57
|
+
optional_append_this = ' --tuples-only'
|
58
|
+
end
|
59
|
+
_ << optional_append_this.to_s
|
60
|
+
_ << ' --command="'
|
61
|
+
_ << i
|
62
|
+
_ << '"' unless _.end_with? '"'
|
63
|
+
result = `#{_}`.chomp
|
64
|
+
erev _ if be_verbose
|
65
|
+
erev result if be_verbose
|
66
|
+
return result
|
67
|
+
end
|
68
|
+
|
69
|
+
end
|
70
|
+
|
71
|
+
if __FILE__ == $PROGRAM_NAME
|
72
|
+
Bioroebe.run_sql_query 'foo bar'
|
73
|
+
end
|
@@ -0,0 +1,19 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/delimiter.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.delimiter?
|
11
|
+
#
|
12
|
+
# This is simply the delimiter used for reading "multiline input"
|
13
|
+
# of the Bioroebe::Shell component.
|
14
|
+
# ========================================================================= #
|
15
|
+
def self.delimiter?
|
16
|
+
'___'
|
17
|
+
end
|
18
|
+
|
19
|
+
end
|
@@ -0,0 +1,71 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/digest.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.digest_this_dna
|
11
|
+
#
|
12
|
+
# Usage examples:
|
13
|
+
#
|
14
|
+
# Bioroebe.digest_this_dna(:lambda_genome, with: :EcoRI)
|
15
|
+
# Bioroebe.digest_this_dna("/root/Bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta", with: :EcoRI)
|
16
|
+
#
|
17
|
+
# ========================================================================= #
|
18
|
+
def self.digest_this_dna(
|
19
|
+
this_DNA_sequence, hash = {}
|
20
|
+
)
|
21
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
22
|
+
require 'bioroebe/constants/files_and_directories.rb'
|
23
|
+
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
24
|
+
restriction_enzymes = Bioroebe.load_and_return_the_restriction_enzymes
|
25
|
+
this_restriction_enzyme = nil
|
26
|
+
nucleotide_sequence = nil
|
27
|
+
if this_DNA_sequence.is_a? Array
|
28
|
+
this_DNA_sequence = this_DNA_sequence.first
|
29
|
+
end
|
30
|
+
if this_DNA_sequence.is_a?(String) and File.exist?(this_DNA_sequence)
|
31
|
+
nucleotide_sequence = ::Bioroebe::ParseFasta.new(this_DNA_sequence).sequence?
|
32
|
+
end
|
33
|
+
# ======================================================================= #
|
34
|
+
# === Handle the hash next (and ensure that it is a Hash)
|
35
|
+
# ======================================================================= #
|
36
|
+
if hash.is_a? Hash
|
37
|
+
# ===================================================================== #
|
38
|
+
# === :with
|
39
|
+
# ===================================================================== #
|
40
|
+
if hash.has_key? :with
|
41
|
+
this_restriction_enzyme = hash.delete(:with).to_s
|
42
|
+
end
|
43
|
+
end
|
44
|
+
target_sequence = restriction_enzymes[this_restriction_enzyme].dup
|
45
|
+
if target_sequence =~ /\d$/ # If it ends with a number.
|
46
|
+
target_sequence.chop!
|
47
|
+
target_sequence.strip!
|
48
|
+
end
|
49
|
+
if nucleotide_sequence.include?(target_sequence)
|
50
|
+
e 'Yes, this sequence is there.'
|
51
|
+
scanned = nucleotide_sequence.scan(
|
52
|
+
/#{target_sequence}/
|
53
|
+
)
|
54
|
+
e "It can be found #{scanned.size.to_s} times."
|
55
|
+
sub_sequences = nucleotide_sequence.split(/#{target_sequence}/)
|
56
|
+
sub_sequences.sort_by {|entry| entry.size }.reverse.each {|sequence|
|
57
|
+
pp sequence.size
|
58
|
+
}
|
59
|
+
else
|
60
|
+
e 'Nothing found.'
|
61
|
+
end
|
62
|
+
end
|
63
|
+
|
64
|
+
end
|
65
|
+
|
66
|
+
if __FILE__ == $PROGRAM_NAME
|
67
|
+
Bioroebe.digest_this_dna(
|
68
|
+
"/home/Temp/bioroebe/fasta/NC_001416.1_Enterobacteria_phage_lambda_complete_genome.fasta",
|
69
|
+
with: :EcoRI
|
70
|
+
)
|
71
|
+
end # rb digest.rb
|
@@ -0,0 +1,146 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/download_and_fetch_data.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
10
|
+
require 'bioroebe/toplevel_methods/esystem.rb'
|
11
|
+
require 'bioroebe/toplevel_methods/fasta_and_fastq.rb'
|
12
|
+
require 'bioroebe/toplevel_methods/log_directory.rb'
|
13
|
+
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
14
|
+
require 'bioroebe/colours/colours.rb'
