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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# =========================================================================== #
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# === Bioroebe::CalculateMeltingTemperature
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# Magnesium (Mg²⁺) makes the complex more stable - the formulas should
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# reflect this fact.
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#
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require 'bioroebe/base/commandline_application/commandline_application.rb'
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module Bioroebe
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# ========================================================================= #
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# === GAS_CONSTANT_R
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# ========================================================================= #
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# === initialize
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)
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reset
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set_sequence(i)
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run if run_already
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# ========================================================================= #
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# ======================================================================= #
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# ======================================================================= #
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end
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@sequence.size
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@result
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# === sequence?
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# ========================================================================= #
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def sequence?
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@sequence
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end; alias input? sequence? # === input?
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# ========================================================================= #
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# === calculate_tm
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#
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# Calculate the melting temperature.
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#
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# Note that there are several different ways how the melting
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# temperature (Tm) of an oligo-nucleotide can be calculated.
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#
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# All of these methods will yield slightly different results.
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#
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# All of these calculations are also theoretical calculations based
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#
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#
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# Now, let's explain the arguments to this method:
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#
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# * ct: concentration of oligo nucleotide(mM) (default 0.5)
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# * na: concentration of Na⁺ (mM) (default 50)
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# * formamide_concentration: concentration of Formamide (mol/L) (default 0)
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# * This method will return a Float.
|
160
|
+
#
|
161
|
+
# ========================================================================= #
|
162
|
+
def calculate_tm(
|
163
|
+
ct = 0.5,
|
164
|
+
na = 50,
|
165
|
+
formamide_concentration = 0
|
166
|
+
)
|
167
|
+
# ======================================================================= #
|
168
|
+
# === How much formamide we threw into this
|
169
|
+
# ======================================================================= #
|
170
|
+
formamide_concentration = formamide_concentration.to_f # concentration of Formamide (mol/L)
|
171
|
+
ct = ct / 1000000.0 # concentration of oligo (mol/L)
|
172
|
+
na = na / 1000.0 # concentration of Na+ (mol/L)
