bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -0
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#!/usr/bin/ruby -w
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# frozen_string_literal: true
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# =========================================================================== #
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# === Bioroebe::ColourScheme
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# =========================================================================== #
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# require 'bioroebe/colours/colour_schemes/array_available_colour_schemes.rb'
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module Bioroebe
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module ColourScheme
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# ========================================================================= #
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# === Bioroebe::ColourScheme::ARRAY_AVAILABLE_COLOUR_SCHEMES
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#
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# Batch-load the various colour addons.
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#
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#
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# buried, helix, hydropathy, strand and turn.
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#
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# nucleotide, taylor and zappo.
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#
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ARRAY_AVAILABLE_COLOUR_SCHEMES = %w(
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buried
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helix
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hydropathy
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strand
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turn
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nucleotide
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taylor
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zappo
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)
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# =========================================================================== #
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# === Color codings for buried amino acids
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#
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# =========================================================================== #
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# require 'bioroebe/colours/buried.rb'
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# =========================================================================== #
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require 'bioroebe/colours/colour_schemes/score.rb'
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class Buried < Score # === Bioroebe::ColourScheme::Buried
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# ======================================================================= #
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# === @colours
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# ======================================================================= #
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@colours = {}
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@colours.default = 'FFFFFF' # return white by default
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# ======================================================================= #
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# === Bioroebe::ColourScheme::Buried.score_to_rgb_hex
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# ======================================================================= #
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percent = score_to_percent(score, min, max)
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rgb_percent_to_hex(0.0, 1.0 - percent, percent)
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end
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# ======================================================================= #
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# === @scores
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# ======================================================================= #
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@scores = { # Hash, with aminoacid->score entries.
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'A' => 0.66,
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'C' => 1.19,
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'D' => 1.46,
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'E' => 0.74,
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'F' => 0.6,
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'G' => 1.56,
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'H' => 0.95,
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'I' => 0.47,
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'K' => 1.01,
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'L' => 0.59,
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'M' => 0.6,
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'N' => 1.56,
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'P' => 1.52,
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'Q' => 0.98,
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'R' => 0.95,
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'S' => 1.43,
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'T' => 0.96,
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'U' => 0,
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'V' => 0.5,
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'W' => 0.96,
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'Y' => 1.14,
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'B' => 1.51,
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'X' => 1.0,
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'Z' => 0.86
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}
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@min = 0.05
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@max = 4.6
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@scores.each { |k,s|
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# ======================================================================= #
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# === Fill up the @colours Hash
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# ======================================================================= #
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@colours[k] = score_to_rgb_hex(s, @min, @max) # Convert the scores into RGB values.
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# =========================================================================== #
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# = Description
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#
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# Popular colour codings for nucleic and amino acids.
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#
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# The Bioroebe::ColourScheme module contains classes that return popular
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# colour codings for nucleic and amino acids in RGB hex format suitable
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# for HTML code.
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#
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# Presently the following schemes are supported:
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#
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# Buried - Buried index
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# Helix - Helix propensity
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# Hydropathy - Hydrophobicity
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# Nucleotide - Nucelotide colour coding
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# Strand - Strand propensity
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# Taylor - Taylor colour coding
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# Turn - Turn propensity
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# Zappo - Zappo colour coding
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#
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# More possible colour schemes may be these variants:
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#
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# BLOSUM62
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# ClustalX
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# Percentage Identity (PID)
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#
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# The colours schemes BLOSUM62, ClustalX, and Percentage Identity
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# are all dependent on the alignment consensus.
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#
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# This data is currently referenced from the "JalView alignment editor".
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#
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# Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
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# "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
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#
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# http://www.jalview.org
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#
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# Currently, the score data for things such as hydropathy, helix, turn,
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# etc. are contained here but should probably be moved elsewhere once a
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# good reference is found for these values.
