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
@@ -1,281 +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/chop_and_cut.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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# === chop (chop tag)
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#
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# We use this method to get rid of some nucleotides, from the 3'
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# end of a nucleotide sequence (aka the "right hand side" of it) by
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# default.
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#
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# The first argument to this method tells us how many nucleotides are
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# to be removed.
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#
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# The second argument determines whether to chop from the right side
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# (the 3' side) or from the left side (the 5' side).
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# ========================================================================= #
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def chop(
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i = 1,
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chop_from_left_or_right_hand_side = :default # The default is the 3' end.
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) # Default will be to chop off one nucleotide.
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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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i = i.first if i.is_a? Array
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if i == '?'
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e 'chop allows us to remove nucleotides from the main sequence.'
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return
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end
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i = 1 if i.nil? # Assign to the default then.
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i = i.to_i # Need a number past this point.
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if i == 0
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erev 'Please add a number, such as 1, or any other value.'
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else
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case chop_from_left_or_right_hand_side
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# ===================================================================== #
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# === :right
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# ===================================================================== #
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when :right,
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:default
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which_end = "3'"
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# ===================================================================== #
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# === :left
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# ===================================================================== #
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when :left
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which_end = "5'"
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end
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if dna_sequence_object?.size > 0
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erev "We will now remove some characters (#{simp(i.to_s)}#{rev}"\
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") from the #{which_end} end of our main string."
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end
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if dna_sequence_object?.size == 0
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erev 'Can not remove anything as the sequence is empty.'
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elsif i > dna_sequence_object?.size
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erev 'We can not remove that many characters, thus we will'
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erev 'simply remove all characters now.'
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reset_string
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else
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# =================================================================== #
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# Finally do the manipulation. We need to honour from which
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# side we will be operating on.
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# =================================================================== #
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case chop_from_left_or_right_hand_side
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# =================================================================== #
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# === :default
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# =================================================================== #
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when :default,
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:right
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# ================================================================= #
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# We also store the chopped-away sequence, but we have to be
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# mindful here since the sequence-object counts the nucleotides
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# differently than ruby counts Arrays.
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# ================================================================= #
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@internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[(-i)+1, i-1].dup
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seq_object?[-i, i] = ''
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# =================================================================== #
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# === :left
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# =================================================================== #
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when :left
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@internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, i].dup
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seq_object?[0, i+1] = ''
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end
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end
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unless dna_sequence_object?.size == 0
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erev "#{rev}The new length of the main string is now: "\
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"#{simp(dna_sequence_object?.size.to_s)}#{rev}."
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end
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show_dna_sequence
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end
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end; alias remove_n_nucleotides chop # === remove_n_nucleotides
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# ========================================================================= #
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# === cut_sequence_in_slices_of
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#
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# This method cuts the sequence into slices of n, where n is the
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# argument to this method.
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#
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# So if you input 10 as argument, then we will put the nucleotides
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# into chunks of 10 nucleotides per row.
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#
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# Usage examples:
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#
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# cut_sequence_in_slices_of 5
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# cut_sequence_in_slices_of 6
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# cut_sequence_in_slices_of 7
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#
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# ========================================================================= #
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def cut_sequence_in_slices_of(threshold = '9')
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_ = dna_sequence_object?
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matches = _.scan(/.{#{threshold}}/)
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matches.each {|entry|
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erev ' '+entry
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}
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end
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# ========================================================================= #
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# === left_chop
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# ========================================================================= #
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def left_chop(i)
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chop(i, :left)
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end
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# ========================================================================= #
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# === cut_at
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#
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# Use this method to chop off or rather cut at a DNA sequence.
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# ========================================================================= #
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def cut_at(
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this_sequence = 'GAATTC',
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be_verbose = true
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)
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main_sequence = dna_sequence_object?
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this_sequence = this_sequence.join.strip if this_sequence.is_a? Array
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if be_verbose
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erev "We will chop away (at) the sequence #{simp(this_sequence)}#{rev}."
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erev 'Note that the sequences all originated from the larger '\
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'parent sequence.'
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end
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results = main_sequence.split(/#{this_sequence}/)
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results.each {|sequence|
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_ = properly_spaced_dna(sequence)
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_ << (' ('+sequence.size.to_s+' nucleotides)').rjust(110 - sequence.size)
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erev _
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}
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end
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# ========================================================================= #
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# === restore_the_last_chop_operation
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#
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# This method will "restore" the last chop operation.
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#
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# Presently it will only append onto the 3' area but in the future
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# this may change, depending on whether we will store the position
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# as well.
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# ========================================================================= #
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def restore_the_last_chop_operation
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if @internal_hash[:array_these_sequences_were_chopped_away].empty?
