bioroebe 0.10.80
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +329 -0
- 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
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +146 -0
- data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +207 -0
- data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +279 -0
- data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +23 -0
- data/lib/bioroebe/gui/gtk3/www_finder/www_finder.config +6 -0
- data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +368 -0
- data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +82 -0
- data/lib/bioroebe/gui/libui/README.md +4 -0
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +114 -0
- data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +112 -0
- 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
- data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +135 -0
- data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +118 -0
- data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +115 -0
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +174 -0
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +132 -0
- data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +89 -0
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +111 -0
- data/lib/bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb +42 -0
- 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
- data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +243 -0
- 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
- data/lib/bioroebe/images/BIOROEBE.png +0 -0
- data/lib/bioroebe/images/BIOROEBE_NEW_LOGO.png +0 -0
- data/lib/bioroebe/images/BlosumMatrixViewer.png +0 -0
- data/lib/bioroebe/images/DnaToAminoacidWidget.png +0 -0
- data/lib/bioroebe/images/PRINTED_AMINOACID_TABLE.png +0 -0
- data/lib/bioroebe/images/class_ConvertAminoacidToDNA.png +0 -0
- data/lib/bioroebe/images/class_SimpleStringComparer.png +0 -0
- data/lib/bioroebe/images/example_of_FASTA_coloured_output.png +0 -0
- data/lib/bioroebe/images/libui_hamming_distance_widget.png +0 -0
- data/lib/bioroebe/images/pretty_DNA_picture.png +0 -0
- data/lib/bioroebe/images/primer_design_widget.png +0 -0
- data/lib/bioroebe/images/restriction_enzyme_commandline_result.png +0 -0
- data/lib/bioroebe/images/ruby-gtk_three_to_one_widget.png +0 -0
- data/lib/bioroebe/images/small_DNA_logo.png +0 -0
- data/lib/bioroebe/images/small_drosophila_image.png +0 -0
- data/lib/bioroebe/java/README.md +6 -0
- data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
- data/lib/bioroebe/java/bioroebe/AllInOne.java +214 -0
- data/lib/bioroebe/java/bioroebe/Base.class +0 -0
- data/lib/bioroebe/java/bioroebe/Base.java +102 -0
- data/lib/bioroebe/java/bioroebe/BisulfiteTreatment.class +0 -0
- data/lib/bioroebe/java/bioroebe/BisulfiteTreatment.java +23 -0
- data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
- data/lib/bioroebe/java/bioroebe/Codons.class +0 -0
- data/lib/bioroebe/java/bioroebe/Codons.java +22 -0
- data/lib/bioroebe/java/bioroebe/Esystem.class +0 -0
- data/lib/bioroebe/java/bioroebe/Esystem.java +47 -0
- data/lib/bioroebe/java/bioroebe/GUI/BaseFrame.class +0 -0
- data/lib/bioroebe/java/bioroebe/GUI/BaseFrame.java +65 -0
- data/lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class +0 -0
- data/lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java +32 -0
- data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
- data/lib/bioroebe/java/bioroebe/IsPalindrome.java +18 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +19 -0
- data/lib/bioroebe/java/bioroebe/README.md +4 -0
- data/lib/bioroebe/java/bioroebe/RemoveFile.class +0 -0
- data/lib/bioroebe/java/bioroebe/RemoveFile.java +24 -0
- data/lib/bioroebe/java/bioroebe/RemoveNumbers.class +0 -0
- data/lib/bioroebe/java/bioroebe/RemoveNumbers.java +14 -0
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +20 -0
- data/lib/bioroebe/java/bioroebe/SaveFile.java +44 -0
- data/lib/bioroebe/java/bioroebe/Sequence.java +28 -0
- data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToCamelcase.java +32 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +15 -0
- data/lib/bioroebe/java/bioroebe/enums/DNA.java +6 -0
- data/lib/bioroebe/java/bioroebe.jar +0 -0
- data/lib/bioroebe/matplotlib/matplotlib_generator.rb +104 -0
- data/lib/bioroebe/misc/quiz/README.md +6 -0
- data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +163 -0
- data/lib/bioroebe/misc/ruler.rb +244 -0
- data/lib/bioroebe/misc/useful_formulas.rb +129 -0
- data/lib/bioroebe/ncbi/efetch.rb +253 -0
- data/lib/bioroebe/ncbi/ncbi.rb +93 -0
- data/lib/bioroebe/ngs/README.md +2 -0
- data/lib/bioroebe/ngs/phred_quality_score_table.rb +123 -0
- data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +166 -0
- data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +135 -0
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +198 -0
- data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +133 -0
- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
- data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +139 -0
- 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
- data/lib/bioroebe/parsers/gff.rb +346 -0
- data/lib/bioroebe/parsers/parse_embl.rb +76 -0
- data/lib/bioroebe/parsers/stride_parser.rb +117 -0
- data/lib/bioroebe/patterns/README.md +5 -0
- 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
- data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +164 -0
- data/lib/bioroebe/pdb/parse_mmCIF_file.rb +63 -0
- data/lib/bioroebe/pdb/parse_pdb_file.rb +1086 -0
- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
- data/lib/bioroebe/perl/README.md +7 -0
- data/lib/bioroebe/perl/local_to_global.pl +694 -0
- data/lib/bioroebe/project/project.rb +264 -0
- data/lib/bioroebe/protein_structure/alpha_helix.rb +96 -0
- data/lib/bioroebe/protein_structure/helical_wheel.rb +205 -0
- data/lib/bioroebe/raw_sequence/README.md +17 -0
- data/lib/bioroebe/raw_sequence/raw_sequence.rb +557 -0
- data/lib/bioroebe/readline/README.md +2 -0
- data/lib/bioroebe/readline/readline.rb +31 -0
- data/lib/bioroebe/regexes/README.md +2 -0
- data/lib/bioroebe/regexes/regexes.rb +34 -0
- data/lib/bioroebe/requires/commandline_application.rb +5 -0
- data/lib/bioroebe/requires/require_all_aminoacids_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_calculate_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_codon_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_colour_scheme_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_count_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_dotplot_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_electron_microscopy_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_enzymes_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_fasta_and_fastq_files.rb +32 -0
