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
data/lib/bioroebe/shell/add.rb
DELETED
@@ -1,108 +0,0 @@
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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/shell/add.rb'
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# =========================================================================== #
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module Bioroebe
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class Shell < ::Bioroebe::CommandlineApplication
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# ========================================================================= #
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# === add_to_end
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#
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# This method will invoke append() if something has to be appended.
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# ========================================================================= #
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def add_to_end(i)
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add_to_start_or_end(i, :end)
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end; alias add add_to_end # === add (add tag)
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# ========================================================================= #
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# === add_to_start
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# ========================================================================= #
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def add_to_start(i)
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add_to_start_or_end(i, :start)
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end; alias left_add add_to_start # === left_add
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-
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# ========================================================================= #
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# === add_to_start_or_end
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#
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# This method can either add to the start or to the end.
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#
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# The default is to append to the nucleotide sequence.
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#
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# We can input a number - in this case, we simply add these many
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# nucleotides onto the main string.
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# ========================================================================= #
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def add_to_start_or_end(
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i = '',
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append_or_prepend = :append
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)
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i = i.join('') if i.is_a? Array
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i = i.dup
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old_length = i.size
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case i.to_s # Easier start/stop entries.
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# ======================================================================= #
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# === Add a start codon.
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# ======================================================================= #
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when 'start',
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'START',
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/ORF/i,
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':start'
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i = ::Bioroebe.start_codon? # Used to be hardcoded -> 'ATG'
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# ======================================================================= #
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# === Add a stop codon.
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# ======================================================================= #
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when /^stop$/i,
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':stop'
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i = ::Bioroebe.stop_codons?.sample
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end
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i.upcase!
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case append_or_prepend
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# ======================================================================= #
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# === :prepend
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# ======================================================================= #
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when :prepend,
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:to_start,
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:start
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if i =~ /^\d+$/ # If input is only numbers.
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erev 'Only numbers were given: Prepending '+
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sfancy(i.to_s)+rev+
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' random nucleotides to the main string now.'
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i.to_i.times { prepend(add_nucleotide) }
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else
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erev "Prepending #{sfancy(i)}#{rev} to the main string."
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prepend(i)
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end
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# ======================================================================= #
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# === :append
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# ======================================================================= #
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when :append,
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:to_end,
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:end
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if i =~ /^\d+$/ # If input is only numbers.
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erev "Only numbers were given: Adding #{sfancy(i.to_s)}#{rev}"\
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" random nucleotides to the main string now."
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i.to_i.times { append(return_random_nucleotide) }
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else
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if only_nucleotides?(i)
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89
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msg = "Adding #{sfancy(i)}#{rev}"
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msg = msg.dup if msg.frozen?
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if ::Bioroebe.is_a_stop_codon? i
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msg << ' (a stop codon)'
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end
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msg << ' to the main string.'
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erev msg
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end
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append(i)
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end
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end
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new_length = string?.size.to_s
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unless new_length.to_i == old_length.to_i
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erev "The new length of the main string is now: "\
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"#{simp(new_length)}#{rev}."
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end
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show_dna_sequence
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end
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end; end
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@@ -1,360 +0,0 @@
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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# require 'bioroebe/shell/assign.rb'
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# =========================================================================== #
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module Bioroebe
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class Shell < ::Bioroebe::CommandlineApplication
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# ========================================================================= #
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# === set_dna_sequence (assign tag, assigning tag)
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#
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# This method can be used to set/assign the main DNA string.
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#
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# It is a fairly long method, mostly because it will do lots of
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# additional tasks, way aside from setting/assigning to a DNA
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# sequence only.
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#
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# As of June 2016, the method will also keep a backup of the
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# generated sequence in a local file as well. This will allow
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# us to "replay" the given sequence on startup of the shell.
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#
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# Note that as of Jun 2016, we will chop off any '"' found in
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# the input String.
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# ========================================================================= #
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def set_dna_sequence(
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i = nil,
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be_verbose = true,
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do_upcase = :check_for_config_value_here
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)
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32
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if is_the_main_sequence_frozen?
