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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# require 'bioroebe/toplevel_methods/rds.rb'
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# =========================================================================== #
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module Bioroebe
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# rds is an abbreviation and is short for "remove double slashes".
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# We will thus get rid of too many '/' tokens in a given string,
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#
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# ========================================================================= #
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def self.rds(i)
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i.squeeze('/')
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end
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end
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/toplevel_methods/remove.rb'
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# Bioroebe.remove_numbers(ARGV)
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# =========================================================================== #
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module Bioroebe
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# ========================================================================= #
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# === Bioroebe.remove_numbers
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#
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# This method will simply remove numbers from the given input at hand.
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#
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# Usage example:
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#
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#
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# ========================================================================= #
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def self.remove_numbers(i = ARGV)
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if i.is_a? Array
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i = i.join
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end
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i.gsub(/[0-9]/,'')
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end; self.instance_eval { alias remove_numbers_from remove_numbers } # === Bioroebe.remove_numbers_from
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# ========================================================================= #
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# === Bioroebe.remove_subsequence
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#
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# This method will remove one or more subsequences from a given
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# String at hand. The String that you wish to modify, should be
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# given as the second argument to this method, called `from`.
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#
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# The first argument to this method can be an Array or a String - in
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# either case, if the variable `from` contains this sequence, it
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# will be removed.
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#
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# Note that only the FIRST occurence found will be removed - the others
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# will be ignored, if they exist.
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#
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# The second argument to this method must be a String.
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#
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# Usage example:
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#
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# Bioroebe.remove_subsequence(["ATCGGTCGAA", "ATCGGTCGAGCGTGT"], 'ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG')
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# Bioroebe.remove_subsequence(array, main_sequence)
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#
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# ========================================================================= #
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def self.remove_subsequence(
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subsequence,
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from # ← Must be a String.
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)
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unless from.is_a? String
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raise 'Please input a String as second argument to this method.'
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end
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unless subsequence.is_a? Array
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subsequence = [subsequence].flatten
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end
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from = from.dup if from.frozen?
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subsequence.each {|this_subsequence|
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from.sub!(/#{this_subsequence}/,'')
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}
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from # Return the, possibly modified, String here.
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end; self.instance_eval { alias remove_subsequences remove_subsequence } # === Bioroebe.remove_subsequences
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end
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if __FILE__ == $PROGRAM_NAME
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require 'colours/autoinclude'
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alias e puts
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main_sequence = 'ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG'
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subsequence1 = 'ATCGGTCGAA'
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subsequence2 = 'ATCGGTCGAGCGTGT'
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e "#{Colours.rev}The main sequence is:"
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e
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e " #{Colours.lightgreen(main_sequence)} (size: #{main_sequence.size})"
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e
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e 'The two subsequences '+Colours.slateblue(subsequence1)+
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' and '+Colours.slateblue(subsequence2)+' will be removed next.'
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e
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e 'And now the resulting new String is:'
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e
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new_string = Bioroebe.remove_subsequence([subsequence1, subsequence2], main_sequence)
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e " #{Colours.lightgreen(new_string)} (size: #{new_string.size})"
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e
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end # removesubsequence
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/toplevel_methods/return_source_code_of_this_method.rb'
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# Bioroebe.return_source_code_of_this_method
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# =========================================================================== #
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module Bioroebe
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# ========================================================================= #
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# === Bioroebe.return_source_code_of_this_method
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#
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# This method will return the source code of a particular method.
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#
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# Note that the method will stop at the first 'end' encountered.
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# ========================================================================= #
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def self.return_source_code_of_this_method(i)
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if i.is_a? Array
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i = i.first
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end
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content = i.source_location
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full_content = File.readlines(
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content[0].to_s
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)[ (content[1]-1) .. -1 ].join.to_s
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if full_content.include? 'end'
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full_content = full_content[0 .. full_content.index('end')+2]
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end
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return full_content
|
29
|
+
end
|
30
|
+
|
31
|
+
end
|
32
|
+
|
33
|
+
if __FILE__ == $PROGRAM_NAME
|
34
|
+
Bioroebe.return_source_code_of_this_method
|
35
|
+
end
|
@@ -0,0 +1,68 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb'