- data/lib/bioroebe/requires/require_all_nucleotides_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_palindromes_files.rb +29 -0
- data/lib/bioroebe/requires/require_all_parser_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_pattern_files.rb +29 -0
- data/lib/bioroebe/requires/require_all_pdb_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_sequence_files.rb +26 -0
- data/lib/bioroebe/requires/require_all_string_matching_files.rb +28 -0
- data/lib/bioroebe/requires/require_all_svg_files.rb +12 -0
- data/lib/bioroebe/requires/require_all_taxonomy_files.rb +35 -0
- data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +32 -0
- data/lib/bioroebe/requires/require_cleave_and_digest.rb +24 -0
- data/lib/bioroebe/requires/require_colours.rb +20 -0
- data/lib/bioroebe/requires/require_encoding.rb +7 -0
- data/lib/bioroebe/requires/require_sequence.rb +7 -0
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +162 -0
- data/lib/bioroebe/requires/require_the_bioroebe_shell.rb +7 -0
- data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +7 -0
- data/lib/bioroebe/requires/require_the_constants.rb +23 -0
- data/lib/bioroebe/requires/require_the_toplevel_methods.rb +29 -0
- data/lib/bioroebe/requires/require_yaml.rb +94 -0
- data/lib/bioroebe/sequence/alignment.rb +214 -0
- data/lib/bioroebe/sequence/dna.rb +211 -0
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +404 -0
- data/lib/bioroebe/sequence/protein.rb +281 -0
- data/lib/bioroebe/sequence/reverse_complement.rb +148 -0
- data/lib/bioroebe/sequence/sequence.rb +706 -0
- data/lib/bioroebe/shell/add.rb +108 -0
- data/lib/bioroebe/shell/assign.rb +360 -0
- data/lib/bioroebe/shell/chop_and_cut.rb +281 -0
- data/lib/bioroebe/shell/colours/colours.rb +235 -0
- data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +1 -0
- data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +1 -0
- data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +1 -0
- data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -0
- data/lib/bioroebe/shell/constants.rb +166 -0
- data/lib/bioroebe/shell/download.rb +335 -0
- data/lib/bioroebe/shell/enable_and_disable.rb +158 -0
- data/lib/bioroebe/shell/enzymes.rb +310 -0
- data/lib/bioroebe/shell/fasta.rb +345 -0
- data/lib/bioroebe/shell/gtk.rb +76 -0
- data/lib/bioroebe/shell/help/class.rb +443 -0
- data/lib/bioroebe/shell/help/help.rb +25 -0
- data/lib/bioroebe/shell/history.rb +132 -0
- data/lib/bioroebe/shell/initialize.rb +217 -0
- data/lib/bioroebe/shell/loop.rb +74 -0
- data/lib/bioroebe/shell/menu.rb +5320 -0
- data/lib/bioroebe/shell/misc.rb +4341 -0
- data/lib/bioroebe/shell/prompt.rb +107 -0
- data/lib/bioroebe/shell/random.rb +289 -0
- data/lib/bioroebe/shell/readline/readline.rb +91 -0
- data/lib/bioroebe/shell/reset.rb +335 -0
- data/lib/bioroebe/shell/scan_and_parse.rb +135 -0
- data/lib/bioroebe/shell/search.rb +337 -0
- data/lib/bioroebe/shell/sequences.rb +200 -0
- data/lib/bioroebe/shell/shell.rb +41 -0
- data/lib/bioroebe/shell/show_report_and_display.rb +2901 -0
- data/lib/bioroebe/shell/startup.rb +127 -0
- data/lib/bioroebe/shell/taxonomy.rb +14 -0
- data/lib/bioroebe/shell/tk.rb +23 -0
- data/lib/bioroebe/shell/user_input.rb +88 -0
- data/lib/bioroebe/shell/xorg.rb +45 -0
- data/lib/bioroebe/siRNA/README.md +2 -0
- data/lib/bioroebe/siRNA/siRNA.rb +93 -0
- data/lib/bioroebe/string_matching/README.md +13 -0
- data/lib/bioroebe/string_matching/find_longest_substring.rb +162 -0
- data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +175 -0
- data/lib/bioroebe/string_matching/hamming_distance.rb +313 -0
- data/lib/bioroebe/string_matching/levensthein.rb +698 -0
- data/lib/bioroebe/string_matching/simple_string_comparer.rb +294 -0
- data/lib/bioroebe/string_matching/smith_waterman.rb +276 -0
- data/lib/bioroebe/svg/README.md +1 -0
- data/lib/bioroebe/svg/glyph.rb +719 -0
- data/lib/bioroebe/svg/mini_feature.rb +111 -0
- data/lib/bioroebe/svg/page.rb +570 -0
- data/lib/bioroebe/svg/primitive.rb +70 -0
- data/lib/bioroebe/svg/svgee.rb +326 -0
- data/lib/bioroebe/svg/track.rb +263 -0
- data/lib/bioroebe/taxonomy/README.md +1 -0
- data/lib/bioroebe/taxonomy/chart.rb +95 -0
- data/lib/bioroebe/taxonomy/class_methods.rb +181 -0
- data/lib/bioroebe/taxonomy/colours.rb +26 -0
- data/lib/bioroebe/taxonomy/constants.rb +218 -0
- data/lib/bioroebe/taxonomy/edit.rb +97 -0
- data/lib/bioroebe/taxonomy/help/help.rb +65 -0
- data/lib/bioroebe/taxonomy/help/helpline.rb +53 -0
- data/lib/bioroebe/taxonomy/info/check_available.rb +143 -0
- data/lib/bioroebe/taxonomy/info/info.rb +337 -0
- data/lib/bioroebe/taxonomy/info/is_dna.rb +150 -0
- data/lib/bioroebe/taxonomy/interactive.rb +1933 -0
- data/lib/bioroebe/taxonomy/menu.rb +905 -0
- data/lib/bioroebe/taxonomy/node.rb +118 -0
- data/lib/bioroebe/taxonomy/parse_fasta.rb +383 -0
- data/lib/bioroebe/taxonomy/shared.rb +287 -0
- data/lib/bioroebe/taxonomy/taxonomy.rb +521 -0
- data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +56 -0
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +715 -0
- data/lib/bioroebe/toplevel_methods/atomic_composition.rb +198 -0
- data/lib/bioroebe/toplevel_methods/base_composition.rb +121 -0
- data/lib/bioroebe/toplevel_methods/blast.rb +153 -0
- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
- data/lib/bioroebe/toplevel_methods/cat.rb +71 -0
- data/lib/bioroebe/toplevel_methods/chunked_display.rb +92 -0
- data/lib/bioroebe/toplevel_methods/cliner.rb +81 -0
- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
- data/lib/bioroebe/toplevel_methods/convert_global_env.rb +39 -0
- data/lib/bioroebe/toplevel_methods/databases.rb +73 -0
- data/lib/bioroebe/toplevel_methods/delimiter.rb +19 -0
- data/lib/bioroebe/toplevel_methods/digest.rb +71 -0
- data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +146 -0
- data/lib/bioroebe/toplevel_methods/e.rb +20 -0
- data/lib/bioroebe/toplevel_methods/editor.rb +21 -0
- data/lib/bioroebe/toplevel_methods/esystem.rb +22 -0
- data/lib/bioroebe/toplevel_methods/exponential_growth.rb +74 -0
- data/lib/bioroebe/toplevel_methods/extract.rb +56 -0
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +353 -0
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +257 -0
- data/lib/bioroebe/toplevel_methods/frequencies.rb +92 -0
- data/lib/bioroebe/toplevel_methods/hamming_distance.rb +60 -0
- data/lib/bioroebe/toplevel_methods/infer.rb +66 -0
- data/lib/bioroebe/toplevel_methods/is_on_roebe.rb +39 -0
- 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 +1,353 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# This file will hold code for FASTA and FASTQ on the toplevel.
