bioroebe 0.10.80 → 0.12.24
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- checksums.yaml +4 -4
- data/README.md +3946 -2817
- data/bin/bioroebe +13 -2
- data/bin/bioroebe_hash +7 -0
- data/bin/codon_to_aminoacid +6 -4
- data/bin/compacter +7 -0
- data/bin/plain_palindrome +7 -0
- data/bioroebe.gemspec +3 -3
- data/doc/README.gen +3918 -2793
- data/doc/quality_control/commandline_applications.md +3 -3
- data/doc/statistics/statistics.md +7 -7
- data/doc/todo/bioroebe_GUI_todo.md +19 -14
- data/doc/todo/bioroebe_java_todo.md +22 -0
- data/doc/todo/bioroebe_todo.md +2075 -2620
- data/lib/bioroebe/C++/DNA.cpp +69 -0
- data/lib/bioroebe/C++/RNA.cpp +58 -0
- data/lib/bioroebe/C++/sequence.cpp +35 -0
- data/lib/bioroebe/abstract/README.md +1 -0
- data/lib/bioroebe/abstract/features.rb +29 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
- data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
- data/lib/bioroebe/base/base_module/base_module.rb +36 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +13 -9
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +24 -19
- data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
- data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
- data/lib/bioroebe/base/commandline_application/reset.rb +5 -3
- data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +42 -0
- data/lib/bioroebe/base/misc.rb +35 -0
- data/lib/bioroebe/base/prototype/misc.rb +15 -9
- data/lib/bioroebe/base/prototype/reset.rb +10 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +10 -2
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +104 -50
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
- data/lib/bioroebe/codons/codons.rb +1 -1
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +208 -59
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
- data/lib/bioroebe/codons/show_codon_tables.rb +8 -3
- data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
- data/lib/bioroebe/colours/rev.rb +4 -1
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
- data/lib/bioroebe/constants/database_constants.rb +1 -1
- data/lib/bioroebe/constants/files_and_directories.rb +31 -4
- data/lib/bioroebe/constants/misc.rb +20 -0
- data/lib/bioroebe/constants/nucleotides.rb +7 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +109 -39
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
- data/lib/bioroebe/cpp +1 -0
- data/lib/bioroebe/crystal/README.md +2 -0
- data/lib/bioroebe/crystal/to_rna.cr +19 -0
- data/lib/bioroebe/data/README.md +11 -8
- data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
- data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
- data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
- data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
- data/lib/bioroebe/data/fasta/human/README.md +2 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +1 -1
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
- data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
- data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
- data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
- data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1518 -7
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
- data/lib/bioroebe/genome/README.md +4 -0
- data/lib/bioroebe/genome/genome.rb +130 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
- data/lib/bioroebe/gui/gtk +1 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +106 -137
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +27 -61
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +1 -1
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +1 -2
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +1 -2
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +46 -29
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +77 -52
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +1 -2
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +100 -23
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +1 -2
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +1 -2
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +43 -30
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +1 -2
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +120 -73
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +1 -2
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +19 -20
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +20 -13
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +1 -2
- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +97 -22
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +3 -73
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +1 -2
- data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +1 -2
- data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +1 -2
- data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +1 -2
- data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.class +0 -0
- data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java +104 -0
- data/lib/bioroebe/gui/javafx/bioroebe.jar +0 -0
- data/lib/bioroebe/gui/javafx/bioroebe.mf +1 -0
- data/lib/bioroebe/gui/javafx/module-info.class +0 -0
- data/lib/bioroebe/gui/javafx/module-info.java +5 -0
- data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
- data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +166 -0
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
- data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
- data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
- data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +94 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
- data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
- data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
- data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
- data/lib/bioroebe/images/images.html +29845 -0
- data/lib/bioroebe/java/README.md +5 -0
- data/lib/bioroebe/java/bioroebe/AllInOne.java +1 -0
- data/lib/bioroebe/java/bioroebe/Base.class +0 -0
- data/lib/bioroebe/java/bioroebe/Base.java +39 -5
- data/lib/bioroebe/java/bioroebe/IsPalindrome.java +23 -5
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +0 -0
- data/lib/bioroebe/java/bioroebe/Sequence.java +28 -3
- data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToCamelcase.java +16 -4
- data/lib/bioroebe/java/bioroebe/ToRNA.java +43 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +6 -0
- data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/BisulfiteTreatment.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{Codons.class → src/Codons.class} +0 -0
- data/lib/bioroebe/java/bioroebe/src/Codons.java +35 -0
- data/lib/bioroebe/java/bioroebe/src/Commandline.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/Commandline.java +101 -0
- data/lib/bioroebe/java/bioroebe/{Esystem.class → src/Esystem.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{Esystem.java → src/Esystem.java} +6 -1
- data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/GenerateRandomDnaSequence.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/GenerateRandomDnaSequence.java} +8 -2
- data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.java +56 -0
- data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/RemoveFile.java} +10 -4
- data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/RemoveNumbers.class} +0 -0
- data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/RemoveNumbers.java} +1 -0
- data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.class +0 -0
- data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.java +75 -0
- data/lib/bioroebe/misc/ruler.rb +11 -2
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
- data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +59 -18
- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
- data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
- data/lib/bioroebe/parsers/gff.rb +1 -9
- data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
- data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
- data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
- data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
- data/lib/bioroebe/project/project.rb +1 -1
- data/lib/bioroebe/python/README.md +1 -0
- data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
- data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
- data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
