bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -0
@@ -0,0 +1,108 @@
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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/shell/add.rb'
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# =========================================================================== #
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module Bioroebe
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class Shell < ::Bioroebe::CommandlineApplication
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# ========================================================================= #
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# === add_to_end
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#
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# ========================================================================= #
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def add_to_end(i)
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add_to_start_or_end(i, :end)
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end; alias add add_to_end # === add (add tag)
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# ========================================================================= #
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# === add_to_start
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# ========================================================================= #
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def add_to_start(i)
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add_to_start_or_end(i, :start)
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end; alias left_add add_to_start # === left_add
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# ========================================================================= #
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# === add_to_start_or_end
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#
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# This method can either add to the start or to the end.
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#
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# The default is to append to the nucleotide sequence.
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#
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# We can input a number - in this case, we simply add these many
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# nucleotides onto the main string.
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# ========================================================================= #
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def add_to_start_or_end(
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i = '',
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append_or_prepend = :append
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)
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i = i.join('') if i.is_a? Array
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i = i.dup
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old_length = i.size
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case i.to_s # Easier start/stop entries.
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# ======================================================================= #
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# === Add a start codon.
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# ======================================================================= #
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when 'start',
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'START',
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/ORF/i,
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':start'
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i = ::Bioroebe.start_codon? # Used to be hardcoded -> 'ATG'
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# ======================================================================= #
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# === Add a stop codon.
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# ======================================================================= #
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when /^stop$/i,
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':stop'
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i = ::Bioroebe.stop_codons?.sample
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end
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i.upcase!
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case append_or_prepend
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# ======================================================================= #
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# === :prepend
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# ======================================================================= #
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when :prepend,
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:to_start,
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:start
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if i =~ /^\d+$/ # If input is only numbers.
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erev 'Only numbers were given: Prepending '+
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sfancy(i.to_s)+rev+
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' random nucleotides to the main string now.'
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i.to_i.times { prepend(add_nucleotide) }
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else
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erev "Prepending #{sfancy(i)}#{rev} to the main string."
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prepend(i)
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end
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# ======================================================================= #
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# === :append
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# ======================================================================= #
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when :append,
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:to_end,
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:end
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if i =~ /^\d+$/ # If input is only numbers.
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erev "Only numbers were given: Adding #{sfancy(i.to_s)}#{rev}"\
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" random nucleotides to the main string now."
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i.to_i.times { append(return_random_nucleotide) }
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else
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if only_nucleotides?(i)
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msg = "Adding #{sfancy(i)}#{rev}"
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msg = msg.dup if msg.frozen?
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if ::Bioroebe.is_a_stop_codon? i
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msg << ' (a stop codon)'
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end
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msg << ' to the main string.'
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erev msg
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end
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append(i)
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end
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end
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new_length = string?.size.to_s
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unless new_length.to_i == old_length.to_i
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erev "The new length of the main string is now: "\
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"#{simp(new_length)}#{rev}."
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end
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show_dna_sequence
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end
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end; end
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#!/usr/bin/ruby -w
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/shell/assign.rb'
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# =========================================================================== #
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module Bioroebe
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class Shell < ::Bioroebe::CommandlineApplication
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# ========================================================================= #
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# === set_dna_sequence (assign tag, assigning tag)
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#
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# This method can be used to set/assign the main DNA string.
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#
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# It is a fairly long method, mostly because it will do lots of
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# additional tasks, way aside from setting/assigning to a DNA
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# sequence only.
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#
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# As of June 2016, the method will also keep a backup of the
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# generated sequence in a local file as well. This will allow
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# us to "replay" the given sequence on startup of the shell.
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#
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# Note that as of Jun 2016, we will chop off any '"' found in
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# the input String.
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# ========================================================================= #
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def set_dna_sequence(
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i = nil,
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be_verbose = true,
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do_upcase = :check_for_config_value_here
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)
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if is_the_main_sequence_frozen?