|
6
|
+
#
|
7
|
+
# The FASTQ component will return the proper offset for use in
|
8
|
+
# FASTQ files (.fastq), for the corresponding quality scheme.
|
9
|
+
# =========================================================================== #
|
10
|
+
# require 'bioroebe/toplevel_methods/fasta_and_fastq.rb'
|
11
|
+
# Bioroebe.simplify_fasta_header
|
12
|
+
# Bioroebe.index_this_fasta_file(ARGV)
|
13
|
+
# Bioroebe.automatically_rename_this_fasta_file(ARGV)
|
14
|
+
# Bioroebe.show_fasta_header(ARGV)
|
15
|
+
# =========================================================================== #
|
16
|
+
module Bioroebe
|
17
|
+
|
18
|
+
require 'bioroebe/requires/require_yaml.rb'
|
19
|
+
require 'bioroebe/constants/files_and_directories.rb'
|
20
|
+
require 'bioroebe/colours/colours.rb'
|
21
|
+
require 'bioroebe/toplevel_methods/log_directory.rb'
|
22
|
+
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
23
|
+
require 'bioroebe/toplevel_methods/rds.rb'
|
24
|
+
require 'bioroebe/toplevel_methods/remove.rb'
|
25
|
+
|
26
|
+
# ========================================================================= #
|
27
|
+
# === Bioroebe.sanitize_this_fasta_file
|
28
|
+
#
|
29
|
+
# This method will modify a .fasta file's sequence header, by appending
|
30
|
+
# the number of aminoacids to this header.
|
31
|
+
#
|
32
|
+
# Usage example:
|
33
|
+
#
|
34
|
+
# Bioroebe.sanitize_this_fasta_file('/root/Bioroebe/fasta/IFNB1-P01574.fasta')
|
35
|
+
#
|
36
|
+
# ========================================================================= #
|
37
|
+
def self.sanitize_this_fasta_file(i)
|
38
|
+
if File.exist? i
|
39
|
+
dataset = File.readlines(i).map(&:strip)
|
40
|
+
header = dataset.first.dup
|
41
|
+
aminoacid_sequence = Bioroebe::ParseFasta.new(i) { :be_silent }.return_n_aminoacids
|
42
|
+
header << ", #{aminoacid_sequence} aminoacids"
|
43
|
+
dataset[0] = header
|
44
|
+
# ===================================================================== #
|
45
|
+
# Now we can save it again.
|
46
|
+
# ===================================================================== #
|
47
|
+
e 'Storing the modified data into '+sfile(i)+'.'
|
48
|
+
write_what_into(dataset.join(N), i)
|
49
|
+
end
|
50
|
+
end
|
51
|
+
|
52
|
+
# ========================================================================= #
|
53
|
+
# === Bioroebe.colourize_this_fasta_dna_sequence
|
54
|
+
#
|
55
|
+
# This toplevel method can be used to colourize a FASTA (DNA)
|
56
|
+
# sequence, e. g. "ATGCGCGTATTA" and so forth.
|
57
|
+
#
|
58
|
+
# Note that this is intended for the commandline, that is to be
|
59
|
+
# displayed on e. g. a KDE Konsole terminal.
|
60
|
+
#
|
61
|
+
# Usage example:
|
62
|
+
#
|
63
|
+
# puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
|
64
|
+
#
|
65
|
+
# ========================================================================= #
|
66
|
+
def self.colourize_this_fasta_dna_sequence(
|
67
|
+
i = nil
|
68
|
+
)
|
69
|
+
if i.nil?
|
70
|
+
e 'Please provide a valid FASTA sequence as input to '\
|
71
|
+
'Bioroebe.colourize_this_fasta_dna_sequence()'
|
72
|
+
return
|
73
|
+
end
|
74
|
+
if i.is_a? Array
|
75
|
+
# ===================================================================== #
|
76
|
+
# Arrays will be joined together.
|
77
|
+
# ===================================================================== #
|
78
|
+
i = i.join(' ').strip
|
79
|
+
end
|
80
|
+
if i.is_a? String
|
81
|
+
# ===================================================================== #
|
82
|
+
# The colours are either defined in a file called
|
83
|
+
# 'colourize_fasta_sequences.yml' or they are simply hardcoded.
|
84
|
+
#
|
85
|
+
# The preferred (and thus default) way is to simply make use
|
86
|
+
# of that .yml file. That works on my home system, so it
|
87
|
+
# should work for other people as well.
|
88
|
+
# ===================================================================== #
|
89
|
+
if use_colours?