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43
|
+
#
|
44
|
+
# = Usage example
|
45
|
+
#
|
46
|
+
# require 'bioroebe'
|
47
|
+
#
|
48
|
+
# seq = 'gattaca'
|
49
|
+
# scheme = Bioroebe::ColourScheme::Zappo
|
50
|
+
# postfix = '</span>'
|
51
|
+
# html = ''.dup
|
52
|
+
# seq.each_byte { |c|
|
53
|
+
# colour = scheme[c.chr]
|
54
|
+
# prefix = %Q(<span style="background:\##{colour};">)
|
55
|
+
# html << prefix + c.chr + postfix
|
56
|
+
# }
|
57
|
+
# puts html
|
58
|
+
#
|
59
|
+
# == Accessing colours
|
60
|
+
#
|
61
|
+
# puts Bioroebe::ColourScheme::Buried['A'] # 00DC22
|
62
|
+
# puts Bioroebe::ColourScheme::Buried[:c] # 00BF3F
|
63
|
+
# puts Bioroebe::ColourScheme::Buried[nil] # nil
|
64
|
+
# puts Bioroebe::ColourScheme::Buried['-'] # FFFFFF
|
65
|
+
# puts Bioroebe::ColourScheme::Buried[7] # FFFFFF
|
66
|
+
# puts Bioroebe::ColourScheme::Buried['junk'] # FFFFFF
|
67
|
+
# puts Bioroebe::ColourScheme::Buried['t'] # 00CC32
|
68
|
+
#
|
69
|
+
# =========================================================================== #
|
70
|
+
# External Resources that may be useful here:
|
71
|
+
#
|
72
|
+
# https://www.jalview.org/help.html
|
73
|
+
#
|
74
|
+
# =========================================================================== #
|
75
|
+
# require 'bioroebe/colour_schemes/colour_scheme.rb'
|
76
|
+
# =========================================================================== #
|
77
|
+
require 'bioroebe/colours/colour_schemes/simple.rb'
|
78
|
+
require 'bioroebe/colours/colour_schemes/score.rb'
|
79
|
+
|
80
|
+
module Bioroebe
|
81
|
+
|
82
|
+
module ColourScheme # === Bioroebe::ColourScheme
|
83
|
+
|
84
|
+
# ========================================================================= #
|
85
|
+
# === Consensus sub-classes
|
86
|
+
#
|
87
|
+
# NOTE todo:
|
88
|
+
#
|
89
|
+
# BLOSUM62
|
90
|
+
# ClustalX
|
91
|
+
# PID
|
92
|
+
#
|
93
|
+
# ========================================================================= #
|
94
|
+
|
95
|
+
# ========================================================================= #
|
96
|
+
# TODO - anyone wants to implement these?
|
97
|
+
# ========================================================================= #
|
98
|
+
class Consensus
|
99
|
+
end
|
100
|
+
|
101
|
+
end; end
|
@@ -0,0 +1,262 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::ColourSchemeDemo