|
15
|
+
|
16
|
+
# ========================================================================= #
|
17
|
+
# === Bioroebe.fetch_data_from_uniprot
|
18
|
+
#
|
19
|
+
# The first argument to this method should be the name of the protein
|
20
|
+
# at hand. Alternatively it can also be just the full URL.
|
21
|
+
#
|
22
|
+
# The second argument specifies whether we will automatically try
|
23
|
+
# to rename this FASTA file. By default this is enabled, largely
|
24
|
+
# because it makes it a bit easier to know what a particular
|
25
|
+
# fasta sequence contains.
|
26
|
+
# ========================================================================= #
|
27
|
+
def self.fetch_data_from_uniprot(
|
28
|
+
i = 'B5ZC00',
|
29
|
+
do_perform_rename_action = true
|
30
|
+
)
|
31
|
+
require 'open-uri'
|
32
|
+
# ======================================================================= #
|
33
|
+
# Support Array as input:
|
34
|
+
# ======================================================================= #
|
35
|
+
if i.is_a? Array
|
36
|
+
i.each {|entry|
|
37
|
+
fetch_data_from_uniprot(entry, do_perform_rename_action)
|
38
|
+
}
|
39
|
+
else
|
40
|
+
if i.frozen?
|
41
|
+
i = i.dup
|
42
|
+
end
|
43
|
+
i.strip!
|
44
|
+
if i.start_with? 'http'
|
45
|
+
remote_url = i
|
46
|
+
else
|
47
|
+
remote_url = "https://www.uniprot.org/uniprot/#{i}".dup
|
48
|
+
end
|
49
|
+
# ======================================================================= #
|
50
|
+
# Next, we will append a trailing ".fasta" part for uniprot, if
|
51
|
+
# the very last part does NOT include a '.' character.
|
52
|
+
# ======================================================================= #
|
53
|
+
_ = File.basename(remote_url)
|
54
|
+
unless _.include?('.')
|
55
|
+
remote_url << '.fasta' unless remote_url.end_with? '.fasta'
|
56
|
+
end
|
57
|
+
# ======================================================================= #
|
58
|
+
# Store this protein sequence at an appropriate location:
|
59
|
+
# ======================================================================= #
|
60
|
+
e
|
61
|
+
erev "Trying to obtain remote data from "\
|
62
|
+
"#{sfancy(remote_url)} #{rev}next:"
|
63
|
+
e
|
64
|
+
store_here = LOCAL_DIRECTORY_FOR_UNIPROT+
|
65
|
+
File.basename(remote_url)
|
66
|
+
# ======================================================================= #
|
67
|
+
# Next create the directory unless it already exists.
|
68
|
+
# ======================================================================= #
|
69
|
+
unless File.directory? LOCAL_DIRECTORY_FOR_UNIPROT
|
70
|
+
mkdir LOCAL_DIRECTORY_FOR_UNIPROT
|
71
|
+
end
|
72
|
+
dataset = URI.open(remote_url).read
|
73
|
+
e "The remote dataset will be stored here: "\
|
74
|
+
"#{sfile(store_here)}"
|
75
|
+
e
|
76
|
+
write_what_into(dataset, store_here)
|
77
|
+
# ======================================================================= #
|
78
|
+
# Next comes a rename action - this will make the .fasta file more
|
79
|
+
# verbose, but I think this may still be helpful, in particular if you
|
80
|
+
# have a lot of .fasta files. There is a switch that controls this
|
81
|
+
# setting though.
|
82
|
+
# ======================================================================= #
|
83
|
+
if do_perform_rename_action
|
84
|
+
# ===================================================================== #
|
85
|
+
# The initially assumed filename may be like this:
|
86
|
+
#
|
87
|
+
# /root/Bioroebe/A2Z669_CSPLT_ORYSI_CASP-like_protein_5A2_OS=Oryza_sativa_subsp_indica_OX=39946_GN=OsI_33147_PE=3_SV=1.fasta
|
88
|
+
#
|
89
|
+
# ===================================================================== #
|
90
|
+
assumed_filename = ::Bioroebe.return_new_filename_based_on_fasta_identifier(store_here)
|
91
|
+
new_filename = LOCAL_DIRECTORY_FOR_UNIPROT+
|
92
|
+
File.basename(assumed_filename)
|
93
|
+
erev "Next renaming `#{sfile(store_here)}#{rev}` to"
|
94
|
+
erev " `#{sfile(new_filename)}`."