|
90
|
+
i = i.dup if i.frozen?
|
91
|
+
this_file = FILE_COLOURIZE_FASTA_SEQUENCES
|
92
|
+
if File.exist? this_file
|
93
|
+
dataset_for_the_colours = YAML.load_file(this_file)
|
94
|
+
dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
|
95
|
+
i.gsub!(
|
96
|
+
/#{this_nucleotide}/,
|
97
|
+
send(this_colour_to_be_used, this_nucleotide)+
|
98
|
+
rev
|
99
|
+
)
|
100
|
+
}
|
101
|
+
else
|
102
|
+
i.gsub!(/A/, "#{teal('A')}#{rev}")
|
103
|
+
i.gsub!(/C/, "#{slateblue('C')}#{rev}")
|
104
|
+
i.gsub!(/G/, "#{royalblue('G')}#{rev}")
|
105
|
+
i.gsub!(/T/, "#{steelblue('T')}#{rev}")
|
106
|
+
i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
|
107
|
+
end
|
108
|
+
end
|
109
|
+
end
|
110
|
+
i
|
111
|
+
end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
|
112
|
+
self.instance_eval { alias colourized_parse_fasta colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
|
113
|
+
|
114
|
+
# ========================================================================= #
|
115
|
+
# === Bioroebe.calculate_weight_of_the_aminoacids_in_this_fasta_file
|
116
|
+
#
|
117
|
+
# This method will return a Hash containing the weight of the
|
118
|
+
# aminoacids in a .fasta file.
|
119
|
+
#
|
120
|
+
# Usage example:
|
121
|
+
#
|
122
|
+
# x = Bioroebe.calculate_weight_of_the_aminoacids_in_this_fasta_file('viruses.fa')
|
123
|
+
#
|
124
|
+
# This may yield a Hash such as the following:
|
125
|
+
#
|
126
|
+
# { "sp|P23046|NSP5_ROTBV" => 21647.5341,
|
127
|
+
# "sp|Q81835|SHDAG_HDVU2" => 22030.6392,
|
128
|
+
# "sp|A5HBD7|ST_POVWU" => 23433.3773,
|
129
|
+
# "sp|Q91FT8|234R_IIV6" => 21076.778 }
|
130
|
+
#
|
131
|
+
# ========================================================================= #
|
132
|
+
def self.calculate_weight_of_the_aminoacids_in_this_fasta_file(fasta_file)
|
133
|
+
if File.exist? fasta_file
|
134
|
+
hash = {}
|
135
|
+
results = Bioroebe.parse_fasta_quietly(fasta_file)
|
136
|
+
short_headers = results.short_headers?
|
137
|
+
sequences = results.sequences?
|
138
|
+
short_headers.each_with_index {|entry, index|
|
139
|
+
sum = 0
|
140
|
+
this_sequence = sequences[index]
|
141
|
+
# Next, convert this sequence into the corresponding mass.
|
142
|
+
this_sequence.chars.each {|this_specific_aminoacid|
|
143
|
+
sum += Bioroebe.weight_of_this_aminoacid?(this_specific_aminoacid)
|
144
|
+
}
|
145
|
+
hash[entry] = sum.round(4)
|
146
|
+
}
|
147
|
+
hash
|
148
|
+
else
|
149
|
+
e 'No file exists at '+fasta_file.to_s+'.'
|
150
|
+
end
|
151
|
+
end
|
152
|
+
|
153
|
+
require 'bioroebe/toplevel_methods/esystem.rb'
|
154
|
+
# ========================================================================= #
|
155
|
+
# === Bioroebe.index_this_fasta_file
|
156
|
+
#
|
157
|
+
# This method will use samtools faidx to index files.
|
158
|
+
# ========================================================================= #
|
159
|
+
def self.index_this_fasta_file(i = ARGV)
|
160
|
+
[i].flatten.compact.each {|this_file|
|
161
|
+
e
|
162
|
+
esystem "samtools faidx #{this_file}"
|
163
|
+
e
|
164
|
+
}
|
165
|
+
end
|
166
|
+
|
167
|
+
# ========================================================================= #
|
168
|
+
# === Bioroebe.return_sequence_from_this_file
|
169
|
+
#
|
170
|
+
# This is mostly an ad-hoc method to quickly read data from a
|
171
|
+
# local fasta file.
|
172
|
+
#
|
173
|
+
# Usage example:
|
174
|
+
#
|
175
|
+
# x = Bioroebe.return_sequence_from_this_file('viruses.fa')
|
176
|
+
#
|
177
|
+
# ========================================================================= #
|
178
|
+
def self.return_sequence_from_this_file(
|
179
|
+
this_file = 'bla.fasta'
|
180
|
+
)
|
181
|
+
if File.exist? this_file
|
182
|
+
dataset = File.readlines(this_file).select {|line|
|
183
|
+
line.start_with? ' '
|
184
|
+
}.map(&:strip).map {|line|
|
185
|
+
Bioroebe.remove_numbers(
|
186
|
+
line.upcase.delete(' ')
|
187
|
+
)
|
188
|
+
}
|
189
|
+
if dataset.is_a? Array
|
190
|
+
dataset = dataset.join
|
191
|
+
end
|
192
|
+
return dataset
|
193
|
+
end
|
194
|
+
end
|
195
|
+
|
196
|
+
# ========================================================================= #
|
197
|
+
# === Bioroebe.return_sanger_offset
|
198
|
+
# ========================================================================= #
|
199
|
+
def self.return_sanger_offset(
|
200
|
+
_ = FILE_FASTQ_QUALITY_SCHEMES
|
201
|
+
)
|
202
|
+
dataset = YAML.load_file(_)
|
203
|
+
entry = dataset['fastq-sanger']
|
204
|
+
offset = entry['offset']
|
205
|
+
return offset
|
206
|
+
end
|
207
|
+
|
208
|
+
# ========================================================================= #
|
209
|
+
# === Bioroebe.return_illumina_offset
|
210
|
+
# ========================================================================= #
|
211
|
+
def self.return_illumina_offset(
|
212
|
+
_ = FILE_FASTQ_QUALITY_SCHEMES
|
213
|
+
)
|
214
|
+
dataset = YAML.load_file(_)
|
215
|
+
entry = dataset['fastq-illumina']
|
216
|
+
offset = entry['offset']
|
217
|
+
return offset
|
218
|
+
end
|
219
|
+
|
220
|
+
# ========================================================================= #
|
221
|
+
# === Bioroebe.return_solexa_offset
|
222
|
+
# ========================================================================= #
|
223
|
+
def self.return_solexa_offset(
|
224
|
+
_ = FILE_FASTQ_QUALITY_SCHEMES
|
225
|
+
)
|
226
|
+
dataset = YAML.load_file(_)
|
227
|
+
entry = dataset['fastq-solexa']
|
228
|
+
offset = entry['offset']