|
6
|
+
# Bioroebe.return_subsequence_based_on_indices
|
7
|
+
# =========================================================================== #
|
8
|
+
module Bioroebe
|
9
|
+
|
10
|
+
# ========================================================================= #
|
11
|
+
# === Bioroebe.return_subsequence_based_on_indices
|
12
|
+
#
|
13
|
+
# This method will return a subsequence that was sliced out from the
|
14
|
+
# given input array of indices (the second argument to this method).
|
15
|
+
#
|
16
|
+
# This method here also allows us to read from an existing File. The
|
17
|
+
# format of that file has to be simple, though - the first line must
|
18
|
+
# be the sequence; and the second line will constitute the array
|
19
|
+
# of indices.
|
20
|
+
#
|
21
|
+
# For a usage example, see the end of this file here please. It has
|
22
|
+
# been written primarily to solve a specific task at Rosalind.
|
23
|
+
# ========================================================================= #
|
24
|
+
def self.return_subsequence_based_on_indices(
|
25
|
+
i, *array_of_indices
|
26
|
+
)
|
27
|
+
if array_of_indices.is_a? Array
|
28
|
+
array_of_indices.map! {|entry| entry.to_i }
|
29
|
+
end
|
30
|
+
result = ''.dup
|
31
|
+
if i and i.is_a?(String) and File.exist?(i)
|
32
|
+
dataset = File.readlines(i).reject {|line| line.strip.empty? }
|
33
|
+
i = dataset.first
|
34
|
+
array_of_indices = dataset.last.split(' ').map(&:to_i)
|
35
|
+
end
|
36
|
+
array_of_indices.each_slice(2).each {|a, b|
|
37
|
+
result << i[a .. b]+' '
|
38
|
+
}
|
39
|
+
result.strip
|
40
|
+
end
|
41
|
+
|
42
|
+
end
|
43
|
+
|
44
|
+
if __FILE__ == $PROGRAM_NAME
|
45
|
+
a = 22 # These four variables determine the sub-indices.
|
46
|
+
b = 27
|
47
|
+
c = 97
|
48
|
+
d = 102
|
49
|
+
if ARGV.empty?
|
50
|
+
test_this_string = 'HumptyDumptysatonawallHumptyDumpty'\
|
51
|
+
'hadagreatfallAlltheKingshorsesandalltheKingsmen'\
|
52
|
+
'CouldntputHumptyDumptyinhisplaceagain.'
|
53
|
+
else
|
54
|
+
test_this_string = ARGV.first
|
55
|
+
if test_this_string and File.file?(test_this_string)
|
56
|
+
dataset = File.readlines(test_this_string)
|
57
|
+
test_this_string = dataset.first
|
58
|
+
splitted = dataset.last.split(' ')
|
59
|
+
a = splitted[0]
|
60
|
+
b = splitted[1]
|
61
|
+
c = splitted[2]
|
62
|
+
d = splitted[3]
|
63
|
+
end
|
64
|
+
end
|
65
|
+
puts Bioroebe.return_subsequence_based_on_indices(
|
66
|
+
test_this_string, a, b, c, d
|
67
|
+
)
|
68
|
+
end # returnsubsequencebasedonindices /HUM.txt
|
@@ -0,0 +1,73 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioreobe/module_methods/rna_splicing.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'bioroebe/toplevel_methods/remove.rb'
|
10
|
+
|
11
|
+
# ========================================================================= #
|
12
|
+
# === Bioroebe.rna_splicing
|
13
|
+
#
|
14
|
+
# This is a VERY primitive method that has been written primarily to
|
15
|
+
# solve a specific question on Rosalind.
|
16
|
+
#
|
17
|
+
# This is NOT how splicing normally works - but it works to solve
|
18
|
+
# the given question at Rosalind.
|
19
|
+
#
|
20
|
+
# Invocation example:
|
21
|
+
#
|
22
|
+
# Bioroebe.rna_splicing('/SPLICING.md')
|
23
|
+
#
|
24
|
+
# ========================================================================= #
|
25
|
+
def self.rna_splicing(i)
|
26
|
+
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
27
|
+
if i and File.exist?(i)
|
28
|
+
# ===================================================================== #
|
29
|
+
# Read in the file should it exist.
|
30
|
+
# ===================================================================== #
|
31
|
+
i = File.read(i).strip
|
32
|
+
end
|
33
|
+
if i.is_a?(String) and i.include?('>')
|
34
|
+
_ = ::Bioroebe::ParseFasta.new(i) { :be_quiet }
|
35
|
+
sequences = _.sequences?