|
173
|
+
len = sequence?.length # .prec_f # base length
|
174
|
+
# ======================================================================= #
|
175
|
+
# === Thermodynamic parameters
|
176
|
+
#
|
177
|
+
# delta_enthalpy ... delta enthalpy
|
178
|
+
# delta_entropy ... delta entropy
|
179
|
+
#
|
180
|
+
# ======================================================================= #
|
181
|
+
|
182
|
+
# ======================================================================= #
|
183
|
+
# === Delta Enthalpy
|
184
|
+
#
|
185
|
+
# Different combinations of nucleotides have a different enthalpy.
|
186
|
+
# ======================================================================= #
|
187
|
+
delta_enthalpy = {
|
188
|
+
'AA' => -9.1, 'TT' => -9.1, 'AT' => -8.6, 'TA' => -6.0,
|
189
|
+
'CA' => -5.8, 'TG' => -5.8, 'GT' => -6.5, 'AC' => -6.5,
|
190
|
+
'CT' => -7.8, 'AG' => -7.8, 'GA' => -5.6, 'TC' => -5.6,
|
191
|
+
'CG' => -11.9, 'GC' => -11.1, 'GG' => -11.0, 'CC' => -11.0
|
192
|
+
}
|
193
|
+
# ======================================================================= #
|
194
|
+
# === Delta entropy
|
195
|
+
# ======================================================================= #
|
196
|
+
delta_entropy = {
|
197
|
+
'AA' => -24.0, 'TT' => -24.0, 'AT' => -23.9, 'TA' => -16.9,
|
198
|
+
'CA' => -12.9, 'TG' => -12.9, 'GT' => -17.3, 'AC' => -17.3,
|
199
|
+
'CT' => -20.8, 'AG' => -20.8, 'GA' => -13.5, 'TC' => -13.5,
|
200
|
+
'CG' => -27.8, 'GC' => -26.7, 'GG' => -26.6, 'CC' => -26.6
|
201
|
+
}
|
202
|
+
tot_h = 0.0
|
203
|
+
tot_s = 0.0
|
204
|
+
# ======================================================================= #
|
205
|
+
# Count up the total enthalpy and entropy.
|
206
|
+
# ======================================================================= #
|
207
|
+
(sequence?.size - 2).times {|counter|
|
208
|
+
enthalpy = @sequence.slice(counter, 2)
|
209
|
+
tot_h += delta_enthalpy[enthalpy]
|
210
|
+
entropy = @sequence.slice(counter, 2)
|
211
|
+
tot_s += delta_entropy[entropy]
|
212
|
+
}
|
213
|
+
# ======================================================================= #
|
214
|
+
# Obtain the amount of AT and GC.
|
215
|
+
# ======================================================================= #
|
216
|
+
at = ::Bioroebe.count_AT(@sequence)
|
217
|
+
gc = ::Bioroebe.count_GC(@sequence)
|
218
|
+
report_total_length # Notify the user of the current total length.
|
219
|
+
# ======================================================================= #
|
220
|
+
# === Show AT and GC counts next, including percentage.
|
221
|
+
# ======================================================================= #
|
222
|
+
erev 'AT count is: '+simp(at.to_s)+rev+' nucleotides ('+
|
223
|
+
sfancy(at * 100 / @sequence.size).to_s+rev+'%)'
|
224
|
+
erev 'GC count is: '+simp(gc.to_s)+rev+' nucleotides ('+
|
225
|
+
sfancy(gc * 100 / @sequence.size).to_s+rev+'%)'
|
226
|
+
# ======================================================================= #
|
227
|
+
# We have to calculate the tm first. We do this by also considering
|
228
|
+
# the gas constant.
|
229
|
+
# ======================================================================= #
|
230
|
+
tm = (
|
231
|
+
(1000 * tot_h) / (-10.8+tot_s+GAS_CONSTANT_R * Math.log(ct/4))
|
232
|
+
) - 273.15 + 16.6 * Math.log10(na)
|
233
|
+
# ======================================================================= #
|
234
|
+
# === First the traditional GC% method.
|
235
|
+
# ======================================================================= #
|
236
|
+
if tm > 80
|
237
|
+
# ===================================================================== #
|
238
|
+
# The traditional GC% method comes next.
|
239
|
+
# ===================================================================== #
|
240
|
+
tm = 81.5+16.6 * Math.log10(na) +
|
241
|
+
41 * ((gc)/len)-500/len-0.62 * formamide_concentration
|
242
|
+
elsif tm < 20
|
243
|
+
# ===================================================================== #
|
244
|
+
# === Wallace Method
|
245
|
+
#
|
246
|
+
# The Wallace method, also known as "2+4 rule of thumb".
|
247
|
+
#
|
248
|
+
# This very simple method assigns 2°C to each A-T pair and 4°C to
|
249
|
+
# each G-C pair. The Tm then is the sum of these values for all
|
250
|
+
# individual pairs in a DNA double strand.
|
251
|
+
#
|
252
|
+
# This takes into account that the G-C bond is stronger than the
|
253
|
+
# A-T bond. Note that the 2+4 rule is valid only for a small
|
254
|
+
# length-range, about 20-40 nt - rather 20, than towards 40,
|
255
|
+
# though.
|
256
|
+
#
|
257
|
+
# The Wallace equation was developed for short DNA oligos of
|
258
|
+
# 14-20 base pairs.
|
259
|
+
#
|
260
|
+
# See documentation at:
|
261
|
+
#
|
262
|
+
# https://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html#equations
|
263
|
+
#
|
264
|
+
# It is very easy to compute, but is of course also very inaccurate.
|
265
|
+
#
|
266
|
+
# Whenever possible, it should be avoided.
|
267
|
+
# ===================================================================== #
|
268
|
+
tm = CalculateMeltingTemperature.wallace_method(at, gc)
|
269
|
+
else
|
270
|
+
# tm = tm
|
271
|
+
end
|
272
|
+
@result = tm
|
273
|
+
return tm
|
274
|
+
end
|
275
|
+
|
276
|
+
# ========================================================================= #
|
277
|
+
# === show_help (help tag)
|
278
|
+
#
|
279
|
+
# To show this help section, try:
|
280
|
+
#
|
281
|
+
# cmt --help
|
282
|
+
#
|
283
|
+
# ========================================================================= #
|
284
|
+
def show_help
|
285
|
+
e
|
286
|
+
opnn; e 'Simply input the DNA sequence.'