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report_that_the_main_sequence_is_frozen
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return
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end
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case do_upcase
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# ======================================================================= #
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# === :check_for_config_value_here
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# ======================================================================= #
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when :check_for_config_value_here,
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|
+
:default
|
42
|
+
if @config and @config.respond_to?(:upcase_nucleotides)
|
43
|
+
do_upcase = @config.upcase_nucleotides
|
44
|
+
else
|
45
|
+
do_upcase = false
|
46
|
+
end
|
47
|
+
# ======================================================================= #
|
48
|
+
# === :do_not_upcase
|
49
|
+
# ======================================================================= #
|
50
|
+
when :do_not_upcase
|
51
|
+
do_upcase = false
|
52
|
+
end
|
53
|
+
if do_upcase
|
54
|
+
shall_we_upcase = do_upcase if @config
|
55
|
+
end
|
56
|
+
# ======================================================================= #
|
57
|
+
# === Sanitize the second variable next
|
58
|
+
# ======================================================================= #
|
59
|
+
case be_verbose
|
60
|
+
# ======================================================================= #
|
61
|
+
# === :be_verbose
|
62
|
+
# ======================================================================= #
|
63
|
+
when :be_verbose
|
64
|
+
be_verbose = true
|
65
|
+
# ======================================================================= #
|
66
|
+
# === :do_not_upcase
|
67
|
+
# ======================================================================= #
|
68
|
+
when :do_not_upcase,
|
69
|
+
:no_upcase,
|
70
|
+
:no_upcasing,
|
71
|
+
shall_we_upcase = false
|
72
|
+
be_verbose = true # Sync this.
|
73
|
+
# ======================================================================= #
|
74
|
+
# === :be_silent
|
75
|
+
# ======================================================================= #
|
76
|
+
when :be_silent,
|
77
|
+
:be_quiet
|
78
|
+
be_verbose = false
|
79
|
+
end
|
80
|
+
if i.nil?
|
81
|
+
# ===================================================================== #
|
82
|
+
# === Hande nil value for the variable i next:
|
83
|
+
#
|
84
|
+
# Here in this entry point, we will handle if the first input
|
85
|
+
# argument is nil.
|
86
|
+
#
|
87
|
+
# If @internal_hash[:misc_sequence] is NOT nil, then it will be used
|
88
|
+
# once, then cleared. Otherwise, we will use dna_sequence?.
|
89
|
+
# ===================================================================== #
|
90
|
+
if @internal_hash[:misc_sequence]
|
91
|
+
i = @internal_hash[:misc_sequence]
|
92
|
+
@internal_hash[:misc_sequence] = nil # Set it to nil again.
|
93
|
+
else
|
94
|
+
i = dna_sequence?
|
95
|
+
end
|
96
|
+
end
|
97
|
+
# ======================================================================= #
|
98
|
+
# === Convert Array into String next
|
99
|
+
# ======================================================================= #
|
100
|
+
i = i.join if i.is_a? Array
|
101
|
+
i = i.to_s # Work on a String past this point here.
|
102
|
+
if i.include? ' ' # Sanitize the input a little bit.
|
103
|
+
i = i.strip.delete(' ')
|
104
|
+
end
|
105
|
+
if i.include? '|' # I think we will not need '|' in our main string.
|
106
|
+
i.delete!('|')
|
107
|
+
end
|
108
|
+
# ======================================================================= #
|
109
|
+
# === If the input has only numbers
|
110
|
+
# ======================================================================= #
|
111
|
+
if i =~ /^\d+$/
|
112
|
+
i = random_dna_sequence(i)
|
113
|
+
end
|
114
|
+
# ======================================================================= #
|
115
|
+
# === Handle Fasta format next
|
116
|
+
# ======================================================================= #
|
117
|
+
if i.start_with?('>') and i.include?(N)
|
118
|
+
erev 'It seems as if you have a FASTA sequence there, as it starts with '\
|
119
|
+
'a > character.'
|
120
|
+
erev 'We will omit this first section (the header) though.'
|
121
|
+
i[0 .. i.index(N)] = '' # This does the chop-off action.
|
122
|
+
end
|
123
|
+
i.delete!('-') if i.include? '-'
|
124
|
+
i.delete!('_') if i.include? '_' # Don't want '_' characters.
|
125
|
+
i.delete!('?') if i.include? '?'