|
36
|
+
main_sequence = sequences.first
|
37
|
+
array_subsequences = sequences[1 .. -1]
|
38
|
+
result = ::Bioroebe.remove_subsequence(array_subsequences, main_sequence)
|
39
|
+
return result
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
43
|
+
end
|
44
|
+
|
45
|
+
if __FILE__ == $PROGRAM_NAME
|
46
|
+
alias e puts
|
47
|
+
if ARGV.empty?
|
48
|
+
use_this_dataset = '>Rosalind_10
|
49
|
+
ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG
|
50
|
+
>Rosalind_12
|
51
|
+
ATCGGTCGAA
|
52
|
+
>Rosalind_15
|
53
|
+
ATCGGTCGAGCGTGT'
|
54
|
+
else
|
55
|
+
use_this_dataset = ARGV.first
|
56
|
+
end
|
57
|
+
e 'Original input is:'
|
58
|
+
e
|
59
|
+
e 'ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG'
|
60
|
+
e
|
61
|
+
result = Bioroebe.rna_splicing use_this_dataset
|
62
|
+
e result
|
63
|
+
# ========================================================================= #
|
64
|
+
# The next code is if you need an aminoacid sequence:
|
65
|
+
# ========================================================================= #
|
66
|
+
e
|
67
|
+
e 'This corresponds to these aminoacids:'
|
68
|
+
e
|
69
|
+
e Bioroebe.to_aa(result)
|
70
|
+
e
|
71
|
+
end # rnasplicing
|
72
|
+
# rnasplicing /RNA_SPLICING.md
|
73
|
+
# rnasplicing /SPLICING.md
|
@@ -0,0 +1,69 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/rnalfold.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
10
|
+
|
11
|
+
# ========================================================================= #
|
12
|
+
# === Bioroebe.rnalfold
|
13
|
+
#
|
14
|
+
# This method allows us to make use of RNALfold. By default the method
|
15
|
+
# will attempt to obtain all .fa files in the current directory; this
|
16
|
+
# should simplify batch-processing.
|
17
|
+
#
|
18
|
+
# Otherwise, the first input argument to this method should be the
|
19
|
+
# file(s) that you wish to manipulate.
|
20
|
+
#
|
21
|
+
# A typical usage example may be:
|
22
|
+
#
|
23
|
+
# Bioroebe.rnalfold { '--zscore=-3 -L 200' }
|
24
|
+
#
|
25
|
+
# ========================================================================= #
|
26
|
+
def self.rnalfold(
|
27
|
+
i = :use_all_fasta_files_in_the_current_directory
|
28
|
+
)
|
29
|
+
require 'bioroebe/colours/sfancy.rb'
|
30
|
+
require 'bioroebe/colours/sfile.rb'
|
31
|
+
# ======================================================================= #
|
32
|
+
# RNALfold will be used (as command).
|
33
|
+
# ======================================================================= #
|
34
|
+
use_this_command = 'RNALfold'.dup
|
35
|
+
case i
|
36
|
+
when :default,
|
37
|
+
:use_all_fasta_files_in_the_current_directory
|
38
|
+
i = Dir['**.fa']
|
39
|
+
end
|
40
|
+
if block_given?
|
41
|
+
yielded = yield
|
42
|
+
# ===================================================================== #
|
43
|
+
# Simply append these block-commands in that case:
|
44
|
+
# ===================================================================== #
|
45
|
+
use_this_command << " #{yielded}"
|
46
|
+
end
|
47
|
+
# ======================================================================= #
|
48
|
+
# We assume that our input is an Array past this point.
|
49
|
+
# ======================================================================= #
|
50
|
+
i.each {|this_file|
|
51
|
+
e "Working on `#{sfancy(this_file)}` next."
|
52
|
+
new_filename = this_file.dup
|
53
|
+
regex_to_use = /-L (\d+)/
|
54
|
+
use_this_command =~ regex_to_use
|
55
|
+
new_filename << '.'+$1.to_s.dup
|
56
|
+
new_filename << '.lfold'
|
57
|
+
_ = use_this_command+' < '+this_file+' > '+new_filename
|
58
|
+
esystem _
|
59
|
+
if File.exist? new_filename
|
60
|
+
e "A new file has been created at `#{sfile(new_filename)}`."