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erev 'Can not restore the last chop-operation as we have not yet'
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erev 'chopped away any nucleotide from the main sequence.'
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else
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this_sequence = @internal_hash[:array_these_sequences_were_chopped_away].pop
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erev 'Now adding the sequence '+
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format_this_nucleotide_sequence(
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this_sequence
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)
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erev 'to our main sequence.'
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main_sequence?.append(this_sequence)
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end
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end
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# ========================================================================= #
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# === chop_to
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#
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# This method will chop up to the first occurence of the given input
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# sequence.
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#
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# If the given input sequence can not be found, no change is made.
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# ========================================================================= #
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def chop_to(i)
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if i.is_a? Array
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i = i.first
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end
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case i
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when 'start'
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i = 'ATG'
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end
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_ = nucleotide_sequence?
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if i.include? 'U'
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# ===================================================================== #
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# Convert Uracil to Thymine next.
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# ===================================================================== #
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erev "The given input sequence includes at the least one "\
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"#{sfancy('U')}#{rev}, which we will convert to #{sfancy('T')}#{rev}."
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i.tr!('U','T')
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end
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if _.include? i
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# ===================================================================== #
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# Ok, we found the search sequence, so now we can chop off the
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# unnecessary sequences.
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# ===================================================================== #
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position = _.index(i)
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erev "Chopping away #{sfancy(position.to_s)}#{rev} nucleotides from "\
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"the left-hand side (5' end) next."
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@internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, position+1]
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seq_object?[0, position+1] = ''
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show_dna_sequence
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else
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erev 'No modification can be made as our target nucleotide sequence'
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erev "does not include the given search string #{sfancy(i)}."
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end
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end
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# ========================================================================= #
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# === cut (cut tag)
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#
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# This method will cut away some part from the DNA string.
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# ========================================================================= #
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def cut(i)
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i = i.to_i
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@sequence[-i,i] = ''
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show_dna_sequence
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end
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# ========================================================================= #
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# === cutseq
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#
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# This can be used to modify the sequence object. It will cut some
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# segment out from the nucleotide.
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#
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# Usage examples:
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#
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# random 30; cutseq 5 8
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# random 30; cutseq 5-8
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#
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# ========================================================================= #
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def cutseq(i = [1,3])
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if i.is_a? Array
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if i.size == 1 and i.first.is_a? String and i.first.include?('-')
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i = [i.first.split('-')].flatten
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end
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if i.empty? # In this case we will ask the user for input.
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erev 'No argument was provided. Please input the start nucleotide position next:'
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start_position = $stdin.gets.chomp.to_i
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erev 'Next, input the end nucleotide position:'
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end_position = $stdin.gets.chomp
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elsif i.size > 1
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start_position = i.first
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end_position = i.last
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end
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end
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# ======================================================================= #
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# === Handle +3 relational position given
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# ======================================================================= #
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if end_position.is_a? String and end_position.include?('+')
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end_position = start_position + end_position.delete('+').to_i
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end
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n_nucleotides_will_be_deleted = (end_position.to_i - start_position.to_i)+1
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# ======================================================================= #
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# Notify the user what we will do next.
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# ======================================================================= #
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erev 'Next cutting away '+simp(n_nucleotides_will_be_deleted.to_s)+
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rev+' nucleotides.'
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sequence_object?[start_position, end_position] = ''
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end
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# ========================================================================= #
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# === cut_with_enzyme
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# ========================================================================= #
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def cut_with_enzyme(i)
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i = i.join(' ').strip if i.is_a? Array
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pp sequence_object?.cut_with_enzyme(i)
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end
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end; end
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@@ -1,166 +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/constants.rb'
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# =========================================================================== #
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module Bioroebe # === Bioroebe::Shell
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class Shell < ::Bioroebe::CommandlineApplication
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# ========================================================================= #
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# Right now we will only add the chemistry_paradise gem, if it is available.
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# ========================================================================= #
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array_failsave_requires = %w(
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chemistry_paradise
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)
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array_failsave_requires.each {|project|
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begin
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require project
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rescue LoadError; end # Silent rescue.
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}
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# ========================================================================= #
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# === NAMESPACE
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# ========================================================================= #
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NAMESPACE = inspect
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# ========================================================================= #
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# === TRUNCATE_AT_N_ELEMENTS
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#
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# If we display nucleotide strings, then by default, these may be very
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# long. So the following constant will act as a threshold.
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# ========================================================================= #
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TRUNCATE_AT_N_ELEMENTS = 2000
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# ========================================================================= #
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# === VALID_WAYS_TO_EXIT
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#
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# All ways to exit will be recorded here.
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#
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# If you need to use more ways, simply append to this Array.
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#
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# This constant may have to be moved into the bio-shell part eventually.