|
126
|
+
i.delete!('#') if i.include? '#' # This was added at 08.05.2016.
|
127
|
+
i.delete!('"') if i.include? '"' # This was added at 02.06.2016.
|
128
|
+
i.gsub!(/\^C/,'') if i.include? '^C'
|
129
|
+
i = i.to_s.dup
|
130
|
+
case i
|
131
|
+
# ======================================================================= #
|
132
|
+
# === :GFP
|
133
|
+
# ======================================================================= #
|
134
|
+
when ':GFP' # ← This means the default GFP sequence.
|
135
|
+
i = return_default_GFP_sequence
|
136
|
+
# ======================================================================= #
|
137
|
+
# === random
|
138
|
+
# ======================================================================= #
|
139
|
+
when /^random$/i,
|
140
|
+
'' # As of 04.01.2015, we will try '' too here.
|
141
|
+
i = random :do_not_show_the_string
|
142
|
+
# ======================================================================= #
|
143
|
+
# === multiline
|
144
|
+
# ======================================================================= #
|
145
|
+
when 'multiline' # Handle multiline input.
|
146
|
+
erev 'Multiline input detected.'
|
147
|
+
erev 'Finish by issuing __ on an empty line. (These are 2 "_" tokens.)'
|
148
|
+
i = $stdin.gets('__')
|
149
|
+
# ===================================================================== #
|
150
|
+
# Next, sanitize it a bit if it starts with a '>' identifier.
|
151
|
+
# ===================================================================== #
|
152
|
+
if i.strip.start_with? '>'
|
153
|
+
i = i[(i.index(N)+1)..-1]
|
154
|
+
end
|
155
|
+
else
|
156
|
+
if i
|
157
|
+
# =================================================================== #
|
158
|
+
# === Next upcase the input if the flag was set
|
159
|
+
# =================================================================== #
|
160
|
+
i.upcase! if shall_we_upcase
|
161
|
+
case mode?
|
162
|
+
# =================================================================== #
|
163
|
+
# === :dna
|
164
|
+
# =================================================================== #
|
165
|
+
when :dna,
|
166
|
+
:rna
|
167
|
+
dna_sequence_object?.set_mode(mode?)
|
168
|
+
# =================================================================== #
|
169
|
+
# === :aminoacids
|
170
|
+
# =================================================================== #
|
171
|
+
when :aminoacids
|
172
|
+
set_aminoacids(i)
|
173
|
+
end
|
174
|
+
else # else input is nil.
|
175
|
+
erev 'Missing Input to assign_sequence(). Please input '\
|
176
|
+
'your DNA string now (Hitting the enter key will '\
|
177
|
+
'finish this):'
|
178
|
+
i = $stdin.gets.chomp
|
179
|
+
i = i.upcase if shall_we_upcase
|
180
|
+
end
|
181
|
+
end
|
182
|
+
i = '' unless i
|
183
|
+
# ======================================================================= #
|
184
|
+
# === Remove possible newlines in the given input
|
185
|
+
# ======================================================================= #
|
186
|
+
i.delete!(N) if i.include? N
|
187
|
+
i.delete!('_') if i.include? '_'
|
188
|
+
# ======================================================================= #
|
189
|
+
# Is faster than .gsub()# if i
|
190
|
+
# i.upcase! # Since as of Feb 2016. Nope, disabled again as of May 2016.
|
191
|
+
# end
|
192
|
+
# ======================================================================= #
|
193
|
+
if File.exist?(i) # Assume a file was given. Read its content then.
|
194
|
+
if i.end_with? '.yml'
|
195
|
+
i = YAML.load_file(i)
|
196
|
+
else
|
197
|
+
i = File.readlines(i).reject {|line|
|
198
|
+
line.start_with? '>'
|
199
|
+
}.join
|
200
|
+
end
|
201
|
+
end
|
202
|
+
# ======================================================================= #
|
203
|
+
# Also get rid of numbers.
|
204
|
+
# ======================================================================= #
|
205
|
+
i = i.dup if i.frozen?