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report_that_the_main_sequence_is_frozen
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return
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end
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36
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case do_upcase
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# ======================================================================= #
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38
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# === :check_for_config_value_here
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# ======================================================================= #
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40
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when :check_for_config_value_here,
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:default
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42
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if @config and @config.respond_to?(:upcase_nucleotides)
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43
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do_upcase = @config.upcase_nucleotides
|
44
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else
|
45
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do_upcase = false
|
46
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-
end
|
47
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# ======================================================================= #
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48
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# === :do_not_upcase
|
49
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# ======================================================================= #
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50
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when :do_not_upcase
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do_upcase = false
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52
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-
end
|
53
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if do_upcase
|
54
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shall_we_upcase = do_upcase if @config
|
55
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end
|
56
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# ======================================================================= #
|
57
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# === Sanitize the second variable next
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58
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# ======================================================================= #
|
59
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case be_verbose
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60
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# ======================================================================= #
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61
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# === :be_verbose
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62
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# ======================================================================= #
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63
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when :be_verbose
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64
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be_verbose = true
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65
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# ======================================================================= #
|
66
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# === :do_not_upcase
|
67
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# ======================================================================= #
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68
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when :do_not_upcase,
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69
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:no_upcase,
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70
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:no_upcasing,
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71
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shall_we_upcase = false
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72
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be_verbose = true # Sync this.
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73
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# ======================================================================= #
|
74
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# === :be_silent
|
75
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-
# ======================================================================= #
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76
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when :be_silent,
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77
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:be_quiet
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78
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be_verbose = false
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79
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-
end
|
80
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if i.nil?
|
81
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# ===================================================================== #
|
82
|
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# === Hande nil value for the variable i next:
|
83
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#
|
84
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# Here in this entry point, we will handle if the first input
|
85
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# argument is nil.
|
86
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#
|
87
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# If @internal_hash[:misc_sequence] is NOT nil, then it will be used
|
88
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# once, then cleared. Otherwise, we will use dna_sequence?.
|
89
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# ===================================================================== #
|
90
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if @internal_hash[:misc_sequence]
|
91
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i = @internal_hash[:misc_sequence]
|
92
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@internal_hash[:misc_sequence] = nil # Set it to nil again.
|
93
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-
else
|
94
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-
i = dna_sequence?
|
95
|
-
end
|
96
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-
end
|
97
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# ======================================================================= #
|
98
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-
# === Convert Array into String next
|
99
|
-
# ======================================================================= #
|
100
|
-
i = i.join if i.is_a? Array
|
101
|
-
i = i.to_s # Work on a String past this point here.
|
102
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if i.include? ' ' # Sanitize the input a little bit.
|
103
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i = i.strip.delete(' ')
|
104
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-
end
|
105
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if i.include? '|' # I think we will not need '|' in our main string.
|
106
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i.delete!('|')
|
107
|
-
end
|
108
|
-
# ======================================================================= #
|
109
|
-
# === If the input has only numbers
|
110
|
-
# ======================================================================= #
|
111
|
-
if i =~ /^\d+$/
|
112
|
-
i = random_dna_sequence(i)
|
113
|
-
end
|
114
|
-
# ======================================================================= #
|
115
|
-
# === Handle Fasta format next
|
116
|
-
# ======================================================================= #
|
117
|
-
if i.start_with?('>') and i.include?(N)
|
118
|
-
erev 'It seems as if you have a FASTA sequence there, as it starts with '\
|
119
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'a > character.'
|
120
|
-
erev 'We will omit this first section (the header) though.'
|
121
|
-
i[0 .. i.index(N)] = '' # This does the chop-off action.
|
122
|
-
end
|
123
|
-
i.delete!('-') if i.include? '-'
|
124
|
-
i.delete!('_') if i.include? '_' # Don't want '_' characters.
|
125
|
-
i.delete!('?') if i.include? '?'
|
126
|
-
i.delete!('#') if i.include? '#' # This was added at 08.05.2016.
|
127
|
-
i.delete!('"') if i.include? '"' # This was added at 02.06.2016.