|
6
|
+
#
|
7
|
+
# A Bioroebe::ColourScheme demo script for Nucleic Acids sequences.
|
8
|
+
#
|
9
|
+
# Usage example:
|
10
|
+
#
|
11
|
+
# (1) If you want to showcase what this class can do, run a command
|
12
|
+
# similar to the following one:
|
13
|
+
#
|
14
|
+
# colour_scheme > /Depot/jjj/foo.html; open /Depot/jjj/foo.html
|
15
|
+
#
|
16
|
+
# Where colour_scheme is an alias to this file here.
|
17
|
+
#
|
18
|
+
# (2) If you want to colourize sequences, try this:
|
19
|
+
#
|
20
|
+
# cat sequence.fasta
|
21
|
+
#
|
22
|
+
# >DNA_sequence
|
23
|
+
# acgtgtgtcatgctagtcgatcgtactagtcgtagctagtca
|
24
|
+
#
|
25
|
+
# colour_scheme sequence.fasta > colourized_sequence.html; open colourized_sequence.html
|
26
|
+
#
|
27
|
+
# =========================================================================== #
|
28
|
+
# require 'bioroebe/colour_schemes/colour_scheme_demo.rb'
|
29
|
+
# =========================================================================== #
|
30
|
+
require 'bioroebe/base/base.rb'
|
31
|
+
require 'bioroebe/colours/colour_schemes/colour_scheme.rb'
|
32
|
+
require 'bioroebe/colours/colour_schemes/array_available_colour_schemes.rb'
|
33
|
+
|
34
|
+
Bioroebe::ColourScheme::ARRAY_AVAILABLE_COLOUR_SCHEMES.each {|this_scheme|
|
35
|
+
require "bioroebe/colours/colour_schemes/#{this_scheme}.rb"
|
36
|
+
}
|
37
|
+
|
38
|
+
module Bioroebe
|
39
|
+
|
40
|
+
class ColourSchemeDemo < ::Bioroebe::Base
|
41
|
+
|
42
|
+
require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
|
43
|
+
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
44
|
+
require 'bioroebe/toplevel_methods/nucleotides.rb'
|
45
|
+
|
46
|
+
# ========================================================================= #
|
47
|
+
# === TITLE
|
48
|
+
# ========================================================================= #
|
49
|
+
TITLE = 'Bioroebe::ColourScheme for DNA sequences'
|
50
|
+
|
51
|
+
# ========================================================================= #
|
52
|
+
# === CDIV
|
53
|
+
# ========================================================================= #
|
54
|
+
CDIV = '</div>'
|
55
|
+
|
56
|
+
# ========================================================================= #
|
57
|
+
# === BODY_TAG
|
58
|
+
# ========================================================================= #
|
59
|
+
BODY_TAG = '<body style="font-size:1.5em">'
|
60
|
+
|
61
|
+
# ========================================================================= #
|
62
|
+
# === MAXIMAL_N_NUCLEOTIDES_PER_ROW
|
63
|
+
# ========================================================================= #
|
64
|
+
MAXIMAL_N_NUCLEOTIDES_PER_ROW = 80
|
65
|
+
|
66
|
+
# ========================================================================= #
|
67
|
+
# === DEFAULT_FASTA_FILE_NAME
|
68
|
+
# ========================================================================= #
|
69
|
+
DEFAULT_FASTA_FILE_NAME = 'tardigrada_fasta.ffn'
|
70
|
+
|
71
|
+
# ========================================================================= #
|
72
|
+
# === initialize
|
73
|
+
#
|
74
|
+
# First argument should be the nucleotide sequence.
|
75
|
+
#
|
76
|
+
# Second argument should be the aminoacid sequence. But it can be
|
77
|
+
# omitted - in that case, we will deduce the aminoacid sequence
|
78
|
+
# from the nucleotide sequence.
|
79
|
+
# ========================================================================= #
|
80
|
+
def initialize(
|
81
|
+
nucleotide_sequence,
|
82
|
+
aminoacid_sequence = nil
|
83
|
+
)
|
84
|
+
reset
|
85
|
+
case aminoacid_sequence
|
86
|
+
when :be_quiet
|
87
|
+
aminoacid_sequence = nil
|
88
|
+
@be_verbose = false
|
89
|
+
end
|
90
|
+
# ======================================================================= #
|
91
|
+
# === Handle the case when the user did not input an aminoacid sequence
|
92
|
+
# ======================================================================= #
|
93
|
+
if aminoacid_sequence.nil?
|
94
|
+
if nucleotide_sequence.respond_to? :translate
|
95
|
+
aminoacid_sequence = nucleotide_sequence.translate # Aminoacid sequence.