- data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
- data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
- data/lib/bioroebe/python/mymodule.py +8 -0
- data/lib/bioroebe/python/protein_to_dna.py +33 -0
- data/lib/bioroebe/python/shell/shell.py +19 -0
- data/lib/bioroebe/python/to_rna.py +14 -0
- data/lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py +137 -0
- data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
- data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
- data/lib/bioroebe/python/toplevel_methods/palindromes.py +52 -0
- data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
- data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
- data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
- data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
- data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
- data/lib/bioroebe/requires/require_cleave_and_digest.rb +3 -1
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
- data/lib/bioroebe/sequence/alignment.rb +14 -4
- data/lib/bioroebe/sequence/dna.rb +1 -0
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
- data/lib/bioroebe/sequence/protein.rb +105 -3
- data/lib/bioroebe/sequence/rna.rb +220 -0
- data/lib/bioroebe/sequence/sequence.rb +128 -40
- data/lib/bioroebe/shell/menu.rb +3815 -3696
- data/lib/bioroebe/shell/misc.rb +9019 -3133
- data/lib/bioroebe/shell/readline/readline.rb +1 -1
- data/lib/bioroebe/shell/shell.rb +1137 -28
- data/lib/bioroebe/siRNA/siRNA.rb +81 -1
- data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
- data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
- data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
- data/lib/bioroebe/taxonomy/constants.rb +4 -3
- data/lib/bioroebe/taxonomy/edit.rb +2 -1
- data/lib/bioroebe/taxonomy/help/help.rb +10 -10
- data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
- data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
- data/lib/bioroebe/taxonomy/info/info.rb +18 -11
- data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
- data/lib/bioroebe/taxonomy/interactive.rb +140 -104
- data/lib/bioroebe/taxonomy/menu.rb +27 -18
- data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
- data/lib/bioroebe/taxonomy/shared.rb +1 -0
- data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
- data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
- data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
- data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
- data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
- data/lib/bioroebe/toplevel_methods/misc.rb +175 -11
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +75 -47
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +3 -3
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
- data/lib/bioroebe/utility_scripts/compacter/compacter.rb +251 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
- data/lib/bioroebe/utility_scripts/permutations.rb +36 -9
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/www/embeddable_interface.rb +121 -58
- data/lib/bioroebe/www/sinatra/sinatra.rb +186 -71
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +17 -17
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
- data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
- data/lib/bioroebe/yaml/genomes/README.md +3 -4
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +5 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +57 -57
- data/spec/README.md +6 -0
- data/spec/project_wide_specification/classes.md +5 -0
- metadata +107 -70
- data/doc/setup.rb +0 -1655
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
- data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
- data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
- data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
- data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
- data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
- data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
- data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
- data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
- data/lib/bioroebe/java/bioroebe.jar +0 -0
- data/lib/bioroebe/shell/add.rb +0 -108
- data/lib/bioroebe/shell/assign.rb +0 -360
- data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
- data/lib/bioroebe/shell/constants.rb +0 -166
- data/lib/bioroebe/shell/download.rb +0 -335
- data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
- data/lib/bioroebe/shell/enzymes.rb +0 -310
- data/lib/bioroebe/shell/fasta.rb +0 -345
- data/lib/bioroebe/shell/gtk.rb +0 -76
- data/lib/bioroebe/shell/history.rb +0 -132
- data/lib/bioroebe/shell/initialize.rb +0 -217
- data/lib/bioroebe/shell/loop.rb +0 -74
- data/lib/bioroebe/shell/prompt.rb +0 -107
- data/lib/bioroebe/shell/random.rb +0 -289
- data/lib/bioroebe/shell/reset.rb +0 -335
- data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
- data/lib/bioroebe/shell/search.rb +0 -337
- data/lib/bioroebe/shell/sequences.rb +0 -200
- data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
- data/lib/bioroebe/shell/startup.rb +0 -127
- data/lib/bioroebe/shell/taxonomy.rb +0 -14
- data/lib/bioroebe/shell/tk.rb +0 -23
- data/lib/bioroebe/shell/user_input.rb +0 -88
- data/lib/bioroebe/shell/xorg.rb +0 -45
- data/lib/bioroebe/utility_scripts/compacter.rb +0 -131
- /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/BisulfiteTreatment.java} +0 -0
- /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/RemoveFile.class} +0 -0
@@ -2,69 +2,185 @@
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# === Bioroebe::ConvertThisCodonToThatAminoacid
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#
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# This class can be used to convert a particular codon, such as 'ATG',
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# into the corresponding aminoacid, in this case being 'M' for
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# Methionin. A String will be returned by this method.
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#
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# The characters in that String will correspond to the one-letter
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# format of aminoacids, such as the example shown above 'M' for
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# Methionin.
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#
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# The method has to handle invalid input arguments as well, to some
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# extent.
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#
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# The method supports both DNA and mRNA as "input".
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#
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# In order for the method to do its job properly, the method will
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# make use of the codon table stored in:
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#
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# Bioroebe.aa_to_rna_codon_table
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#
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# Also note that this method can easily be used to translate
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# other frames - simply provide the proper input to it.
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#
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# Note that this method will return the result - it will NOT
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# output the result.
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#
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# Usage examples:
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#
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# Bioroebe::ConvertThisCodonToThatAminoacid.new
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# puts Bioroebe.codon_to_aminoacid('ATG') # => "M"
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# puts Bioroebe.codon_to_aminoacid('GUG') # => "V"
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# puts Bioroebe.decode_this_codon('CCG') # => "P"