|
229
|
+
return offset
|
230
|
+
end
|
231
|
+
|
232
|
+
# ========================================================================= #
|
233
|
+
# === Bioroebe.automatically_rename_this_fasta_file
|
234
|
+
#
|
235
|
+
# This method will automatically (try to) rename an existing
|
236
|
+
# fasta file, by tapping into the method called
|
237
|
+
# .return_new_filename_based_on_fasta_identifier().
|
238
|
+
# ========================================================================= #
|
239
|
+
def self.automatically_rename_this_fasta_file(fasta_file)
|
240
|
+
fasta_file = [fasta_file].flatten.compact
|
241
|
+
fasta_file.each {|this_fasta_file|
|
242
|
+
if File.exist? this_fasta_file
|
243
|
+
new_filename = return_new_filename_based_on_fasta_identifier(this_fasta_file)
|
244
|
+
erev "Renaming #{sfile(this_fasta_file)}#{rev} "\
|
245
|
+
"to #{sfile(new_filename)} #{rev}next."
|
246
|
+
Bioroebe.rename(this_fasta_file, new_filename)
|
247
|
+
else
|
248
|
+
no_file_exists_at(this_fasta_file)
|
249
|
+
end
|
250
|
+
}
|
251
|
+
end
|
252
|
+
|
253
|
+
# ========================================================================= #
|
254
|
+
# === Bioroebe.return_new_filename_based_on_fasta_identifier
|
255
|
+
#
|
256
|
+
# This method will give us a new filename suggestion, which
|
257
|
+
# we can use to then rename a FASTA file (.fa).
|
258
|
+
#
|
259
|
+
# Usage example:
|
260
|
+
#
|
261
|
+
# Bioroebe.return_new_filename_based_on_fasta_identifier "NC_008253.fna" # => "NC_008253.1_Escherichia_coli_536.fasta"
|
262
|
+
# Bioroebe.return_new_filename_based_on_fasta_identifier ">NC_000866.4 Enterobacteria phage T4, complete genome" # => "NC_008253.1_Escherichia_coli_536.fasta"
|
263
|
+
#
|
264
|
+
# ========================================================================= #
|
265
|
+
def self.return_new_filename_based_on_fasta_identifier(i)
|
266
|
+
if i.is_a? Array
|
267
|
+
i.flatten!
|
268
|
+
i.compact!
|
269
|
+
i = i.first
|
270
|
+
end
|
271
|
+
fasta_identifier = File.readlines(i).first
|
272
|
+
if fasta_identifier
|
273
|
+
if fasta_identifier.include? '|'
|
274
|
+
splitted = fasta_identifier.split('|')
|
275
|
+
elsif fasta_identifier.start_with?('>') # else may look like ">NC_000866.4 Enterobacteria phage T4, complete genome\n"
|
276
|
+
splitted = fasta_identifier.delete('>,').split(' ')
|
277
|
+
nm_identifier = splitted[0]
|
278
|
+
name_of_the_sequence = splitted[1 .. -1].join(' ').strip
|
279
|
+
end
|
280
|
+
if fasta_identifier.include? '|'
|
281
|
+
case splitted.size
|
282
|
+
when 3
|
283
|
+
nm_identifier = splitted[1]
|
284
|
+
name_of_the_sequence = splitted[2]
|
285
|
+
else
|
286
|
+
nm_identifier = splitted[3] # Such as "NM_007315.3"
|
287
|
+
name_of_the_sequence = splitted[4] # Such as "Homo sapiens signal transducer and activator of transcription 1 (STAT1)"
|
288
|
+
end
|
289
|
+
end
|
290
|
+
if nm_identifier
|
291
|
+
nm_identifier.strip!
|
292
|
+
name_of_the_sequence.strip!
|
293
|
+
if name_of_the_sequence.include? ','
|
294
|
+
name_of_the_sequence = name_of_the_sequence[0 .. name_of_the_sequence.index(',')].strip
|
295
|
+
end
|
296
|
+
name_of_the_sequence.tr!(' ()/','_')
|
297
|
+
name_of_the_sequence.tr!(',','')
|
298
|
+
name_of_the_sequence.tr!('.','') # We need no '.' characters.
|
299
|
+
name_of_the_sequence.squeeze!('_') # We want only one '_'.
|
300
|
+
name_of_the_sequence.squeeze!('-')
|
301
|
+
name_of_the_sequence.chop! if name_of_the_sequence.end_with? '_'
|
302
|
+
new_filename = nm_identifier+'_'+name_of_the_sequence+'.fasta'
|
303
|
+
# =================================================================== #
|
304
|
+
# Next, prepend the target directory.
|
305
|
+
# =================================================================== #
|
306
|
+
new_filename.prepend(log_dir?)
|
307
|
+
# =================================================================== #
|
308
|
+
# And get rid of any possible dual '//'.
|
309
|
+
# =================================================================== #
|
310
|
+
new_filename = rds(new_filename)
|
311
|
+
else
|
312
|
+
e swarn('Something went wrong - we did not find a valid NCBI entry.')
|
313
|
+
return nil
|
314
|
+
end
|
315
|
+
else
|
316
|
+
erev "No FASTA identifier could be found for #{sfile(i)}#{rev}."