|
96
|
+
elsif nucleotide_sequence.is_a? String
|
97
|
+
aminoacid_sequence = ::Bioroebe::DnaToAminoacidSequence.new(
|
98
|
+
nucleotide_sequence, :return_silently
|
99
|
+
)
|
100
|
+
end
|
101
|
+
end
|
102
|
+
_ = ['<html>',
|
103
|
+
'<header>', '<title>', TITLE, '</title>', '</header>',
|
104
|
+
BODY_TAG, '<h1>', TITLE, '</h1>']
|
105
|
+
_ << ['<div>', '<h2>', 'Simple colors', '</h2>']
|
106
|
+
%w( Nucleotide ).each { |scheme|
|
107
|
+
_ << display_scheme(scheme, nucleotide_sequence, '')
|
108
|
+
}
|
109
|
+
_ << [CDIV]
|
110
|
+
%w( Zappo Taylor ).each { |scheme|
|
111
|
+
_ << display_scheme(scheme, '', aminoacid_sequence)
|
112
|
+
}
|
113
|
+
_ << [CDIV]
|
114
|
+
_ << ['<div>', '<h2>', 'Score colors', '</h2>']
|
115
|
+
%w( Buried Helix Hydropathy Strand Turn ).each { |score|
|
116
|
+
_ << display_scheme(score, "", aminoacid_sequence)
|
117
|
+
}
|
118
|
+
_ << [CDIV]+['</body>','</html>']
|
119
|
+
@result = _
|
120
|
+
report_result if @be_verbose
|
121
|
+
end
|
122
|
+
|
123
|
+
# ========================================================================= #
|
124
|
+
# === reset
|
125
|
+
# ========================================================================= #
|
126
|
+
def reset
|
127
|
+
super()
|
128
|
+
# ======================================================================= #
|
129
|
+
# === @be_verbose
|
130
|
+
# ======================================================================= #
|
131
|
+
@be_verbose = true
|
132
|
+
end
|
133
|
+
|
134
|
+
# ========================================================================= #
|
135
|
+
# === br
|
136
|
+
#
|
137
|
+
# Returns folded sequence with <br> HTML tag.
|
138
|
+
#
|
139
|
+
# The second argument keeps track when to add a <br> tag and a newline.
|
140
|
+
# ========================================================================= #
|
141
|
+
def br(
|
142
|
+
i, width = MAXIMAL_N_NUCLEOTIDES_PER_ROW
|
143
|
+
)
|
144
|
+
return "<br\n>" if i % width == 0
|
145
|
+
return '' # Else return an empty string.
|
146
|
+
end
|
147
|
+
|
148
|
+
# ========================================================================= #
|
149
|
+
# === display_scheme
|
150
|
+
#
|
151
|
+
# This method will properly show the sequence. It will use a <div>
|
152
|
+
# tag for this.
|
153
|
+
#
|
154
|
+
# Returns scheme wise html doc.
|
155
|
+
# ========================================================================= #
|
156
|
+
def display_scheme(
|
157
|
+
scheme,
|
158
|
+
nucleotide_sequence,
|
159
|
+
aminoacid_sequence
|
160
|
+
)
|
161
|
+
html = ''.dup
|
162
|
+
# ======================================================================= #
|
163
|
+
# === Obtain the relevant constant next
|
164
|
+
# ======================================================================= #
|
165
|
+
constant = ::Bioroebe::ColourScheme.const_get(scheme)
|
166
|
+
[ nucleotide_sequence, aminoacid_sequence ].each { |sequence|
|
167
|
+
html << display(sequence, constant)
|
168
|
+
}
|
169
|
+
result = ['<div>', "<h3>#{constant}</h3>", html, CDIV]
|
170
|
+
return result
|
171
|
+
end
|
172
|
+
|
173
|
+
# ========================================================================= #
|
174
|
+
# === display
|
175
|
+
#
|
176
|
+
# This method will return the sequence html doc, which equates to
|
177
|
+
# a <p> tag in HTML.
|
178
|
+
# ========================================================================= #
|
179
|
+
def display(sequence, cs)
|
180
|
+
# ======================================================================= #
|
181
|
+
# Open the <p> tag first:
|
182
|
+
# ======================================================================= #
|
183
|
+
html = '<p style="font-family: monospace; padding-left: 1.25em;">'.dup
|
184
|
+
close_span_tag = '</span>'
|
185
|
+
index = 0 # Index.