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# puts Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
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# puts Bioroebe.codon_to_aminoacid('ATGA') # => "M"
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# puts Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
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# puts Bioroebe.convert_this_codon_to_that_aminoacid('ATGA') # => "M"
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#
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# Commandline usage example:
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#
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# dcodon TTT TTC # => ["TTY"]
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#
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# =========================================================================== #
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# require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
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# =========================================================================== #
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require 'bioroebe/base/commandline_application/commandline_application.rb'
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module Bioroebe
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class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # === Bioroebe::ConvertThisCodonToThatAminoacid
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require 'bioroebe/codons/codon_table.rb'
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# ========================================================================= #
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# ===
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#
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# === initialize
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# ========================================================================= #
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def initialize(
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i = ARGV, # This should be an Array.
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run_already = true,
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&block
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)
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reset
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set_commandline_arguments(i)
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# ========================================================================= #
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# === Handle blocks next
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# ========================================================================= #
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if block_given?
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yielded = yield
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case yielded
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# ======================================================================= #
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# === :be_quiet
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# ======================================================================= #
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when :be_quiet
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be_quiet
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end
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end
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run if run_already
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end
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# ========================================================================= #
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# === reset (reset tag)
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# ========================================================================= #
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def reset
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super()
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reset_the_internal_hash
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# ======================================================================= #
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# === @shall_we_replace_stop_codons
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# ======================================================================= #
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@shall_we_replace_stop_codons = :default
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# ======================================================================= #
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# === :with_trailer
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# ======================================================================= #
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@internal_hash[:with_trailer] = false
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end
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# ========================================================================= #
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-
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-
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-
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# === menu (menu tag)
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# ========================================================================= #
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def menu(
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i = commandline_arguments_starting_with_a_hyphen?
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)
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-
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if i.is_a? Array
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i.each {|entry| menu(entry) }
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else
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case i # case tag
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# ===================================================================== #
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# === codon_to_aa --with-trailer
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# ===================================================================== #
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when /^-?-?with(-|_)?trailer$/i
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@internal_hash[:with_trailer] = true
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# ===================================================================== #
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# === codon_to_aa --help
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# ===================================================================== #
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when /^-?-?help$/i
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show_help
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exit
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end
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end
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end
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# ========================================================================= #
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# === show_help (help tag)
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# ========================================================================= #
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def show_help
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e
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e " --with-trailer # display any result via 5'- and -3' padding"
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e
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end
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# ========================================================================= #
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# === with_trailer?