|
206
|
+
i.gsub!(/\d/,'')
|
207
|
+
# ======================================================================= #
|
208
|
+
# The DNA Sequence will be stored in the Sequence object directly.
|
209
|
+
# The nil is required for now, because otherwise set_input() will
|
210
|
+
# upcase the input by default.
|
211
|
+
# ======================================================================= #
|
212
|
+
if dna_sequence_object?.nil?
|
213
|
+
_ = Bioroebe::Sequence.new(i.dup) { :is_DNA }
|
214
|
+
@internal_hash[:array_dna_sequence] << _
|
215
|
+
else
|
216
|
+
# ===================================================================== #
|
217
|
+
# Assign it here.
|
218
|
+
# ===================================================================== #
|
219
|
+
dna_sequence_object?.set_input(i.dup, nil) # We can re-use the old @sequence object.
|
220
|
+
end
|
221
|
+
# ======================================================================= #
|
222
|
+
# === :coding_area
|
223
|
+
#
|
224
|
+
# Whenever the DNA sequence is modified like that, we will also reset
|
225
|
+
# the "coding_area" entry in the internal Hash to the initial nil state.
|
226
|
+
# ======================================================================= #
|
227
|
+
@internal_hash[:coding_area] = nil
|
228
|
+
# ======================================================================= #
|
229
|
+
# === Report that we will perform an assignment next
|
230
|
+
# ======================================================================= #
|
231
|
+
if be_verbose # Check for verbosity
|
232
|
+
case mode?
|
233
|
+
when :dna
|
234
|
+
if i.empty?
|
235
|
+
erev 'Nothing was assigned yet.'
|
236
|
+
else
|
237
|
+
erev 'Setting DNA sequence to ('+
|
238
|
+
sfancy(i.size.to_s)+
|
239
|
+
rev+' nucleotides):'
|
240
|
+
show_string
|
241
|
+
end
|
242
|
+
end
|
243
|
+
end
|
244
|
+
# ======================================================================= #
|
245
|
+
# === Set the Xorg Buffer next
|
246
|
+
# ======================================================================= #
|
247
|
+
if @config and @config.respond_to?(:additionally_set_xorg_buffer) and
|
248
|
+
@config.additionally_set_xorg_buffer
|
249
|
+
begin
|
250
|
+
set_xorg_buffer(i)
|
251
|
+
rescue NoMethodError; end
|
252
|
+
end
|
253
|
+
unless i.empty? # We do not save empty nucleotide Strings.
|
254
|
+
result = i.to_s.dup
|
255
|
+
# ===================================================================== #
|
256
|
+
# We will save into a file next.
|
257
|
+
# ===================================================================== #
|
258
|
+
this_file = "#{log_dir?}dna_string.yml"
|
259
|
+
dna_sequence_object?.save_sequence_to_this_file(this_file) # Save it here.
|
260
|
+
# ===================================================================== #
|
261
|
+
# Since as of Jun 2016, we will also create a new RNA string.
|
262
|
+
#
|
263
|
+
# This has been disabled as of December 2021. It was too strange
|
264
|
+
# to automatically create a RNA string.
|
265
|
+
# ===================================================================== #
|
266
|
+
# if @internal_hash[:array_rna_sequence]
|
267
|
+
# @internal_hash[:array_rna_sequence].last.set_sequence(result)
|
268
|
+
# end
|
269
|
+
# ===================================================================== #
|
270
|
+
# === Automatically assign the aminoacid sequence as well
|
271
|
+
# ===================================================================== #
|
272
|
+
_ = translate_dna_into_aminoacid(result)
|
273
|
+
set_aminoacids(_, nil, :be_quiet)
|
274
|
+
return result
|
275
|
+
end
|
276
|
+
end; alias set_dna_string set_dna_sequence # === set_dna_string
|
277
|
+
alias set_string set_dna_sequence # === set_dna_sequence
|
278
|
+
alias set_main_sequence set_dna_sequence # === set_main_sequence (set_main_sequence tag)
|
279
|
+
alias set_sequence set_dna_sequence # === set_sequence (set_sequence tag)
|
280
|
+
alias set_dna set_dna_sequence # === set_dna
|
281
|
+
alias set_assign set_dna_sequence # === set_dna
|
282
|
+
alias assign_sequence set_dna_sequence # === assign_sequence
|
283
|
+
alias assign_dna_sequence set_dna_sequence # === assign_dna_sequence
|
284
|
+
alias assign_this_dna_sequence set_dna_sequence # === assign_this_dna_sequence
|
285
|
+
alias assign set_dna_sequence # === assign
|
286
|
+
|
287
|
+
require 'bioroebe/aminoacids/create_random_aminoacids.rb'