|
317
|
+
end
|
318
|
+
end
|
319
|
+
|
320
|
+
# ========================================================================= #
|
321
|
+
# === Bioroebe.show_fasta_header
|
322
|
+
#
|
323
|
+
# This ad-hoc method can be used to quickly show the first line of an
|
324
|
+
# assumed .fasta file.
|
325
|
+
# ========================================================================= #
|
326
|
+
def self.show_fasta_header(of_this_file)
|
327
|
+
if of_this_file.is_a? Array
|
328
|
+
of_this_file = of_this_file.first
|
329
|
+
end
|
330
|
+
e File.readlines(of_this_file).first
|
331
|
+
end
|
332
|
+
|
333
|
+
end
|
334
|
+
|
335
|
+
if __FILE__ == $PROGRAM_NAME
|
336
|
+
alias e puts
|
337
|
+
# ========================================================================= #
|
338
|
+
# And show the offsets in use as well:
|
339
|
+
# ========================================================================= #
|
340
|
+
e Bioroebe.return_sanger_offset
|
341
|
+
e Bioroebe.return_solexa_offset
|
342
|
+
e Bioroebe.return_illumina_offset
|
343
|
+
e Bioroebe.colourize_this_fasta_sequence(
|
344
|
+
'ATGAAATCGCGCGTGCCGCGCGCGC'\
|
345
|
+
'GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCTGCGCGCGCGCGCG'\
|
346
|
+
'CGCGCGCGTGCCGCGCGCAGGCGGCGGCGGCGGCGGCGGCG'
|
347
|
+
)
|
348
|
+
if ARGV.empty?
|
349
|
+
e 'Please supply a file path.'
|
350
|
+
else
|
351
|
+
e Bioroebe.return_new_filename_based_on_fasta_identifier(ARGV)
|
352
|
+
end
|
353
|
+
end
|
@@ -0,0 +1,257 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'fileutils'
|
10
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
11
|
+
require 'bioroebe/toplevel_methods/log_directory.rb'
|
12
|
+
require 'bioroebe/colours/rev.rb'
|
13
|
+
require 'bioroebe/colours/sfile.rb'
|
14
|
+
require 'bioroebe/colours/sdir.rb'
|
15
|
+
|
16
|
+
# ========================================================================= #
|
17
|
+
# === Bioroebe.pwd (pwd tag)
|
18
|
+
#
|
19
|
+
# Feedback the current working directory (it will be returned, as a
|
20
|
+
# String).
|
21
|
+
# ========================================================================= #
|
22
|
+
def self.pwd
|
23
|
+
"#{Dir.pwd}/".squeeze('/')
|
24
|
+
end; self.instance_eval { alias return_pwd pwd } # === Bioroebe.return_pwd
|
25
|
+
|
26
|
+
# ========================================================================= #
|
27
|
+
# === pwd
|
28
|
+
# ========================================================================= #
|
29
|
+
def pwd
|
30
|
+
::Bioroebe.pwd
|
31
|
+
end
|
32
|
+
|
33
|
+
# ========================================================================= #
|
34
|
+
# === Bioroebe.no_file_exists_at
|
35
|
+
# ========================================================================= #
|
36
|
+
def self.no_file_exists_at(i)
|
37
|
+
erev "No file exists at `#{sfile(i)}#{rev}`."
|
38
|
+
end
|
39
|
+
|
40
|
+
# ========================================================================= #
|
41
|
+
# === Bioroebe.mv
|
42
|
+
#
|
43
|
+
# This method can be used to rename or move a (local) file.
|
44
|
+
# ========================================================================= #
|
45
|
+
def self.mv(old, new)
|
46
|
+
FileUtils.mv(old, new)
|
47
|
+
end; self.instance_eval { alias rename mv } # === Bioroebe.rename
|
48
|
+
|
49
|
+
# ========================================================================= #
|
50
|
+
# === Bioroebe.create_file
|
51
|
+
#
|
52
|
+
# This method can be used to create a file.
|
53
|
+
# ========================================================================= #
|
54
|
+
def self.create_file(i)
|
55
|
+
FileUtils.touch(i) unless File.file?(i)
|
56
|
+
end
|
57
|
+
|
58
|
+
# ========================================================================= #
|
59
|
+
# === Bioroebe.append_what_into
|
60
|
+
#
|
61
|
+
# This method can be used to append content onto a file.
|
62
|
+
# ========================================================================= #
|
63
|
+
def self.append_what_into(
|
64
|
+
what = 'Hello world!',
|
65
|
+
into = 'test.md'
|
66
|
+
)
|
67
|
+
unless File.exist? into
|
68
|
+
base_dir = File.dirname(into)
|
69
|
+
unless File.directory? base_dir
|
70
|
+
e rev+
|
71
|
+
'No directory exists at '+sdir(base_dir)+
|
72
|
+
rev+'. Thus creating it now.'
|
73
|
+
create_directory(base_dir)
|
74
|
+
end
|
75
|
+
e rev+
|
76
|
+
'No file exists at '+sfile(into)+rev+
|
77
|
+
'. Thus creating it now.'
|
78
|
+
create_file(into)
|
79
|
+
end
|
80
|
+
File.open(into, 'a') { |file|
|
81
|
+
file << what
|
82
|
+
}
|
83
|
+
end
|
84
|
+
|
85
|
+
# ========================================================================= #
|
86
|
+
# === Bioroebe.write_what_into
|
87
|
+
#
|
88
|
+
# This method will simply write the content of the variable `what`
|
89
|
+
# into the file called `into`.
|
90
|
+
# ========================================================================= #
|
91
|
+
def self.write_what_into(
|
92
|
+
what = 'Hello world!',
|
93
|
+
into = 'test.md'
|
94
|
+
)
|
95
|
+
base_directory = File.dirname(into)
|
96
|
+
if File.directory? base_directory
|
97
|
+
File.open(into, 'w') { |file|
|
98
|
+
file << what
|
99
|
+
}
|
100
|
+
else
|
101
|
+
e "No directory exists at #{base_directory}. Thus, "\
|
102
|
+
"no file could be saved."