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# ========================================================================= #
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def with_trailer?
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@internal_hash[:with_trailer]
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end
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# ========================================================================= #
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# === report (report tag)
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# ========================================================================= #
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def report
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e @result if be_verbose?
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end
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# ========================================================================= #
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# === result?
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# ========================================================================= #
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def result?
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@result
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end; alias sequence? result? # === sequence?
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# ========================================================================= #
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# === run (run tag)
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# ========================================================================= #
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def run
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i = commandline_arguments?
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menu( # Pass all arguments that start with -- next.
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commandline_arguments_starting_with_a_hyphen(i)
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)
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case @shall_we_replace_stop_codons
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# ======================================================================= #
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# === :default
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# ======================================================================= #
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when :default
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-
shall_we_replace_stop_codons = true
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@shall_we_replace_stop_codons = true
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end
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if i.is_a? Array
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-
i = i.join
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i = reject_hyphens(i).join
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end
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i = i.to_s.dup
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i.upcase!
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i.tr!('U','T') # We need DNA here, so U becomes T.
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use_this_codon_table = codon_table_dataset?.dup
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# ======================================================================= #
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# Obtain the dataset from the correct codon_table next.
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# ======================================================================= #
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-
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if i.size < 3
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scanned = i.scan(/./)
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else
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scanned = i.scan(/.../)
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end
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scanned.map! {|potential_codon|
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if use_this_codon_table.has_key? potential_codon
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potential_codon = use_this_codon_table[potential_codon]
|
@@ -80,23 +196,56 @@ module Bioroebe
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}
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result = scanned
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result = result.join if result.is_a? Array
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-
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-
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-
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-
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-
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if with_trailer?
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result = result.dup
|
201
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+
result.prepend("5'-")
|
202
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result << "-3'"
|
203
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end
|
204
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@result = result
|
205
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report
|
206
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end
|
207
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+
|
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# ========================================================================= #
|
209
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# === Bioroebe::ConvertThisCodonToThatAminoacid[]
|
210
|
+
#
|
211
|
+
# Usage example:
|
212
|
+
#
|
213
|
+
# Bioroebe::ConvertThisCodonToThatAminoacid[]
|
214
|
+
#
|
215
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+
# ========================================================================= #
|
216
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+
def self.[](i = ARGV)
|
217
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+
new(i).result?
|
218
|
+
end
|
219
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+
|
220
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+
end
|
221
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+
|
222
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# =========================================================================== #
|
223
|
+
# === Bioroebe.convert_this_codon_to_that_aminoacid
|
224
|
+
# =========================================================================== #
|
225
|
+
def self.convert_this_codon_to_that_aminoacid(i = ARGV)
|
226
|
+
Bioroebe::ConvertThisCodonToThatAminoacid.new(i) { :be_quiet }
|
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+
end; self.instance_eval { alias decode_this_codon convert_this_codon_to_that_aminoacid } # === Bioroebe.decode_this_codon
|
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|
+
self.instance_eval { alias convert_dna_to_protein_sequence convert_this_codon_to_that_aminoacid } # === Bioroebe.convert_dna_to_protein_sequence
|
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|
+
self.instance_eval { alias translate_dna_into_aminoacid convert_this_codon_to_that_aminoacid } # === Bioroebe.translate_dna_into_aminoacid
|
230
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+
self.instance_eval { alias dna_to_aa convert_this_codon_to_that_aminoacid } # === Bioroebe.dna_to_aa
|
231
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self.instance_eval { alias codon_to_aminoacid convert_this_codon_to_that_aminoacid } # === Bioroebe.codon_to_aminoacid
|
89
232
|
|
90
233
|
end
|
91
234
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|
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if __FILE__ == $PROGRAM_NAME
|
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alias e puts
|
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-
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95
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-
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-
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-
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-
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99
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-
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-
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101
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-
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102
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-
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237
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if ARGV.empty?