|
186
|
+
if sequence.is_a? ::Bioroebe::DnaToAminoacidSequence
|
187
|
+
sequence = sequence.sequence? # We need the String here.
|
188
|
+
end
|
189
|
+
sequence.each_byte {|char|
|
190
|
+
colour = cs[char.chr]
|
191
|
+
open_span_tag = '<span style="background:#'+colour+';">'
|
192
|
+
html << open_span_tag+char.chr.to_s+close_span_tag
|
193
|
+
html << br(index += 1) # Increment the index too.
|
194
|
+
}
|
195
|
+
html+'</p>'
|
196
|
+
end
|
197
|
+
|
198
|
+
# ========================================================================= #
|
199
|
+
# === result?
|
200
|
+
# ========================================================================= #
|
201
|
+
def result?
|
202
|
+
_ = @result
|
203
|
+
_ = _.join("\n") if _.is_a? Array
|
204
|
+
return _
|
205
|
+
end
|
206
|
+
|
207
|
+
# ========================================================================= #
|
208
|
+
# === report_result
|
209
|
+
# ========================================================================= #
|
210
|
+
def report_result
|
211
|
+
e result? # Call it by default.
|
212
|
+
end
|
213
|
+
|
214
|
+
# ========================================================================= #
|
215
|
+
# === Bioroebe::ColourSchemeDemo.create_demo_file
|
216
|
+
#
|
217
|
+
# The following class method can be used to create a demo file.
|
218
|
+
#
|
219
|
+
# It assumes that a fasta file will exist at the base directory.
|
220
|
+
# ========================================================================= #
|
221
|
+
def self.create_demo_file(
|
222
|
+
at_this_location = "#{log_dir?}#{DEFAULT_FASTA_FILE_NAME}"
|
223
|
+
)
|
224
|
+
# ======================================================================= #
|
225
|
+
# === We must first check whether the file in question exists
|
226
|
+
# ======================================================================= #
|
227
|
+
if File.exist? at_this_location
|
228
|
+
sequence = ::Bioroebe.parse_fasta_file(at_this_location).sequence?
|
229
|
+
what = self.new(sequence, :be_quiet).result?
|
230
|
+
into = '/Depot/j/colourized_sequence.html'
|
231
|
+
write_what_into(what, into)
|
232
|
+
return into
|
233
|
+
else
|
234
|
+
puts 'No file could be found at `'+
|
235
|
+
::Colours.sfile(at_this_location)+rev+'`.'
|
236
|
+
return nil
|
237
|
+
end
|
238
|
+
end
|
239
|
+
|
240
|
+
# ========================================================================= #
|
241
|
+
# === Bioroebe::ColourSchemeDemo.rev
|
242
|
+
# ========================================================================= #
|
243
|
+
def self.rev
|
244
|
+
::Bioroebe.rev
|
245
|
+
end
|
246
|
+
|
247
|
+
end; end
|
248
|
+
|
249
|
+
if __FILE__ == $PROGRAM_NAME
|
250
|
+
# =========================================================================== #
|
251
|
+
# Must be ported into Bioroebe eventually.
|
252
|
+
# =========================================================================== #
|
253
|
+
file = ARGV.shift
|
254
|
+
if file # If an argument was suuplied.
|
255
|
+
nucleotide_sequence = Bioroebe.parse_fasta_file(file).sequence?
|
256
|
+
else # Else use a random sequence.
|
257
|
+
nucleotide_sequence = Bioroebe.create_random_dna_sequence(250)
|
258
|
+
end
|
259
|
+
Bioroebe::ColourSchemeDemo.new(nucleotide_sequence)
|
260
|
+
end # cscheme > /Depot/j/foo.html
|
261
|
+
# cscheme /root/bioroebe/NM_001180897.3_Saccharomyces_cerevisiae_S288c_Aga2p_AGA2.fasta > /Depot/j/colourized_sequence.html; open /Depot/j/colourized_sequence.html
|
262
|
+
# cscheme /root/Bioroebe/1fat.fasta > /Depot/j/foo.html; oib /Depot/j/foo.html
|
@@ -0,0 +1,65 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::ColourScheme::Helix