|
128
|
-
i.gsub!(/\^C/,'') if i.include? '^C'
|
129
|
-
i = i.to_s.dup
|
130
|
-
case i
|
131
|
-
# ======================================================================= #
|
132
|
-
# === :GFP
|
133
|
-
# ======================================================================= #
|
134
|
-
when ':GFP' # ← This means the default GFP sequence.
|
135
|
-
i = return_default_GFP_sequence
|
136
|
-
# ======================================================================= #
|
137
|
-
# === random
|
138
|
-
# ======================================================================= #
|
139
|
-
when /^random$/i,
|
140
|
-
'' # As of 04.01.2015, we will try '' too here.
|
141
|
-
i = random :do_not_show_the_string
|
142
|
-
# ======================================================================= #
|
143
|
-
# === multiline
|
144
|
-
# ======================================================================= #
|
145
|
-
when 'multiline' # Handle multiline input.
|
146
|
-
erev 'Multiline input detected.'
|
147
|
-
erev 'Finish by issuing __ on an empty line. (These are 2 "_" tokens.)'
|
148
|
-
i = $stdin.gets('__')
|
149
|
-
# ===================================================================== #
|
150
|
-
# Next, sanitize it a bit if it starts with a '>' identifier.
|
151
|
-
# ===================================================================== #
|
152
|
-
if i.strip.start_with? '>'
|
153
|
-
i = i[(i.index(N)+1)..-1]
|
154
|
-
end
|
155
|
-
else
|
156
|
-
if i
|
157
|
-
# =================================================================== #
|
158
|
-
# === Next upcase the input if the flag was set
|
159
|
-
# =================================================================== #
|
160
|
-
i.upcase! if shall_we_upcase
|
161
|
-
case mode?
|
162
|
-
# =================================================================== #
|
163
|
-
# === :dna
|
164
|
-
# =================================================================== #
|
165
|
-
when :dna,
|
166
|
-
:rna
|
167
|
-
dna_sequence_object?.set_mode(mode?)
|
168
|
-
# =================================================================== #
|
169
|
-
# === :aminoacids
|
170
|
-
# =================================================================== #
|
171
|
-
when :aminoacids
|
172
|
-
set_aminoacids(i)
|
173
|
-
end
|
174
|
-
else # else input is nil.
|
175
|
-
erev 'Missing Input to assign_sequence(). Please input '\
|
176
|
-
'your DNA string now (Hitting the enter key will '\
|
177
|
-
'finish this):'
|
178
|
-
i = $stdin.gets.chomp
|
179
|
-
i = i.upcase if shall_we_upcase
|
180
|
-
end
|
181
|
-
end
|
182
|
-
i = '' unless i
|
183
|
-
# ======================================================================= #
|
184
|
-
# === Remove possible newlines in the given input
|
185
|
-
# ======================================================================= #
|
186
|
-
i.delete!(N) if i.include? N
|
187
|
-
i.delete!('_') if i.include? '_'
|
188
|
-
# ======================================================================= #
|
189
|
-
# Is faster than .gsub()# if i
|
190
|
-
# i.upcase! # Since as of Feb 2016. Nope, disabled again as of May 2016.
|
191
|
-
# end
|
192
|
-
# ======================================================================= #
|
193
|
-
if File.exist?(i) # Assume a file was given. Read its content then.
|
194
|
-
if i.end_with? '.yml'
|
195
|
-
i = YAML.load_file(i)
|
196
|
-
else
|
197
|
-
i = File.readlines(i).reject {|line|
|
198
|
-
line.start_with? '>'
|
199
|
-
}.join
|
200
|
-
end
|
201
|
-
end
|
202
|
-
# ======================================================================= #
|
203
|
-
# Also get rid of numbers.
|
204
|
-
# ======================================================================= #
|
205
|
-
i = i.dup if i.frozen?
|
206
|
-
i.gsub!(/\d/,'')
|
207
|
-
# ======================================================================= #
|
208
|
-
# The DNA Sequence will be stored in the Sequence object directly.
|
209
|
-
# The nil is required for now, because otherwise set_input() will
|
210
|
-
# upcase the input by default.
|
211
|
-
# ======================================================================= #
|
212
|
-
if dna_sequence_object?.nil?