|
287
|
+
e
|
288
|
+
end
|
289
|
+
|
290
|
+
# ========================================================================= #
|
291
|
+
# === report_result
|
292
|
+
# ========================================================================= #
|
293
|
+
def report_result
|
294
|
+
round_to_n_numbers = 5
|
295
|
+
report_molecular_weight
|
296
|
+
erev "The melting temperature of `#{simp(return_possibly_truncated_input)}"\
|
297
|
+
"#{rev}` is #{sfancy(@result.round(round_to_n_numbers).to_s)}#{rev} °C."
|
298
|
+
if @sequence.to_s.empty?
|
299
|
+
erev 'Notification: it seems as if you did not pass any nucleotide '\
|
300
|
+
'string to this.'
|
301
|
+
erev 'You could try to "assign" a string or generate a random one '\
|
302
|
+
'via "assign random".'
|
303
|
+
end
|
304
|
+
end; alias report report_result # === report (report tag)
|
305
|
+
|
306
|
+
# ========================================================================= #
|
307
|
+
# === report_molecular_weight
|
308
|
+
#
|
309
|
+
# This method will report the molecular weight of the nucleotides at
|
310
|
+
# hand, in Dalton.
|
311
|
+
# ========================================================================= #
|
312
|
+
def report_molecular_weight
|
313
|
+
molecular_weight = 0
|
314
|
+
hash = {}
|
315
|
+
if File.exist? FILE_NUCLEOTIDES
|
316
|
+
dataset = YAML.load_file(FILE_NUCLEOTIDES)
|
317
|
+
end
|
318
|
+
unless Object.const_defined? :ChemistryParadise
|
319
|
+
begin
|
320
|
+
require 'chemistry_paradise/utility_scripts/calculate_atomic_mass.rb'
|
321
|
+
rescue LoadError; end
|
322
|
+
end
|
323
|
+
hash['A'] = ::ChemistryParadise.return_molmasse(dataset['Desoxyadenosin'])
|
324
|
+
hash['T'] = ::ChemistryParadise.return_molmasse(dataset['Desoxythymidin'])
|
325
|
+
hash['C'] = ::ChemistryParadise.return_molmasse(dataset['Desoxycytidin'])
|
326
|
+
hash['G'] = ::ChemistryParadise.return_molmasse(dataset['Desoxyguanosin'])
|
327
|
+
internal_PO2_group = 62.972
|
328
|
+
index = 0
|
329
|
+
sequence?.split(//).each {|this_nucleotide|
|
330
|
+
add_this = hash[this_nucleotide].to_f
|
331
|
+
case index
|
332
|
+
when 0
|
333
|
+
else # Else add an internal PO2 group, its weight that is.
|
334
|
+
add_this += internal_PO2_group
|
335
|
+
end
|
336
|
+
molecular_weight += add_this
|
337
|
+
index += 1
|
338
|
+
}
|
339
|
+
erev "Molecular weight: "\
|
340
|
+
"#{sfancy(molecular_weight.to_s)}"\
|
341
|
+
"#{rev}"