|
6
|
+
# =========================================================================== #
|
7
|
+
# === Color codings for helix propensity.
|
8
|
+
# =========================================================================== #
|
9
|
+
require 'bioroebe/colours/colour_schemes/score.rb'
|
10
|
+
|
11
|
+
module Bioroebe::ColourScheme
|
12
|
+
|
13
|
+
class Helix < Score # === Bioroebe::ColourScheme::Helix
|
14
|
+
|
15
|
+
# ========================================================================= #
|
16
|
+
# === @colours
|
17
|
+
# ========================================================================= #
|
18
|
+
@colours = {}
|
19
|
+
|
20
|
+
# ========================================================================= #
|
21
|
+
# === @scores
|
22
|
+
# ========================================================================= #
|
23
|
+
@scores = {
|
24
|
+
'A' => 1.42,
|
25
|
+
'C' => 0.70,
|
26
|
+
'D' => 1.01,
|
27
|
+
'E' => 1.51,
|
28
|
+
'F' => 1.13,
|
29
|
+
'G' => 0.57,
|
30
|
+
'H' => 1.00,
|
31
|
+
'I' => 1.08,
|
32
|
+
'K' => 1.16,
|
33
|
+
'L' => 1.21,
|
34
|
+
'M' => 1.45,
|
35
|
+
'N' => 0.67,
|
36
|
+
'P' => 0.57,
|
37
|
+
'Q' => 1.11,
|
38
|
+
'R' => 0.98,
|
39
|
+
'S' => 0.77,
|
40
|
+
'T' => 0.83,
|
41
|
+
'U' => 0.00,
|
42
|
+
'V' => 1.06,
|
43
|
+
'W' => 1.08,
|
44
|
+
'Y' => 0.69,
|
45
|
+
|
46
|
+
'B' => 0.84,
|
47
|
+
'X' => 1.00,
|
48
|
+
'Z' => 1.31
|
49
|
+
}
|
50
|
+
@min = 0.57
|
51
|
+
@max = 1.51
|
52
|
+
@scores.each {|k,s|
|
53
|
+
@colours[k] = score_to_rgb_hex(s, @min, @max)
|
54
|
+
}
|
55
|
+
@colours.default = 'FFFFFF' # Return white by default.
|
56
|
+
|
57
|
+
# ========================================================================= #
|
58
|
+
# === Bioroebe::ColourScheme::Helix.score_to_rgb_hex
|
59
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+
# ========================================================================= #
|
60
|
+
def self.score_to_rgb_hex(score, min, max)
|
61
|
+
percent = score_to_percent(score, min, max)
|
62
|
+
rgb_percent_to_hex(percent, 1.0-percent, percent)
|
63
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+
end
|
64
|
+
|
65
|
+
end; end
|
@@ -0,0 +1,70 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::ColourScheme::Hydropathy