|
213
|
-
_ = Bioroebe::Sequence.new(i.dup) { :is_DNA }
|
214
|
-
@internal_hash[:array_dna_sequence] << _
|
215
|
-
else
|
216
|
-
# ===================================================================== #
|
217
|
-
# Assign it here.
|
218
|
-
# ===================================================================== #
|
219
|
-
dna_sequence_object?.set_input(i.dup, nil) # We can re-use the old @sequence object.
|
220
|
-
end
|
221
|
-
# ======================================================================= #
|
222
|
-
# === :coding_area
|
223
|
-
#
|
224
|
-
# Whenever the DNA sequence is modified like that, we will also reset
|
225
|
-
# the "coding_area" entry in the internal Hash to the initial nil state.
|
226
|
-
# ======================================================================= #
|
227
|
-
@internal_hash[:coding_area] = nil
|
228
|
-
# ======================================================================= #
|
229
|
-
# === Report that we will perform an assignment next
|
230
|
-
# ======================================================================= #
|
231
|
-
if be_verbose # Check for verbosity
|
232
|
-
case mode?
|
233
|
-
when :dna
|
234
|
-
if i.empty?
|
235
|
-
erev 'Nothing was assigned yet.'
|
236
|
-
else
|
237
|
-
erev 'Setting DNA sequence to ('+
|
238
|
-
sfancy(i.size.to_s)+
|
239
|
-
rev+' nucleotides):'
|
240
|
-
show_string
|
241
|
-
end
|
242
|
-
end
|
243
|
-
end
|
244
|
-
# ======================================================================= #
|
245
|
-
# === Set the Xorg Buffer next
|
246
|
-
# ======================================================================= #
|
247
|
-
if @config and @config.respond_to?(:additionally_set_xorg_buffer) and
|
248
|
-
@config.additionally_set_xorg_buffer
|
249
|
-
begin
|
250
|
-
set_xorg_buffer(i)
|
251
|
-
rescue NoMethodError; end
|
252
|
-
end
|
253
|
-
unless i.empty? # We do not save empty nucleotide Strings.
|
254
|
-
result = i.to_s.dup
|
255
|
-
# ===================================================================== #
|
256
|
-
# We will save into a file next.
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# ===================================================================== #
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258
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this_file = "#{log_dir?}dna_string.yml"
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259
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dna_sequence_object?.save_sequence_to_this_file(this_file) # Save it here.
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260
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# ===================================================================== #
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261
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# Since as of Jun 2016, we will also create a new RNA string.
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262
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#
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263
|
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# This has been disabled as of December 2021. It was too strange
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264
|
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# to automatically create a RNA string.
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265
|
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# ===================================================================== #
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266
|
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# if @internal_hash[:array_rna_sequence]
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267
|
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# @internal_hash[:array_rna_sequence].last.set_sequence(result)
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268
|
-
# end
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269
|
-
# ===================================================================== #
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270
|
-
# === Automatically assign the aminoacid sequence as well
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271
|
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# ===================================================================== #
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272
|
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_ = translate_dna_into_aminoacid(result)
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273
|
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set_aminoacids(_, nil, :be_quiet)
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274
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return result
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275
|
-
end
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276
|
-
end; alias set_dna_string set_dna_sequence # === set_dna_string
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277
|
-
alias set_string set_dna_sequence # === set_dna_sequence
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278
|
-
alias set_main_sequence set_dna_sequence # === set_main_sequence (set_main_sequence tag)
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279
|
-
alias set_sequence set_dna_sequence # === set_sequence (set_sequence tag)
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280
|
-
alias set_dna set_dna_sequence # === set_dna
|
281
|
-
alias set_assign set_dna_sequence # === set_dna
|
282
|
-
alias assign_sequence set_dna_sequence # === assign_sequence
|
283
|
-
alias assign_dna_sequence set_dna_sequence # === assign_dna_sequence
|
284
|
-
alias assign_this_dna_sequence set_dna_sequence # === assign_this_dna_sequence
|
285
|
-
alias assign set_dna_sequence # === assign
|
286
|
-
|
287
|
-
require 'bioroebe/aminoacids/create_random_aminoacids.rb'