|
342
|
+
end
|
343
|
+
|
344
|
+
# ========================================================================= #
|
345
|
+
# === run (run tag)
|
346
|
+
# ========================================================================= #
|
347
|
+
def run
|
348
|
+
calculate_tm
|
349
|
+
end
|
350
|
+
|
351
|
+
# ========================================================================== #
|
352
|
+
# === CalculateMeltingTemperature.show_formulas
|
353
|
+
#
|
354
|
+
# The Wallace Method:
|
355
|
+
#
|
356
|
+
# http://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html#equations
|
357
|
+
# http://openwetware.org/wiki/Primer_Tm_estimation_methods
|
358
|
+
#
|
359
|
+
# This method will simply show the Wallace-Formula.
|
360
|
+
#
|
361
|
+
# The shorthand notation is:
|
362
|
+
#
|
363
|
+
# Tm = 2°C(A+T) + 4°C(G+C)
|
364
|
+
#
|
365
|
+
# Note that this is also known as the "GCx4+ATx2" rule. It works for DNA
|
366
|
+
# oligomers not longer than 13 nucleotides. This rule also does not take
|
367
|
+
# into account the order of nucleotides in the sequence, so it really
|
368
|
+
# is not the ideal solution.
|
369
|
+
# ========================================================================== #
|
370
|
+
def self.show_formulas
|
371
|
+
Colours.e
|
372
|
+
' Tm = 2°C(A+T) + 4°C(G+C) # <-- The Wallace-Formula, proposed in 1979'
|
373
|
+
end
|
374
|
+
|
375
|
+
# ========================================================================= #
|
376
|
+
# === CalculateMeltingTemperature.wallace_method
|
377
|
+
#
|
378
|
+
# The argument "at" means the sum of a and t, and "gc" means the sum
|
379
|
+
# of g and c.
|
380
|
+
#
|
381
|
+
# So for instance, the string TGCTCA has 3 AT, and 3 GC, so the method
|
382
|
+
# will yield to us:
|
383
|
+
#
|
384
|
+
# 18
|
385
|
+
#
|
386
|
+
# ========================================================================= #
|
387
|
+
def self.wallace_method(at, gc)
|
388
|
+
result = 4 * (gc) + 2 * (at)
|
389
|
+
result
|
390
|
+
end
|
391
|
+
|
392
|
+
end; end
|
393
|
+
|
394
|
+
if __FILE__ == $PROGRAM_NAME
|
395
|
+
_ = Bioroebe::CalculateMeltingTemperature.new(ARGV)