|
6
|
+
#
|
7
|
+
# Colour codings for hydrophobicity.
|
8
|
+
#
|
9
|
+
# Hydropathy index can be seen in:
|
10
|
+
#
|
11
|
+
# Kyte, J., and Doolittle, R.F., J. Mol. Biol. 1157, 105-132, 1982
|
12
|
+
#
|
13
|
+
# =========================================================================== #
|
14
|
+
require 'bioroebe/colours/colour_schemes/score.rb'
|
15
|
+
|
16
|
+
module Bioroebe::ColourScheme
|
17
|
+
|
18
|
+
class Hydropathy < Score # === Bioroebe::ColourScheme::Hydropathy
|
19
|
+
|
20
|
+
# ========================================================================= #
|
21
|
+
# === @colours
|
22
|
+
# ========================================================================= #
|
23
|
+
@colours = {}
|
24
|
+
|
25
|
+
# ========================================================================= #
|
26
|
+
# === @scores
|
27
|
+
# ========================================================================= #
|
28
|
+
@scores = {
|
29
|
+
'A' => 1.8,
|
30
|
+
'C' => 2.5,
|
31
|
+
'D' => -3.5,
|
32
|
+
'E' => -3.5,
|
33
|
+
'F' => 2.8,
|
34
|
+
'G' => -0.4,
|
35
|
+
'H' => -3.2,
|
36
|
+
'I' => 4.5,
|
37
|
+
'K' => -3.9,
|
38
|
+
'L' => 3.8,
|
39
|
+
'M' => 1.9,
|
40
|
+
'N' => -3.5,
|
41
|
+
'P' => -1.6,
|
42
|
+
'Q' => -3.5,
|
43
|
+
'R' => -4.5,
|
44
|
+
'S' => -0.8,
|
45
|
+
'T' => -0.7,
|
46
|
+
'U' => 0.0,
|
47
|
+
'V' => 4.2,
|
48
|
+
'W' => -0.9,
|
49
|
+
'Y' => -1.3,
|
50
|
+
|
51
|
+
'B' => -3.5,
|
52
|
+
'X' => -0.49,
|
53
|
+
'Z' => -3.5
|
54
|
+
}
|
55
|
+
@min = -3.9
|
56
|
+
@max = 4.5
|
57
|
+
@scores.each { |k, s|
|
58
|
+
@colours[k] = score_to_rgb_hex(s, @min, @max)
|
59
|
+
}
|
60
|
+
@colours.default = 'FFFFFF' # Use white by default.
|
61
|
+
|
62
|
+
# ======================================================================= #
|
63
|
+
# === Bioroebe::ColourScheme::Hydropathy.score_to_rgb_hex
|
64
|
+
# ======================================================================= #
|
65
|
+
def self.score_to_rgb_hex(score, min, max)
|
66
|
+
percent = score_to_percent(score, min, max)
|
67
|
+
rgb_percent_to_hex(percent, 0.0, 1.0-percent)
|
68
|
+
end
|
69
|
+
|
70
|
+
end; end
|
@@ -0,0 +1,47 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::ColourScheme::Helix::Nucleotide
|
6
|
+
#
|
7
|
+
# Colour codings for nucleotides.
|
8
|
+
#
|
9
|
+
# Since this class resides within class Helix, we need to enable
|
10
|
+
# an alias towards the main ColourScheme namespace.
|
11
|
+
#
|
12
|
+
# Very simple colour-scheme. See here:
|
13
|
+
#
|
14
|
+
# http://www.jalview.org/help/html/colourSchemes/nucleotide.html
|
15
|
+
#
|
16
|
+
# =========================================================================== #
|
17
|
+
require 'bioroebe/colours/colour_schemes/score.rb'
|
18
|
+
require 'bioroebe/colours/colour_schemes/simple.rb'
|
19
|
+
|
20
|
+
module Bioroebe
|
21
|
+
|
22
|
+
module ColourScheme
|
23
|
+
|
24
|
+
class Helix < Score
|
25
|
+
|
26
|
+
class Nucleotide < Simple # === Bioroebe::ColourScheme::Helix::Nucleotide
|
27
|
+
|
28
|
+
# ========================================================================= #
|
29
|
+
# === @colours
|
30
|
+
# ========================================================================= #
|
31
|
+
@colours = {
|
32
|
+
'A' => '64F73F',
|
33
|
+
'C' => 'FFB340',
|
34
|
+
'G' => 'EB413C',
|
35
|
+
'T' => '3C88EE',
|
36
|
+
'U' => '3C88EE',
|
37
|
+
}
|
38
|
+
@colours.default = 'FFFFFF' # Use white by default.
|
39
|
+
|
40
|
+
end; end
|
41
|
+
|
42
|
+
# =========================================================================== #
|
43
|
+
# === Bioroebe::ColourScheme::Nucleotide
|
44
|
+
# =========================================================================== #
|
45
|
+
Nucleotide = NA = Nuc = Helix::Nucleotide # Assign some aliases.
|
46
|
+
|
47
|
+
end; end
|