|
288
|
-
# ========================================================================= #
|
289
|
-
# === set_aminoacids (assign protein tag, set aminoacids tag)
|
290
|
-
#
|
291
|
-
# Assign a protein sequence here. The first argument shall be the
|
292
|
-
# aminoacid sequence in question.
|
293
|
-
#
|
294
|
-
# Usage example:
|
295
|
-
#
|
296
|
-
# assign_protein FLIMVSPTAYHQNKDECWRGX*
|
297
|
-
#
|
298
|
-
# ========================================================================= #
|
299
|
-
def set_aminoacids(
|
300
|
-
i = :random,
|
301
|
-
how_many_to_generate = 1000, # Will only be applied if the input is :random or :generate
|
302
|
-
be_verbose = true
|
303
|
-
)
|
304
|
-
# ======================================================================= #
|
305
|
-
# === Sanitize the third argument next
|
306
|
-
# ======================================================================= #
|
307
|
-
case be_verbose
|
308
|
-
when :be_silent,
|
309
|
-
:be_quiet
|
310
|
-
be_verbose = false
|
311
|
-
end
|
312
|
-
i = :random unless i
|
313
|
-
case i
|
314
|
-
# ======================================================================= #
|
315
|
-
# === :random
|
316
|
-
# ======================================================================= #
|
317
|
-
when :random,
|
318
|
-
:generate
|
319
|
-
i = Bioroebe.create_random_aminoacids(how_many_to_generate) # Generate them here.
|
320
|
-
end
|
321
|
-
i = i.join if i.is_a? Array
|
322
|
-
if i =~ /^\d+$/ # only numbers
|
323
|
-
i = Bioroebe.create_random_aminoacids(i)
|
324
|
-
end
|
325
|
-
if be_verbose
|
326
|
-
erev "Now assigning aminoacid sequence to: #{sfancy(i.to_s)}"
|
327
|
-
end
|
328
|
-
if i.is_a? String # Convert it into a Sequence object here.
|
329
|
-
i = ::Bioroebe.sequence(i) { :aminoacid }
|
330
|
-
end
|
331
|
-
# ======================================================================= #
|
332
|
-
# Do the assignment next.
|
333
|
-
# ======================================================================= #
|
334
|
-
if @internal_hash[:array_aminoacid_sequence].empty?
|
335
|
-
@internal_hash[:array_aminoacid_sequence] << i
|
336
|
-
else
|
337
|
-
@internal_hash[:array_aminoacid_sequence].pop
|
338
|
-
@internal_hash[:array_aminoacid_sequence] << i
|
339
|
-
end
|
340
|
-
end; alias assign_aminoacid_sequence set_aminoacids # === assign_aminoacid_sequence
|
341
|
-
alias assign_protein_sequence set_aminoacids # === assign_protein_sequence
|
342
|
-
alias set_aminoacid_sequence set_aminoacids # === set_aminoacid_sequence
|
343
|
-
|
344
|
-
# ========================================================================= #
|
345
|
-
# === report_that_a_string_must_be_assigned_first
|
346
|
-
# ========================================================================= #
|
347
|
-
def report_that_a_string_must_be_assigned_first
|
348
|
-
erev 'No sequence has been assigned yet. Please first "'+
|
349
|
-
sfancy('assign')+rev+'" a string.'
|
350
|
-
end
|
351
|
-
|
352
|
-
# ========================================================================= #
|
353
|
-
# === assign_sequence2
|
354
|
-
# ========================================================================= #
|
355
|
-
def assign_sequence2(i)
|
356
|
-
i = i.join(' ') if i.is_a? Array
|
357
|
-
@internal_hash[:sequence2] = Bioroebe::Sequence.new(i)
|
358
|
-
end
|
359
|
-
|
360
|
-
end; end
|