|
238
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# ======================================================================= #
|
239
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+
# pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
|
240
|
+
# pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
|
241
|
+
# ======================================================================= #
|
242
|
+
e 'GUGGUG → '+Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
|
243
|
+
e 'ATG → '+Bioroebe.codon_to_aminoacid('ATG') # => "M"
|
244
|
+
e 'GUG → '+Bioroebe.codon_to_aminoacid('GUG') # => "V"
|
245
|
+
e 'CCG → '+Bioroebe.decode_this_codon('CCG') # => "P"
|
246
|
+
e 'ATGA → '+Bioroebe.codon_to_aminoacid('ATGA') # => "M"
|
247
|
+
e 'ATGA → '+Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
|
248
|
+
else
|
249
|
+
_ = Bioroebe::ConvertThisCodonToThatAminoacid.new(ARGV)
|
250
|
+
end
|
251
|
+
end # convertthiscodontothataminoacid GGT GGC AAA AGU GCG
|
@@ -27,11 +27,6 @@ class PossibleCodonsForThisAminoacid < ::Bioroebe::CommandlineApplication # ===
|
|
27
27
|
|
28
28
|
require 'bioroebe/codons/codon_table.rb'
|
29
29
|
|
30
|
-
# ========================================================================= #
|
31
|
-
# === NAMESPACE
|
32
|
-
# ========================================================================= #
|
33
|
-
NAMESPACE = inspect
|
34
|
-
|
35
30
|
# ========================================================================= #
|
36
31
|
# === SHOW_ADDITIONAL_HINTS
|
37
32
|
#
|
@@ -93,10 +88,7 @@ class PossibleCodonsForThisAminoacid < ::Bioroebe::CommandlineApplication # ===
|
|
93
88
|
# ========================================================================= #
|
94
89
|
def reset
|
95
90
|
super()
|
96
|
-
|
97
|
-
# === @namespace
|
98
|
-
# ======================================================================= #
|
99
|
-
@namespace = NAMESPACE
|
91
|
+
infer_the_namespace
|
100
92
|
# ======================================================================= #
|
101
93
|
# === @try_to_identify_purines_and_pyrimidines
|
102
94
|
# ======================================================================= #
|
@@ -37,6 +37,7 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
|
|
37
37
|
else
|
38
38
|
first = show_what
|
39
39
|
end
|
40
|
+
first = first.to_s.delete('-')
|
40
41
|
case first.to_sym
|
41
42
|
# ======================================================================= #
|
42
43
|
# === :human
|
@@ -56,7 +57,9 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
|
|
56
57
|
:headers,
|
57
58
|
'--headers'
|
58
59
|
::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
|
59
|
-
e number.to_s.rjust(3)
|
60
|
+
e turquoise(number.to_s.rjust(3))
|
61
|
+
+') '+
|
62
|
+
long_name.ljust(70)
|
60
63
|
}
|
61
64
|
end
|
62
65
|
end
|
@@ -113,7 +116,8 @@ end
|
|
113
116
|
# =========================================================================== #
|
114
117
|
def self.show_codon_tables(how = :headers)
|
115
118
|
ShowCodonTables.new(how)
|
116
|
-
end
|
119
|
+
end; self.instance_eval { alias show_the_codon_tables show_codon_tables } # === Bioroebe.show_the_codon_tables
|
120
|
+
self.instance_eval { alias show_the_codontables show_codon_tables } # === Bioroebe.the_codon_tables
|
117
121
|
|
118
122
|
# =========================================================================== #
|
119
123
|
# === Bioroebe.available_codon_tables?
|
@@ -127,4 +131,5 @@ end
|
|
127
131
|
if __FILE__ == $PROGRAM_NAME
|
128
132
|
Bioroebe::ShowCodonTables.new(ARGV)
|
129
133
|
end # showcodontables
|
130
|
-
# showcodontables human
|
134
|
+
# showcodontables human
|
135
|
+
# showcodontables everything
|
@@ -24,6 +24,7 @@ module Bioroebe
|
|
24
24
|
class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCodonUsage
|
25
25
|
|
26
26
|
require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
|
27
|
+
require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
|
27
28
|
|
28
29
|
# ========================================================================= #
|
29
30
|
# === initialize
|
@@ -133,12 +134,13 @@ class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCo
|
|
133
134
|
# ========================================================================= #
|
134
135
|
def report_the_top_five_codons(from_this_dataset)
|
135
136
|
e
|
136
|
-
|
137
|
+
erev 'The '+mediumpurple('top five codons')+
|
138
|
+
rev+' in use, sorted by frequency, are:'
|
137
139
|
e
|
138
140
|
top_five = from_this_dataset.sort_by {|key, values| values }.reverse[0..4]
|
139
141
|
top_five.each {|name_of_codon, how_many_of_them|
|
140
142
|
_ = name_of_codon.upcase
|
141
|
-
this_codon = codon_to_aminoacid(_)
|
143
|
+
this_codon = codon_to_aminoacid(_).sequence?