|
288
|
+
# ========================================================================= #
|
289
|
+
# === set_aminoacids (assign protein tag, set aminoacids tag)
|
290
|
+
#
|
291
|
+
# Assign a protein sequence here. The first argument shall be the
|
292
|
+
# aminoacid sequence in question.
|
293
|
+
#
|
294
|
+
# Usage example:
|
295
|
+
#
|
296
|
+
# assign_protein FLIMVSPTAYHQNKDECWRGX*
|
297
|
+
#
|
298
|
+
# ========================================================================= #
|
299
|
+
def set_aminoacids(
|
300
|
+
i = :random,
|
301
|
+
how_many_to_generate = 1000, # Will only be applied if the input is :random or :generate
|
302
|
+
be_verbose = true
|
303
|
+
)
|
304
|
+
# ======================================================================= #
|
305
|
+
# === Sanitize the third argument next
|
306
|
+
# ======================================================================= #
|
307
|
+
case be_verbose
|
308
|
+
when :be_silent,
|
309
|
+
:be_quiet
|
310
|
+
be_verbose = false
|
311
|
+
end
|
312
|
+
i = :random unless i
|
313
|
+
case i
|
314
|
+
# ======================================================================= #
|
315
|
+
# === :random
|
316
|
+
# ======================================================================= #
|
317
|
+
when :random,
|
318
|
+
:generate
|
319
|
+
i = Bioroebe.create_random_aminoacids(how_many_to_generate) # Generate them here.
|
320
|
+
end
|
321
|
+
i = i.join if i.is_a? Array
|
322
|
+
if i =~ /^\d+$/ # only numbers
|
323
|
+
i = Bioroebe.create_random_aminoacids(i)
|
324
|
+
end
|
325
|
+
if be_verbose
|
326
|
+
erev "Now assigning aminoacid sequence to: #{sfancy(i.to_s)}"
|
327
|
+
end
|
328
|
+
if i.is_a? String # Convert it into a Sequence object here.
|
329
|
+
i = ::Bioroebe.sequence(i) { :aminoacid }
|
330
|
+
end
|
331
|
+
# ======================================================================= #
|
332
|
+
# Do the assignment next.
|
333
|
+
# ======================================================================= #
|
334
|
+
if @internal_hash[:array_aminoacid_sequence].empty?
|
335
|
+
@internal_hash[:array_aminoacid_sequence] << i
|
336
|
+
else
|
337
|
+
@internal_hash[:array_aminoacid_sequence].pop
|
338
|
+
@internal_hash[:array_aminoacid_sequence] << i
|
339
|
+
end
|
340
|
+
end; alias assign_aminoacid_sequence set_aminoacids # === assign_aminoacid_sequence
|
341
|
+
alias assign_protein_sequence set_aminoacids # === assign_protein_sequence
|
342
|
+
alias set_aminoacid_sequence set_aminoacids # === set_aminoacid_sequence
|
343
|
+
|
344
|
+
# ========================================================================= #
|
345
|
+
# === report_that_a_string_must_be_assigned_first
|
346
|
+
# ========================================================================= #
|
347
|
+
def report_that_a_string_must_be_assigned_first
|
348
|
+
erev 'No sequence has been assigned yet. Please first "'+
|
349
|
+
sfancy('assign')+rev+'" a string.'
|
350
|
+
end
|
351
|
+
|
352
|
+
# ========================================================================= #
|
353
|
+
# === assign_sequence2
|
354
|
+
# ========================================================================= #
|
355
|
+
def assign_sequence2(i)
|
356
|
+
i = i.join(' ') if i.is_a? Array
|
357
|
+
@internal_hash[:sequence2] = Bioroebe::Sequence.new(i)
|
358
|
+
end
|
359
|
+
|
360
|
+
end; end
|