|
103
|
+
end
|
104
|
+
end; self.instance_eval { alias save_file write_what_into } # === Bioroebe.save_file
|
105
|
+
self.instance_eval { alias save_what_where write_what_into } # === Bioroebe.save_what_where
|
106
|
+
|
107
|
+
# ========================================================================= #
|
108
|
+
# === Bioroebe.remove_file
|
109
|
+
#
|
110
|
+
# Use this method to remove a file.
|
111
|
+
# ========================================================================= #
|
112
|
+
def self.remove_file(
|
113
|
+
i, be_verbose = false
|
114
|
+
)
|
115
|
+
if File.exist? i
|
116
|
+
File.delete(i)
|
117
|
+
if be_verbose
|
118
|
+
this_file = "#{return_pwd}#{i}"
|
119
|
+
e 'File '+sfile(this_file)+' exists, '\
|
120
|
+
'we will thus remove it now.'
|
121
|
+
end
|
122
|
+
end
|
123
|
+
end; self.instance_eval { alias remove remove_file } # === Bioroebe.remove
|
124
|
+
|
125
|
+
# ========================================================================= #
|
126
|
+
# === Bioroebe.change_directory
|
127
|
+
#
|
128
|
+
# This method allows us to change the directory.
|
129
|
+
#
|
130
|
+
# Bioroebe.cd() is an alias to the method here.
|
131
|
+
# ========================================================================= #
|
132
|
+
def self.change_directory(
|
133
|
+
i = '$HOME',
|
134
|
+
be_verbose = false
|
135
|
+
)
|
136
|
+
case be_verbose
|
137
|
+
when :do_report_current_directory,
|
138
|
+
:be_verbose
|
139
|
+
be_verbose = true
|
140
|
+
end
|
141
|
+
case i # Do some sanitizing here. (case tag)
|
142
|
+
# ======================================================================= #
|
143
|
+
# === :home_directory
|
144
|
+
# ======================================================================= #
|
145
|
+
when :home_directory,
|
146
|
+
:default,
|
147
|
+
nil # ← Nil is also assumed to refer to this :default value.
|
148
|
+
# ===================================================================== #
|
149
|
+
# In this case we will try to cd into the base-directory of the
|
150
|
+
# Bioroebe shell.
|
151
|
+
# ===================================================================== #
|
152
|
+
i = log_dir?
|
153
|
+
# ======================================================================= #
|
154
|
+
# === :download_dir
|
155
|
+
# ======================================================================= #
|
156
|
+
when :download_dir,':download_dir',
|
157
|
+
:download_directory,':download_directory'
|
158
|
+
i = download_dir?
|
159
|
+
# ======================================================================= #
|
160
|
+
# Bioroebe.save_dir? is defined in bioroebe/toplevel_methods/store_here.rb.
|
161
|
+
# ======================================================================= #
|
162
|
+
when 'base',
|
163
|
+
'logdir'
|
164
|
+
# ===================================================================== #
|
165
|
+
# Enter the main log dir, unless a file exists with the same name.
|
166
|
+
# ===================================================================== #
|
167
|
+
i = save_dir? unless File.exist? i
|
168
|
+
end
|
169
|
+
i << '/' unless i.end_with? '/'
|
170
|
+
if File.directory? i
|
171
|
+
e sdir(i) if be_verbose # Also colourize the directory and output it.
|
172
|
+
Dir.chdir(i)
|
173
|
+
else
|
174
|
+
if be_verbose
|
175
|
+
erev "No directory called `#{sdir(i)}#{rev}` exists,"
|
176
|
+
erev 'thus we can not cd to this target.'
|
177
|
+
end
|
178
|
+
end
|
179
|
+
end; self.instance_eval { alias cd change_directory } # === Bioroebe.cd
|
180
|
+
self.instance_eval { alias chdir change_directory } # === Bioroebe.chdir
|
181
|
+
|
182
|
+
# ========================================================================= #
|
183
|
+
# === Bioroebe.pdb_directory?
|
184
|
+
#
|
185
|
+
# This refers to the local pdb/ directory.
|
186
|
+
# ========================================================================= #
|
187
|
+
def self.pdb_directory?
|
188
|
+
return "#{log_dir?}pdb/"
|
189
|
+
end
|
190
|
+
|
191
|
+
# ========================================================================= #
|
192
|
+
# === Bioroebe.ensure_that_the_base_directories_exist
|
193
|
+
#
|
194
|
+
# This method will ensure that the base directory for the
|
195
|
+
# Bioroebe project exist.
|
196
|
+
# ========================================================================= #
|
197
|
+
def self.ensure_that_the_base_directories_exist
|
198
|
+
# ======================================================================= #
|
199
|
+
# We also need to create the temp directory, as well as having to
|
200
|
+
# notify the user that this will be done. The taxonomy subdirectory
|
201
|
+
# will also be created.
|
202
|
+
# ======================================================================= #
|
203
|
+
use_this_log_dir = log_dir?
|
204
|
+
unless File.exist? use_this_log_dir
|
205
|
+
erev "The base directory at `#{sdir(use_this_log_dir)}#{rev}` does not exist."
|
206
|
+
erev 'It will thus be created next.'
|
207
|
+
mkdir use_this_log_dir
|
208
|
+
end
|
209
|
+
# ======================================================================= #
|
210
|
+
# === Ensure that the Downloads/ directory exists
|
211
|
+
# ======================================================================= #
|
212
|
+
_ = "#{use_this_log_dir}Downloads/"
|
213
|
+
unless File.exist? _
|
214
|
+
erev "The directory at `#{sdir(_)}#{rev}` does not exist."
|
215
|
+
erev 'It will thus be created next.'
|
216
|
+
mkdir _
|
217
|
+
end
|
218
|
+
# ======================================================================= #
|
219
|
+
# === Ensure that the pdb/ directory exists
|
220
|
+
# ======================================================================= #
|
221
|
+
_ = "#{use_this_log_dir}pdb/"
|
222
|
+
unless File.exist? _
|
223
|
+
erev "The directory at `#{sdir(_)}#{rev}` does not exist."
|
224
|
+
erev 'It will thus be created next.'
|
225
|
+
mkdir _
|
226
|
+
end
|
227
|
+
autogenerated_sql_files_dir =
|
228
|
+
AUTOGENERATED_SQL_FILES_DIR
|
229
|
+
unless Dir.exist? autogenerated_sql_files_dir
|
230
|
+
erev 'The directory at `'+sdir(autogenerated_sql_files_dir)+
|
231
|
+
rev+'` does not exist.'