|
396
|
+
_.report_result
|
397
|
+
end # cmelt ATTTAAATTATATA
|
398
|
+
# cmelt GGCCCTATATTTA
|
data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb
ADDED
@@ -0,0 +1,304 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides
|
6
|
+
#
|
7
|
+
# The code collected in this file deals primarily with "Salt-Adjusted Tm".
|
8
|
+
#
|
9
|
+
# Tm stands for "melting temperature". This is a formula that also takes
|
10
|
+
# into consideration the concentration of e. g. Sodium or similar salts.
|
11
|
+
#
|
12
|
+
# Typical concentrations of [Na⁺] are 50 mM. Typical primer concentrations
|
13
|
+
# are 250 pM.
|
14
|
+
#
|
15
|
+
# The formula that is used here is applicable for DNA sequences that
|
16
|
+
# are longer than 13 nucleotides.
|
17
|
+
#
|
18
|
+
# The code in this file in particula implements the following formula:
|
19
|
+
#
|
20
|
+
# Tm = 100.5 + (41 * (yG+zC) / (wA+xT+yG+zC)) - (820/(wA+xT+yG+zC)) + 16.6 * log10([Na+])
|
21
|
+
#
|
22
|
+
# In the above formula, w, x, y, z are the number of the bases A, T, G, C
|
23
|
+
# in the given sequence. So if G occurs 5 times, the above formula
|
24
|
+
# would read (5xG ... and so forth.
|
25
|
+
|
26
|
+
# Since this is a fairly long formula, the code below will break it
|
27
|
+
# down into a few subcomponents, to make it easier to understand
|
28
|
+
# what is going on.
|
29
|
+
#
|
30
|
+
# When should this variant of calculating the melting temperature be
|
31
|
+
# used? When the primers are in the range of about 18-25mers
|
32
|
+
# (Howley et al. 1979).
|
33
|
+
# =========================================================================== #
|
34
|
+
# require 'bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb'
|
35
|
+
# =========================================================================== #
|
36
|
+
require 'bioroebe/base/base.rb'
|
37
|
+
|
38
|
+
module Bioroebe
|
39
|
+
|
40
|
+
class CalculateMeltingTemperatureForMoreThanThirteenNucleotides < Base # === Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides
|
41
|
+
|
42
|
+
# ========================================================================= #
|
43
|
+
# === NAMESPACE
|
44
|
+
# ========================================================================= #
|
45
|
+
NAMESPACE = inspect
|
46
|
+
|
47
|
+
# ========================================================================= #
|
48
|
+
# === BASE_VALUE
|
49
|
+
# ========================================================================= #
|
50
|
+
BASE_VALUE = 100.5
|
51
|
+
|
52
|
+
# ========================================================================= #
|
53
|
+
# === initialize
|
54
|
+
# ========================================================================= #
|
55
|
+
def initialize(
|
56
|
+
i = ARGV,
|
57
|
+
run_already = true
|
58
|
+
)
|
59
|
+
reset
|
60
|
+
set_nucleotide_sequence(i)
|
61
|
+
if block_given?
|
62
|
+
yielded = yield
|
63
|
+
case yielded
|
64
|
+
# ===================================================================== #
|
65
|
+
# === :do_not_report_anything
|
66
|
+
# ===================================================================== #
|
67
|
+
when :do_not_report_anything
|
68
|
+
@do_report = false
|
69
|
+
end
|
70
|
+
end
|
71
|
+
run if run_already
|
72
|
+
end
|
73
|
+
|
74
|
+
# ========================================================================= #
|
75
|
+
# === reset
|
76
|
+
# ========================================================================= #
|
77
|
+
def reset
|
78
|
+
super()
|
79
|
+
# ======================================================================= #
|
80
|
+
# === @namespace
|
81
|
+
# ======================================================================= #
|
82
|
+
@namespace = NAMESPACE
|
83
|
+
# ======================================================================= #
|
84
|
+
# === @nucleotide_sequence
|
85
|
+
# ======================================================================= #
|
86
|
+
@nucleotide_sequence = nil
|
87
|
+
# ======================================================================= #
|
88
|
+
# === @do_report
|
89
|
+
# ======================================================================= #
|
90
|
+
@do_report = true
|
91
|
+
# ======================================================================= #
|
92
|
+
# Set the default sodium concentration next.
|
93
|
+
# ======================================================================= #
|
94
|
+
set_sodium_concentration(:default)
|
95
|
+
end
|
96
|
+
|
97
|
+
# ========================================================================= #
|
98
|
+
# === set_nucleotide_sequence
|
99
|
+
# ========================================================================= #
|
100
|
+
def set_nucleotide_sequence(i)
|
101
|
+
if i.is_a? Array
|
102
|
+
i = i.join.strip
|
103
|
+
end
|
104
|
+
i = i.dup if i.frozen?
|
105
|
+
i.delete!(' ')
|
106
|
+
@nucleotide_sequence = i
|
107
|
+
end
|
108
|
+
|
109
|
+
# ========================================================================= #
|
110
|
+
# === count_frequencies_of_the_nucleotides
|
111
|
+
# ========================================================================= #
|
112
|
+
def count_frequencies_of_the_nucleotides
|
113
|
+
_ = @nucleotide_sequence
|
114
|
+
@n_A = _.count('A')
|
115
|
+
@n_T = _.count('T')
|
116
|
+
@n_G = _.count('G')
|
117
|
+
@n_C = _.count('C')
|
118
|
+
end
|
119
|
+
|
120
|
+
# ========================================================================= #
|
121
|
+
# === nucleotide_sequence?
|
122
|
+
# ========================================================================= #
|
123
|
+
def nucleotide_sequence?
|
124
|
+
@nucleotide_sequence
|
125
|
+
end; alias input_sequence? nucleotide_sequence? # === input_sequence?