|
95
|
+
::Bioroebe.mv(store_here, new_filename)
|
96
|
+
return new_filename
|
97
|
+
end
|
98
|
+
return store_here
|
99
|
+
end
|
100
|
+
end
|
101
|
+
|
102
|
+
# ========================================================================= #
|
103
|
+
# === Bioroebe.wget_download
|
104
|
+
#
|
105
|
+
# This variant will always use "wget" - hence the name.
|
106
|
+
# ========================================================================= #
|
107
|
+
def self.wget_download(target)
|
108
|
+
esystem "wget #{target}"
|
109
|
+
end
|
110
|
+
|
111
|
+
# ========================================================================= #
|
112
|
+
# === Bioroebe.download
|
113
|
+
# ========================================================================= #
|
114
|
+
def self.download(
|
115
|
+
from_these_URLs
|
116
|
+
)
|
117
|
+
require 'open-uri'
|
118
|
+
array_these_urls = [from_these_URLs].flatten.compact
|
119
|
+
array_these_urls.each {|remote_url|
|
120
|
+
# ===================================================================== #
|
121
|
+
# First, we must determine the remote file listing here.
|
122
|
+
# Due to convenience we will simply use curl here.
|
123
|
+
# ===================================================================== #
|
124
|
+
cmd = "curl -s \"#{remote_url}\" --list-only"
|
125
|
+
# e cmd
|
126
|
+
remote_files = `#{cmd}`.split("\n")
|
127
|
+
remote_files.each {|this_remote_file|
|
128
|
+
target = remote_url+this_remote_file
|
129
|
+
e "Downloading `#{this_remote_file}` next. '"\
|
130
|
+
"(Full target: '#{target})"
|
131
|
+
wget_download(target)
|
132
|
+
}
|
133
|
+
}
|
134
|
+
end
|
135
|
+
|
136
|
+
end
|
137
|
+
|
138
|
+
if __FILE__ == $PROGRAM_NAME
|
139
|
+
Bioroebe.download(ARGV)
|
140
|
+
Bioroebe.fetch_data_from_uniprot(ARGV)
|
141
|
+
end # bioroebedownload ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
|
142
|
+
# fetchdatafromuniprot
|
143
|
+
# fetchdatafromuniprot B5ZC00
|
144
|
+
# fetchdatafromuniprot A2Z669
|
145
|
+
# fetchdatafromuniprot P07204_TRBM_HUMAN
|
146
|
+
# fetchdatafromuniprot P20840_SAG1_YEAST
|
@@ -0,0 +1,20 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/e.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.e
|
11
|
+
# ========================================================================= #
|
12
|
+
def self.e(i = '')
|
13
|
+
puts i
|
14
|
+
end
|
15
|
+
|
16
|
+
end
|
17
|
+
|
18
|
+
if __FILE__ == $PROGRAM_NAME
|
19
|
+
Bioroebe.e('Hello world!')
|
20
|
+
end
|
@@ -0,0 +1,21 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/editor.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.editor?
|
11
|
+
# ========================================================================= #
|
12
|
+
def self.editor?
|
13
|
+
require 'bioroebe/configuration/constants.rb'
|
14
|
+
::Bioroebe::Configuration::DEFAULT_EDITOR_TO_USE
|
15
|
+
end
|
16
|
+
|
17
|
+
end
|
18
|
+
|
19
|
+
if __FILE__ == $PROGRAM_NAME
|
20
|
+
puts Bioroebe.editor? # Would output "bluefish" on my home setup.
|
21
|
+
end
|
@@ -0,0 +1,22 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/esystem.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.esystem
|
11
|
+
# ========================================================================= #
|
12
|
+
def self.esystem(i)
|
13
|
+
puts i.to_s
|
14
|
+
system i.to_s
|
15
|
+
end
|
16
|
+
|
17
|
+
end
|
18
|
+
|
19
|
+
if __FILE__ == $PROGRAM_NAME
|
20
|
+
puts 'Running `ls` next:'
|
21
|
+
Bioroebe.esystem 'ls'
|
22
|
+
end
|
@@ -0,0 +1,74 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/exponential_growth.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.calculate_exponential_growth
|
11
|
+
#
|
12
|
+
# This method can be used to calculate how many bacteria will exist after
|
13
|
+
# n cell divisions (provided that we know, and supply to this method,
|
14
|
+
# how many bacteria existed when we started our calculation).
|
15
|
+
# ========================================================================= #
|
16
|
+
def self.calculate_exponential_growth(
|
17
|
+
number_of_cells = 10,
|
18
|
+
number_of_divisions = 10
|
19
|
+
)
|
20
|
+
if number_of_cells.nil?
|
21
|
+
number_of_cells = 10 # Default value.
|
22
|
+
end
|
23
|
+
if number_of_divisions.nil?
|
24
|
+
number_of_divisions = 10 # Default value.