|
142
144
|
colourized_this_codon = turquoise(this_codon)
|
143
145
|
e rev+' - '+
|
144
146
|
teal(_)+
|
@@ -184,10 +186,19 @@ end
|
|
184
186
|
|
185
187
|
# =========================================================================== #
|
186
188
|
# === Bioroebe.codon_frequencies_of_this_sequence
|
189
|
+
#
|
190
|
+
# Usage example:
|
191
|
+
#
|
192
|
+
# x = Bioroebe.codon_frequencies_of_this_sequence('ATGGGCGGGGTGATGGCAATGCCTTTAATGCCGCCAAAAAAAAAAAAAAAA')
|
193
|
+
#
|
194
|
+
# Will yield this Hash:
|
195
|
+
#
|
196
|
+
# {"AAA"=>5, "ATG"=>4, "CCA"=>1, "CCG"=>1, "TTA"=>1, "CCT"=>1, "GCA"=>1, "GTG"=>1, "GGG"=>1, "GGC"=>1}
|
197
|
+
#
|
187
198
|
# =========================================================================== #
|
188
199
|
def self.codon_frequencies_of_this_sequence(i = ARGV)
|
189
|
-
Bioroebe::ShowCodonUsage.new(i) { :be_quiet }
|
190
|
-
end
|
200
|
+
Bioroebe::ShowCodonUsage.new(i) { :be_quiet }.result?
|
201
|
+
end; self.instance_eval { alias hash_frequencies codon_frequencies_of_this_sequence } # === Bioroebe.hash_frequencies
|
191
202
|
|
192
203
|
end
|
193
204
|
|
data/lib/bioroebe/colours/rev.rb
CHANGED
@@ -17,7 +17,10 @@ module Bioroebe
|
|
17
17
|
# ========================================================================= #
|
18
18
|
def self.rev
|
19
19
|
if @use_colours
|
20
|
-
|
20
|
+
unless Object.const_defined?(:Colours)
|
21
|
+
require 'colours'
|
22
|
+
end
|
23
|
+
return ::Colours::GREEN # Default colour goes in here.
|
21
24
|
end
|
22
25
|
return ''
|
23
26
|
end
|
@@ -3,6 +3,7 @@
|
|
3
3
|
# frozen_string_literal: true
|
4
4
|
# =========================================================================== #
|
5
5
|
# require 'bioroebe/constants/aminoacids_and_proteins.rb'
|
6
|
+
# Bioroebe.filter_away_invalid_aminoacids
|
6
7
|
# =========================================================================== #
|
7
8
|
module Bioroebe
|
8
9
|
|
@@ -89,7 +89,7 @@ module Postgresql # === Bioroebe::Postgresql
|
|
89
89
|
DROP_TABLE_FASTA = 'DROP TABLE fasta;'
|
90
90
|
|
91
91
|
# ========================================================================= #
|
92
|
-
# === POSTGRE_DROP_FASTA_COMMAND
|
92
|
+
# === Bioroebe::Postgresql::POSTGRE_DROP_FASTA_COMMAND
|
93
93
|
# ========================================================================= #
|
94
94
|
POSTGRE_DROP_FASTA_COMMAND = DROP_FASTA_TABLE = DROP_TABLE_FASTA
|
95
95
|
|
@@ -165,15 +165,23 @@ module Bioroebe
|
|
165
165
|
end
|
166
166
|
|
167
167
|
# ========================================================================= #
|
168
|
-
# ===
|
168
|
+
# === Bioroebe.fasta_dir?
|
169
|
+
# ========================================================================= #
|
170
|
+
def self.fasta_dir?