|
61
|
+
end
|
62
|
+
}
|
63
|
+
end
|
64
|
+
|
65
|
+
end
|
66
|
+
|
67
|
+
if __FILE__ == $PROGRAM_NAME
|
68
|
+
Bioroebe.rnalfold { '--zscore=-3 -L 200' }
|
69
|
+
end # bioroebernalfold
|
@@ -0,0 +1,116 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# The file here will contain code that is related to "find"-ing something,
|
6
|
+
# typically within another string or object or dataset.
|
7
|
+
# =========================================================================== #
|
8
|
+
# require 'bioroebe/toplevel_methods/searching_and_finding.rb'
|
9
|
+
# Bioroebe.find_substring 'GATATATGCATATACTT', 'ATAT' # => [2, 4, 10]
|
10
|
+
# =========================================================================== #
|
11
|
+
module Bioroebe
|
12
|
+
|
13
|
+
# ========================================================================= #
|
14
|
+
# === Bioroebe.find_substring
|
15
|
+
#
|
16
|
+
# This method can be used to find a substring within a larger String.
|
17
|
+
#
|
18
|
+
# For example, in the below default values, the substring "ATAT"
|
19
|
+
# would exist at the positions 2, 4 and 10, if compared to the
|
20
|
+
# larger parent string "GATATATGCATATACTT".
|
21
|
+
#
|
22
|
+
# The following display may help you see this more easily, in
|
23
|
+
# regards to the substring matches:
|
24
|
+
#
|
25
|
+
# GATATATGCATATACTT
|
26
|
+
# ATATAT ATAT
|
27
|
+
#
|
28
|
+
# If you look closely, you will be able to see that "ATAT" can
|
29
|
+
# be found three times in the string above.
|
30
|
+
#
|
31
|
+
# Indices in this context start at position 1, not 0. This is
|
32
|
+
# mostly done to refer to nucleotides or aminoacids, which
|
33
|
+
# also typically start at the first letter. Position 0 makes
|
34
|
+
# no sense for a nucleotide - what would "nucleotide 0" even
|
35
|
+
# refer to?
|
36
|
+
#
|
37
|
+
# The first argument to this method may also be the path to a
|
38
|
+
# locally existing file, such as "/rosalind_subs.txt". In
|
39
|
+
# fact this method has been largely motivated by Rosalind
|
40
|
+
# tasks.
|
41
|
+
#
|
42
|
+
# The method will return an Array with the positions of all
|
43
|
+
# substrings that are found in the full_string variable. See
|
44
|
+
# the usage example below for how this may be.
|
45
|
+
#
|
46
|
+
# Usage example:
|
47
|
+
#
|
48
|
+
# Bioroebe.find_substring 'GATATATGCATATACTT', 'ATAT' # => [2, 4, 10]
|
49
|
+
#
|
50
|
+
# ========================================================================= #
|
51
|
+
def self.find_substring(
|
52
|
+
full_string = 'GATATATGCATATACTT', # ← The full String comes here.
|
53
|
+
this_substring = :default # ← The substring we are searching for comes here.
|
54
|
+
)
|
55
|
+
if full_string.is_a? Array
|
56
|
+
# ===================================================================== #
|
57
|
+
# Presently this method will only work on the first member of an Array.
|
58
|
+
# ===================================================================== #
|
59
|
+
full_string = full_string.first
|
60
|
+
end
|
61
|
+
if full_string and File.file?(full_string) and
|
62
|
+
this_substring == :default
|
63
|
+
# ===================================================================== #
|
64
|
+
# In this case it is ok to read from that file.
|
65
|
+
# ===================================================================== #
|
66
|
+
_ = File.read(full_string)
|
67
|
+
splitted = _.split("\n")
|
68
|
+
full_string = splitted.first
|
69
|
+
this_substring = splitted.last
|
70
|
+
end
|
71
|
+
case this_substring
|
72
|
+
# ======================================================================= #
|
73
|
+
# Use a default value in this case. In reality users should supply
|
74
|
+
# their own substring when they use this method here.
|
75
|
+
# ======================================================================= #
|
76
|
+
when :default,
|
77
|
+
nil
|
78
|
+
this_substring = 'ATAT'
|
79
|
+
else
|
80
|
+
if this_substring.empty?
|
81
|
+
this_substring = 'ATAT'
|
82
|
+
end
|
83
|
+
end
|
84
|
+
if full_string.nil? or full_string.empty?
|
85
|
+
full_string = 'GATATATGCATATACTT' # ← Use the default in this case.