|
126
|
+
|
127
|
+
# ========================================================================= #
|
128
|
+
# === report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
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129
|
+
# ========================================================================= #
|
130
|
+
def report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
|
131
|
+
if @do_report
|
132
|
+
erev 'This nucleotide sequence has '+
|
133
|
+
sfancy(@nucleotide_sequence.size.to_s)+
|
134
|
+
rev+
|
135
|
+
' nucleotides. ('+orange(input_sequence?)+rev+')'
|
136
|
+
erev "The nucleotide-frequencies are: "\
|
137
|
+
"#{simp(n_A?.to_s+'xA')}#{rev}, "\
|
138
|
+
"#{simp(n_T?.to_s+'xT')}#{rev}, "\
|
139
|
+
"#{simp(n_G?.to_s+'xG')}#{rev}, "\
|
140
|
+
"#{simp(n_C?.to_s+'xC')}#{rev}"
|
141
|
+
end
|
142
|
+
end
|
143
|
+
|
144
|
+
# ========================================================================= #
|
145
|
+
# === n_A?
|
146
|
+
# ========================================================================= #
|
147
|
+
def n_A?
|
148
|
+
@n_A
|
149
|
+
end
|
150
|
+
|
151
|
+
# ========================================================================= #
|
152
|
+
# === n_T?
|
153
|
+
# ========================================================================= #
|
154
|
+
def n_T?
|
155
|
+
@n_T
|
156
|
+
end
|
157
|
+
|
158
|
+
# ========================================================================= #
|
159
|
+
# === n_G?
|
160
|
+
# ========================================================================= #
|
161
|
+
def n_G?
|
162
|
+
@n_G
|
163
|
+
end
|
164
|
+
|
165
|
+
# ========================================================================= #
|
166
|
+
# === n_C?
|
167
|
+
# ========================================================================= #
|
168
|
+
def n_C?
|
169
|
+
@n_C
|
170
|
+
end
|
171
|
+
|
172
|
+
# ========================================================================= #
|
173
|
+
# === n_nucleotides_in_total?
|
174
|
+
# ========================================================================= #
|
175
|
+
def n_nucleotides_in_total?
|
176
|
+
input_sequence?.size
|
177
|
+
end
|
178
|
+
|
179
|
+
# ========================================================================= #
|
180
|
+
# === calculate_Tm_value
|
181
|
+
# ========================================================================= #
|
182
|
+
def calculate_Tm_value
|
183
|
+
result = BASE_VALUE
|
184
|
+
# ======================================================================= #
|
185
|
+
# Next, we will calculate the middle part:
|
186
|
+
#
|
187
|
+
# (1) (41 * (yG+zC) / (wA+xT+yG+zC))
|
188
|
+
#
|
189
|
+
# ======================================================================= #
|
190
|
+
middle_value1 = ( 41.0 * (n_G?+n_C?) / n_nucleotides_in_total? )
|
191
|
+
# ======================================================================= #
|
192
|
+
# And this is the second middle value:
|
193
|
+
#
|
194
|
+
# (820/(wA+xT+yG+zC)) + 16.6 * log10([Na+])
|
195
|
+
#
|
196
|
+
# ======================================================================= #
|
197
|
+
middle_value2 = ( 820.0 / n_nucleotides_in_total? )
|
198
|
+
result += ( middle_value1 - middle_value2)
|
199
|
+
# ======================================================================= #
|
200
|
+
# And the last part is the log result of the concentration of sodium:
|
201
|
+
# ======================================================================= #
|
202
|
+
log_result = 16.6 * log10(concentration_of_sodium)
|
203
|
+
result += log_result
|
204
|
+
@tm_value = result.round(3)
|
205
|
+
end
|
206
|
+
|
207
|
+
# ========================================================================= #
|
208
|
+
# === tm_value?
|
209
|
+
# ========================================================================= #
|
210
|
+
def tm_value?
|
211
|
+
@tm_value
|
212
|
+
end
|
213
|
+
|
214
|
+
# ========================================================================= #
|
215
|
+
# === concentration_of_sodium
|
216
|
+
#
|
217
|
+
# This reflects [Na+], that is the concentration of sodium.
|
218
|
+
#
|
219
|
+
# For now it is hardcoded towards 50.0. In the future this may have
|
220
|
+
# to be adjusted.
|
221
|
+
# ========================================================================= #
|
222
|
+
def concentration_of_sodium
|
223
|
+
@sodium_concentration # This is mMol so 50m Mol is 0.050 Mol.