|
171
|
+
"#{Bioroebe.log_dir?}fasta/"
|
172
|
+
end
|
173
|
+
|
174
|
+
# ========================================================================= #
|
175
|
+
# === Bioroebe.file_fastq_quality_schemes
|
169
176
|
#
|
170
177
|
# This constant will point to a location such as this one here:
|
171
178
|
#
|
172
179
|
# /Programs/Ruby/2.6.4/lib/ruby/site_ruby/2.6.0/bioroebe/yaml/fastq_quality_schemes.yml
|
173
180
|
#
|
174
181
|
# ========================================================================= #
|
175
|
-
|
176
|
-
"#{project_yaml_directory?}fastq_quality_schemes.yml"
|
182
|
+
def self.file_fastq_quality_schemes
|
183
|
+
"#{project_yaml_directory?}fasta_and_fastq/fastq_quality_schemes.yml"
|
184
|
+
end
|
177
185
|
|
178
186
|
# ========================================================================= #
|
179
187
|
# === Bioroebe.file_talens
|
@@ -318,10 +326,17 @@ module Bioroebe
|
|
318
326
|
# ========================================================================= #
|
319
327
|
# === Bioroebe.file_restriction_enzymes
|
320
328
|
# ========================================================================= #
|
321
|
-
def file_restriction_enzymes
|
329
|
+
def self.file_restriction_enzymes
|
322
330
|
FILE_RESTRICTION_ENZYMES
|
323
331
|
end
|
324
332
|
|
333
|
+
# ========================================================================= #
|
334
|
+
# === file_restriction_enzymes
|
335
|
+
# ========================================================================= #
|
336
|
+
def file_restriction_enzymes
|
337
|
+
::Bioroebe.file_restriction_enzymes
|
338
|
+
end
|
339
|
+
|
325
340
|
# ========================================================================= #
|
326
341
|
# === Bioroebe.blosum_directory?
|
327
342
|
# ========================================================================= #
|
@@ -553,6 +568,18 @@ module Bioroebe
|
|
553
568
|
"#{project_yaml_directory?}aminoacids/molecular_weight.yml"
|
554
569
|
end
|
555
570
|
|
571
|
+
# ========================================================================= #
|
572
|
+
# === Bioroebe.file_amino_acids_long_name_to_one_letter
|
573
|
+
#
|
574
|
+
# This method will return a String such as:
|
575
|
+
#
|
576
|
+
# "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml"
|
577
|
+
#
|
578
|
+
# ========================================================================= #
|
579
|
+
def self.file_amino_acids_long_name_to_one_letter
|
580
|
+
"#{project_yaml_directory?}aminoacids/amino_acids_long_name_to_one_letter.yml"
|
581
|
+
end
|
582
|
+
|
556
583
|
end
|
557
584
|
|
558
585
|
if __FILE__ == $PROGRAM_NAME
|
@@ -43,6 +43,26 @@ module Bioroebe
|
|
43
43
|
# ========================================================================= #
|
44
44
|
TOKEN = '|'
|
45
45
|
|
46
|
+
# ========================================================================= #
|
47
|
+
# === VALID_WAYS_TO_EXIT
|
48
|
+
#
|
49
|
+
# All ways to exit will be recorded here.
|
50
|
+
#
|
51
|
+
# If you need to use more ways, simply append to this Array.
|
52
|
+
#
|
53
|
+
# This constant may have to be moved into the bio-shell part eventually.
|
54
|
+
# ========================================================================= #
|
55
|
+
VALID_WAYS_TO_EXIT = %w(
|
56
|
+
quit q exit qq :q qt
|
57
|
+
bye
|
58
|
+
rda
|
59
|
+
r2
|
60
|
+
tq
|
61
|
+
sq
|
62
|
+
exit_program
|
63
|
+
exitprogram
|
64
|
+
)
|
65
|
+
|
46
66
|
# ========================================================================= #
|
47
67
|
# === NAMES_ENTRIES
|
48
68
|
#
|
@@ -107,6 +107,13 @@ module Bioroebe
|
|
107
107
|
ALLOWED_DNA_NUCLEOTIDES
|
108
108
|
end; self.instance_eval { alias dna? allowed_dna_nucleotides? } # === Bioroebe.dna?
|
109
109
|
|
110
|
+
# ========================================================================= #
|
111
|
+
# === Bioroebe.return_DNA_nucleotides
|
112
|
+
# ========================================================================= #
|
113
|
+
def self.return_DNA_nucleotides
|
114
|
+
return DNA_NUCLEOTIDES
|
115
|
+
end
|
116
|
+
|
110
117
|
end
|
111
118
|
|
112
119
|
if __FILE__ == $PROGRAM_NAME
|