|
86
|
+
end
|
87
|
+
result = Array.new.tap { |indexes|
|
88
|
+
final_index_position = full_string.size - this_substring.size
|
89
|
+
i = 0
|
90
|
+
while (i < final_index_position)
|
91
|
+
index = full_string.to_s.index(this_substring.to_s, i)
|
92
|
+
break if index.nil?
|
93
|
+
i = index + 1
|
94
|
+
indexes << i
|
95
|
+
end
|
96
|
+
}
|
97
|
+
result = nil if result.empty? # ← We will try this here; could also return an empty Array, though.
|
98
|
+
result # Return our findings here.
|
99
|
+
end; self.instance_eval { alias find_substring_indices find_substring } # === Bioroebe.find_substring_indices
|
100
|
+
|
101
|
+
end
|
102
|
+
|
103
|
+
if __FILE__ == $PROGRAM_NAME
|
104
|
+
if File.exist?(ARGV.first)
|
105
|
+
# ======================================================================= #
|
106
|
+
# Handle locally existing files first.
|
107
|
+
# ======================================================================= #
|
108
|
+
puts Bioroebe.find_substring(ARGV.first).join(' ').strip
|
109
|
+
else
|
110
|
+
puts Bioroebe.find_substring(ARGV[0], ARGV[1]).join(' ').strip
|
111
|
+
end
|
112
|
+
end # findsubstring TATATA AT
|
113
|
+
# findsubstring TATATATA AT
|
114
|
+
# findsubstring GATATATGCATATACTT ATAT
|
115
|
+
# findsubstring GATATATGCATATACTT ATAT
|
116
|
+
# findsubstring /rosalind_subs.txt
|
@@ -0,0 +1,37 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/shuffleseq.rb'
|
6
|
+
# Bioroebe.shuffleseq
|
7
|
+
# =========================================================================== #
|
8
|
+
module Bioroebe
|
9
|
+
|
10
|
+
# ========================================================================= #
|
11
|
+
# === Bioroebe.shuffleseq
|
12
|
+
#
|
13
|
+
# This method simulates the Emboss shuffleseq-functionality. It will
|
14
|
+
# take the input string, such as an assumed DNA sequence, and simply
|
15
|
+
# re-arrange it as-is.
|
16
|
+
#
|
17
|
+
# You can read this here:
|
18
|
+
#
|
19
|
+
# https://www.bioinformatics.nl/cgi-bin/emboss/shuffleseq
|
20
|
+
#
|
21
|
+
# Usage example:
|
22
|
+
#
|
23
|
+
# Bioroebe.shuffleseq 'ATCGATCG' # => "AGTTACGC"
|
24
|
+
#
|
25
|
+
# ========================================================================= #
|
26
|
+
def self.shuffleseq(i = ARGV)
|
27
|
+
if i.is_a? Array
|
28
|
+
i = i.join(' ').strip
|
29
|
+
end
|
30
|
+
return i.chars.shuffle.join
|
31
|
+
end; self.instance_eval { alias randomize_the_sequence shuffleseq } # === Bioroebe.randomize_the_sequence
|
32
|
+
|
33
|
+
end
|
34
|
+
|
35
|
+
if __FILE__ == $PROGRAM_NAME
|
36
|
+
puts Bioroebe.shuffleseq(ARGV)
|
37
|
+
end # shuffleseq ATCGATCG
|
@@ -0,0 +1,53 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/statistics.rb'
|
6
|
+
# Bioroebe.show_exon_statistics
|
7
|
+
# =========================================================================== #
|
8
|
+
module Bioroebe
|
9
|
+
|
10
|
+
require 'bioroebe/colours/colours.rb'
|
11
|
+
require 'bioroebe/toplevel_methods/e.rb'
|
12
|
+
require 'bioroebe/toplevel_methods/esystem.rb'