|
232
|
+
erev 'It will thus be created next.'
|
233
|
+
mkdir(autogenerated_sql_files_dir)
|
234
|
+
end
|
235
|
+
end
|
236
|
+
|
237
|
+
# ========================================================================= #
|
238
|
+
# === Bioroebe.mkdir (mkdir tag)
|
239
|
+
# ========================================================================= #
|
240
|
+
def self.mkdir(i)
|
241
|
+
FileUtils.mkdir_p(i)
|
242
|
+
end; self.instance_eval { alias create_directory mkdir } # === Bioroebe.create_directory
|
243
|
+
self.instance_eval { alias mkdir_p mkdir } # === Bioroebe.mkdir_p
|
244
|
+
|
245
|
+
# ========================================================================= #
|
246
|
+
# === mkdir
|
247
|
+
# ========================================================================= #
|
248
|
+
def mkdir(i)
|
249
|
+
::Bioroebe.mkdir(i)
|
250
|
+
end
|
251
|
+
|
252
|
+
end
|
253
|
+
|
254
|
+
if __FILE__ == $PROGRAM_NAME
|
255
|
+
Bioroebe.ensure_that_the_base_directories_exist
|
256
|
+
Bioroebe.write_what_into(ARGV[0], ARGV[1])
|
257
|
+
end
|
@@ -0,0 +1,92 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/frequencies.rb'
|
6
|
+
# Bioroebe.aminoacid_frequency
|
7
|
+
# =========================================================================== #
|
8
|
+
module Bioroebe
|
9
|
+
|
10
|
+
require 'bioroebe/project/project.rb'
|
11
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
12
|
+
require 'bioroebe/colours/colours.rb'
|
13
|
+
|
14
|
+
# ========================================================================= #
|
15
|
+
# === Bioroebe.calculate_the_frequencies_of_this_species
|
16
|
+
# ========================================================================= #
|
17
|
+
def self.calculate_the_frequencies_of_this_species(
|
18
|
+
i = :homo_sapiens
|
19
|
+
)
|
20
|
+
require 'bioroebe/sequence/dna.rb'
|
21
|
+
require 'yaml'
|
22
|
+
if i and i.is_a?(Array) and i.empty?
|
23
|
+
i << :homo_sapiens
|
24
|
+
end
|
25
|
+
hash_aminoacids = {}
|
26
|
+
hash_aminoacids.default = 0
|
27
|
+
if i.is_a? Array
|
28
|
+
i = i.first
|
29
|
+
end
|
30
|
+
case i.to_sym
|
31
|
+
# ======================================================================= #
|
32
|
+
# === :homo_sapiens
|
33
|
+
# ======================================================================= #
|
34
|
+
when :homo_sapiens,
|
35
|
+
:homo,
|
36
|
+
:human
|
37
|
+
i = "#{::Bioroebe.project_base_directory?}"\
|
38
|
+
"codon_tables/frequencies/9606_Homo_sapiens.yml"
|
39
|
+
end
|
40
|
+
hash = YAML.load_file(i)
|
41
|
+
# "GAC"=>25.1
|
42
|
+
hash.each_pair {|key, value|
|
43
|
+
this_aminoacid = Bioroebe.to_aa(key)
|
44
|
+
hash_aminoacids[this_aminoacid] += value
|
45
|
+
}
|
46
|
+
e
|
47
|
+
# ======================================================================= #
|
48
|
+
# Convert it into percent:
|
49
|
+
# ======================================================================= #
|
50
|
+
hash_aminoacids.each_pair {|key, value_for_percentage|
|
51
|
+
value_for_percentage = ((value_for_percentage * 100.0) / 1000.0).round(3).to_s
|
52
|
+
value_for_percentage = '%.2f' % value_for_percentage
|
53
|
+
e ' '+
|
54
|
+
steelblue(key).to_s+' '+
|
55
|
+
royalblue(
|
56
|
+
value_for_percentage.rjust(6)+'%'
|
57
|
+
)
|
58
|
+
}
|
59
|
+
e
|
60
|
+
end
|
61
|
+
|
62
|
+
# ========================================================================= #
|
63
|
+
# === Bioroebe.aminoacid_frequency
|
64
|
+
#
|
65
|
+
# Usage example:
|
66
|
+
#
|
67
|
+
# Bioroebe.aminoacid_frequency('MVTDEGAIYFTKDAARNWKAAVEETVSATLNRTVSSGITGASYYTGTFST')
|
68
|
+
#
|
69
|
+
# Would yield the following Hash:
|
70
|
+
#
|
71
|
+
# {"M"=>1, "V"=>4, "T"=>9, "D"=>2, "E"=>3, "G"=>4, "A"=>7, "I"=>2, "Y"=>3, "F"=>2, "K"=>2, "R"=>2, "N"=>2, "W"=>1, "S"=>5, "L"=>1}
|
72
|
+
#
|
73
|
+
# ========================================================================= #
|
74
|
+
def self.aminoacid_frequency(
|
75
|
+
of_this_sequence = ''
|
76
|
+
)
|
77
|
+
if of_this_sequence.is_a? Array
|
78
|
+
of_this_sequence = of_this_sequence.first
|
79
|
+
end
|
80
|
+
chars = of_this_sequence.split(//)
|
81
|
+
hash = {}
|
82
|
+
hash.default = 0
|
83
|
+
chars.each {|this_char| hash[this_char] += 1 }
|
84
|
+
return hash
|
85
|
+
end; self.instance_eval { alias aminoacid_frequencies aminoacid_frequency } # === Bioroebe.aminoacid_frequencies
|
86
|
+
|
87
|
+
end
|
88
|
+
|
89
|
+
if __FILE__ == $PROGRAM_NAME
|
90
|
+
Bioroebe.calculate_the_frequencies_of_this_species(ARGV)
|
91
|
+
pp Bioroebe.aminoacid_frequency('MVTDEGAIYFTKDAARNWKAAVEETVSATLNRTVSSGITGASYYTGTFST')
|
92
|
+
end # calculatethefrequenciesofthisspecies
|