|
25
|
+
end
|
26
|
+
# ======================================================================= #
|
27
|
+
# === Hashes
|
28
|
+
#
|
29
|
+
# Handle Hash as input given.
|
30
|
+
# ======================================================================= #
|
31
|
+
if number_of_cells.is_a? Hash
|
32
|
+
if number_of_cells.has_key? :n_divisions
|
33
|
+
number_of_divisions = number_of_cells.delete(:n_divisions)
|
34
|
+
end
|
35
|
+
if number_of_cells.has_key? :number_of_cells
|
36
|
+
number_of_cells = number_of_cells.delete(:number_of_cells)
|
37
|
+
elsif number_of_cells.has_key? :n_cells
|
38
|
+
number_of_cells = number_of_cells.delete(:n_cells)
|
39
|
+
end
|
40
|
+
end
|
41
|
+
# ======================================================================= #
|
42
|
+
# We need numbers, aka integers - there are no "1.3" cells.
|
43
|
+
# ======================================================================= #
|
44
|
+
number_of_cells = number_of_cells.to_i
|
45
|
+
number_of_divisions = number_of_divisions.to_i
|
46
|
+
total_amount_of_cells = 0
|
47
|
+
total_amount_of_cells = number_of_cells * (2 ** number_of_divisions)
|
48
|
+
return total_amount_of_cells
|
49
|
+
end
|
50
|
+
|
51
|
+
# ========================================================================= #
|
52
|
+
# === Bioroebe.calculate_original_amount_of_cells_of_exponential_growth
|
53
|
+
#
|
54
|
+
# The first argument, number_of_cells, means "how many cells do we have
|
55
|
+
# now/currently". This is necessary, in order to calculate how many
|
56
|
+
# cells we used to have initially.
|
57
|
+
# ========================================================================= #
|
58
|
+
def self.calculate_original_amount_of_cells_of_exponential_growth(
|
59
|
+
number_of_cells = 1600, # 1600 cells to start with.
|
60
|
+
number_of_divisions = 5 # 5 generations by default.
|
61
|
+
)
|
62
|
+
number_of_cells = number_of_cells.to_i
|
63
|
+
number_of_divisions = number_of_divisions.to_i
|
64
|
+
initial_amount_of_cells_was = 0
|
65
|
+
initial_amount_of_cells_was = number_of_cells / ( 2 ** number_of_divisions )
|
66
|
+
return initial_amount_of_cells_was
|
67
|
+
end
|
68
|
+
|
69
|
+
end
|
70
|
+
|
71
|
+
if __FILE__ == $PROGRAM_NAME
|
72
|
+
puts Bioroebe.calculate_exponential_growth(ARGV[0], ARGV[1])
|
73
|
+
# puts Bioroebe.calculate_original_amount_of_cells_of_exponential_growth()
|
74
|
+
end # calculateexponentialgrowth 10 10
|
@@ -0,0 +1,56 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/extract.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
10
|
+
require 'bioroebe/toplevel_methods/esystem.rb'
|
11
|
+
require 'bioroebe/toplevel_methods/verbose.rb'
|
12
|
+
|
13
|
+
# ========================================================================= #
|
14
|
+
# === Bioroebe.extract
|
15
|
+
#
|
16
|
+
# This method can be used to quickly extract a local archive.
|
17
|
+
# ========================================================================= #
|
18
|
+
def self.extract(
|
19
|
+
i = ARGV
|
20
|
+
)
|
21
|
+
require 'bioroebe/colours/sfancy.rb'
|
22
|
+
require 'bioroebe/colours/swarn.rb'
|
23
|
+
if i.is_a? Array
|
24
|
+
i = i.join(' ').strip
|
25
|
+
end
|
26
|
+
unless i.include?('/')
|
27
|
+
unless File.exist? i
|
28
|
+
i = return_pwd+
|
29
|
+
File.basename(i)
|
30
|
+
end
|
31
|
+
end
|
32
|
+
if File.exist? i
|
33
|
+
case i
|
34
|
+
when /bz2$/
|
35
|
+
_ = "tar -xfv #{i}"
|
36
|
+
when /xz$/
|
37
|
+
_ = "tar -xvf #{i}"
|
38
|
+
end
|
39
|
+
if be_verbose?
|
40
|
+
e "Now extracting `#{sfancy((i).squeeze('/'))}`."
|
41
|
+
esystem(_)
|
42
|
+
e 'Done extracting!'
|
43
|
+
else
|
44
|
+
system _
|
45
|
+
end
|
46
|
+
else
|
47
|
+
ewarn "Can not extract #{sfile(i)} because it does "\
|
48
|
+
"not appear to exist."
|
49
|
+
end
|
50
|
+
end
|
51
|
+
|
52
|
+
end
|
53
|
+
|
54
|
+
if __FILE__ == $PROGRAM_NAME
|
55
|
+
Bioroebe.extract(ARGV)
|
56
|
+
end # ruby extract.rb /home/x/src/htop/htop-3.0.5.tar.xz
|