|
13
|
+
require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
|
14
|
+
|
15
|
+
# ========================================================================= #
|
16
|
+
# === Bioroebe.show_exon_statistics
|
17
|
+
#
|
18
|
+
# This is mostly "throw-away" code; it will quickly tell us how many
|
19
|
+
# exons may span over some junction.
|
20
|
+
#
|
21
|
+
# It was specifically created to analyze a .gtf file.
|
22
|
+
#
|
23
|
+
# Invocation example:
|
24
|
+
#
|
25
|
+
# bioroebe --show-exon-statistics-for=/tmp/praktikum/Mouse/chromosome_8/parsed/cdna.8.L100.global.gtf
|
26
|
+
#
|
27
|
+
# ========================================================================= #
|
28
|
+
def self.show_exon_statistics(these_files)
|
29
|
+
[these_files].flatten.compact.each {|this_file|
|
30
|
+
if File.exist? this_file
|
31
|
+
result = `cat #{this_file} | awk '{print $12}' | sort | uniq -c | sort -k1n | awk '{print $1}' | sort | uniq -c | less`
|
32
|
+
e gold(' n exons')
|
33
|
+
splitted = result.split("\n")
|
34
|
+
# =================================================================== #
|
35
|
+
# splitted may look like this:
|
36
|
+
#
|
37
|
+
# [" 89839 1", " 26031 2", " 1136 3", " 24 4"]
|
38
|
+
#
|
39
|
+
# =================================================================== #
|
40
|
+
splitted.each {|line|
|
41
|
+
e line.sub(/( \d+)$/, gold('\1'))
|
42
|
+
}
|
43
|
+
else
|
44
|
+
no_file_exists_at(this_file)
|
45
|
+
end
|
46
|
+
}
|
47
|
+
end
|
48
|
+
|
49
|
+
end
|
50
|
+
|
51
|
+
if __FILE__ == $PROGRAM_NAME
|
52
|
+
Bioroebe.show_exon_statistics(ARGV)
|
53
|
+
end # showexonstatistics /tmp/praktikum/Mouse/chromosome_8/parsed/cdna.8.L100.global.gtf
|
@@ -0,0 +1,62 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# require 'bioroebe/toplevel_methods/sum_of_odd_integers.rb'
|
6
|
+
# =========================================================================== #
|
7
|
+
module Bioroebe
|
8
|
+
|
9
|
+
# ========================================================================= #
|
10
|
+
# === Bioroebe.sum_of_odd_integers
|
11
|
+
#
|
12
|
+
# This method was primarily written to solve a specific problem at
|
13
|
+
# Rosalind.
|
14
|
+
#
|
15
|
+
# This method will probably not be hugely important for every-day
|
16
|
+
# tasks, but I will leave it here nonetheless in the event that
|
17
|
+
# others want to solve problems at Rosalind and may find this
|
18
|
+
# method useful.
|
19
|
+
#
|
20
|
+
# The method will calculate the "sum of odd integers". A local
|
21
|
+
# file can be provided - see the code at File.read() in the
|
22
|
+
# method. For more use cases, see the end of this .rb file.
|
23
|
+
# ========================================================================= #
|
24
|
+
def self.sum_of_odd_integers(
|
25
|
+
starting_point = 100,
|
26
|
+
end_point = 200
|
27
|
+
)
|
28
|
+
if starting_point and File.file?(starting_point)
|
29
|
+
case end_point
|
30
|
+
# ===================================================================== #
|
31
|
+
# === :default
|
32
|
+
# ===================================================================== #
|
33
|
+
when :default,
|
34
|
+
nil
|
35
|
+
dataset = File.read(starting_point).strip
|
36
|
+
splitted = dataset.split(' ')
|
37
|
+
starting_point = splitted.first
|
38
|
+
end_point = splitted.last
|
39
|
+
end
|
40
|
+
end
|
41
|
+
result = 0
|
42
|
+
# ======================================================================= #
|
43
|
+
# We need our start and end point to be Integers past this point:
|
44
|
+
# ======================================================================= #
|
45
|
+
starting_point = starting_point.to_i
|
46
|
+
end_point = end_point.to_i
|
47
|
+
(starting_point .. end_point).each {|number|
|
48
|
+
result += number if number.odd?
|
49
|
+
}
|
50
|
+
result
|
51
|
+
end
|
52
|
+
|
53
|
+
end
|
54
|
+
|
55
|
+
if __FILE__ == $PROGRAM_NAME
|
56
|
+
if ARGV.empty?
|
57
|
+
puts Bioroebe.sum_of_odd_integers
|
58
|
+
else
|
59
|
+
puts Bioroebe.sum_of_odd_integers(ARGV[0], ARGV[1])
|
60
|
+
end
|
61
|
+
end # sumofoddintegers 4068 8689
|
62
|
+
# sumofoddintegers /SUM_OF_ODD_INTEGERS.txt
|