|
224
|
+
end
|
225
|
+
|
226
|
+
# ========================================================================= #
|
227
|
+
# === set_sodium_concentration
|
228
|
+
# ========================================================================= #
|
229
|
+
def set_sodium_concentration(i = :default)
|
230
|
+
case i
|
231
|
+
when :default
|
232
|
+
i = 0.050
|
233
|
+
end
|
234
|
+
@sodium_concentration = i
|
235
|
+
end
|
236
|
+
|
237
|
+
# ========================================================================= #
|
238
|
+
# === log10
|
239
|
+
# ========================================================================= #
|
240
|
+
def log10(i)
|
241
|
+
Math.log10(i)
|
242
|
+
end
|
243
|
+
|
244
|
+
# ========================================================================= #
|
245
|
+
# === report_the_tm_value (report tag)
|
246
|
+
# ========================================================================= #
|
247
|
+
def report_the_tm_value
|
248
|
+
if @do_report
|
249
|
+
erev 'The calculated Tm value (salt-adjusted Tm) '\
|
250
|
+
'is: '+sfancy(@tm_value)+rev+'°C'
|
251
|
+
end
|
252
|
+
end; alias report report_the_tm_value # === report
|
253
|
+
|
254
|
+
# ========================================================================= #
|
255
|
+
# === run
|
256
|
+
# ========================================================================= #
|
257
|
+
def run
|
258
|
+
count_frequencies_of_the_nucleotides
|
259
|
+
e if @do_report
|
260
|
+
report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
|
261
|
+
calculate_Tm_value
|
262
|
+
report_the_tm_value
|
263
|
+
e if @do_report
|
264
|
+
end
|
265
|
+
|
266
|
+
end
|
267
|
+
|
268
|
+
# =========================================================================== #
|
269
|
+
# === Bioroebe.calculate_melting_temperature_for_more_than_thirteen_nucleotides
|
270
|
+
#
|
271
|
+
# An alias exists for this method, called Bioroebe.melting_Temperature().
|
272
|
+
#
|
273
|
+
# Usage example for the latter:
|
274
|
+
#
|
275
|
+
# x = Bioroebe.melting_temperature('CCGTGTCGTACATCG')
|
276
|
+
#
|
277
|
+
# =========================================================================== #
|
278
|
+
def self.calculate_melting_temperature_for_more_than_thirteen_nucleotides(i)
|
279
|
+
::Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides.new(i)
|
280
|
+
end; self.instance_eval { alias melting_temperature calculate_melting_temperature_for_more_than_thirteen_nucleotides } # === Bioroebe.melting_temperature
|
281
|
+
|
282
|
+
# =========================================================================== #
|
283
|
+
# === Bioroebe.salt_adjusted_tm
|
284
|
+
#
|
285
|
+
# This method will just return the Tm value, as a float (number).
|
286
|
+
#
|
287
|
+
# The input to this method should be your DNA sequence at hand,
|
288
|
+
# e. g. the PCR-primer.
|
289
|
+
#
|
290
|
+
# Invocation example:
|
291
|
+
#
|
292
|
+
# result = Bioroebe.salt_adjusted_tm # => 48.836
|
293
|
+
#
|
294
|
+
# =========================================================================== #
|
295
|
+
def self.salt_adjusted_tm(i = 'CCGTGTCGTACATCG')
|
296
|
+
_ = ::Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides.new(i) { :do_not_report_anything }
|
297
|
+
_.tm_value?
|
298
|
+
end
|
299
|
+
|
300
|
+
end
|
301
|
+
|
302
|
+
if __FILE__ == $PROGRAM_NAME
|
303
|
+
Bioroebe.calculate_melting_temperature_for_more_than_thirteen_nucleotides(ARGV)
|
304
|
+
end # calculatemeltingtemperatureformorethanthirteennucleotides CCG TGT CGT ACA TCG
|