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# ========================================================================= #
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45
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VALID_WAYS_TO_EXIT = %w(
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quit q exit qq :q qt
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bye
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rda
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r2
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tq
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sq
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exit_program
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exitprogram
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)
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56
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# ========================================================================= #
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57
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# === DEFAULT_PADDING
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58
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# ========================================================================= #
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59
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DEFAULT_PADDING = ' ' # This is left-padding.
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60
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-
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61
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# ========================================================================= #
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62
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# === MAIN_EDITOR
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63
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#
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64
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# Which editor to use.
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# ========================================================================= #
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66
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if ENV['IS_ROEBE']
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MAIN_EDITOR = 'bluefish'
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else # else assume that we may be on windows.
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MAIN_EDITOR = 'notepad++.exe'
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end; MY_EDITOR = MAIN_EDITOR # === MY_EDITOR
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-
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72
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# ========================================================================= #
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# === HOME_DIRECTORY_OF_USER_X
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#
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# Hardcoded path - only useful on my home setup, though.
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# ========================================================================= #
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HOME_DIRECTORY_OF_USER_X = '/home/x/'
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# ========================================================================= #
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# === RUBY_SRC
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#
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# Hardcoded. This is only useful on my home system.
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83
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# ========================================================================= #
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84
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if ENV['RSRC']
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RUBY_SRC = "#{ENV['RSRC']}/"
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else
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|
-
RUBY_SRC = "#{HOME_DIRECTORY_OF_USER_X}programming/ruby/src/"
|
88
|
-
end
|
89
|
-
|
90
|
-
# ========================================================================= #
|
91
|
-
# === RUBY_BIOROEBE
|
92
|
-
#
|
93
|
-
# This allows a user to designate another home directory.
|
94
|
-
# ========================================================================= #
|
95
|
-
if ENV['RUBY_BIOROEBE']
|
96
|
-
BIOROEBE = ENV['RUBY_BIOROEBE'].to_s
|
97
|
-
else
|
98
|
-
BIOROEBE = ENV['HOME']
|
99
|
-
end
|
100
|
-
|
101
|
-
# ========================================================================= #
|
102
|
-
# === BIOSHELL_SAVE_FILE
|
103
|
-
#
|
104
|
-
# Designate the default location for the save-file, a markdown file.
|
105
|
-
# ========================================================================= #
|
106
|
-
if Dir.exist? ::Bioroebe.log_dir?
|
107
|
-
BIOSHELL_SAVE_FILE = "#{::Bioroebe.log_dir?}shell_file.md"
|
108
|
-
else
|
109
|
-
BIOSHELL_SAVE_FILE = '/home/Temp/bioroebe/shell_file.md'
|
110
|
-
end
|
111
|
-
|
112
|
-
# ========================================================================= #
|
113
|
-
# === HOME_DIR
|
114
|
-
#
|
115
|
-
# This probably is not used a lot anymore these days.
|
116
|
-
# ========================================================================= #
|
117
|
-
if RUBY_SRC # This is valid at home.
|
118
|
-
HOME_DIR = "#{ENV['RSRC']}/bioroebe/lib/bioroebe/"
|
119
|
-
else
|
120
|
-
begin
|
121
|
-
home_dir = File.expand_path('~')
|
122
|
-
rescue Exception
|
123
|
-
home_dir = '/root/'
|
124
|
-
end
|
125
|
-
HOME_DIR = home_dir+'.gem/gems/bioroebe-'+
|
126
|
-
Bioroebe.version?.to_s+'/lib/bioroebe/'
|
127
|
-
end
|
128
|
-
|
129
|
-
require 'bioroebe/project/project.rb'
|
130
|
-
# ========================================================================= #
|
131
|
-
# === FILE_USE_SILENT_STARTUP
|
132
|
-
# ========================================================================= #
|
133
|
-
FILE_USE_SILENT_STARTUP =
|
134
|
-
"#{::Bioroebe.project_base_directory?}shell/configuration/use_silent_startup.yml"
|
135
|
-
|
136
|
-
# ========================================================================= #
|
137
|
-
# === SHALL_WE_DEBUG
|
138
|
-
# ========================================================================= #
|
139
|
-
SHALL_WE_DEBUG = false
|
140
|
-
|
141
|
-
_ = ::Bioroebe.project_yaml_directory?+
|
142
|
-
'default_dna_input.yml' # cat $RUBY_BIO/YAML/default_dna_input.yml
|
143
|
-
# ========================================================================= #
|
144
|
-
# === DEFAULT_DNA_INPUT_YAML_FILE
|
145
|
-
# ========================================================================= #
|
146
|
-
DEFAULT_DNA_INPUT_YAML_FILE = YAML.load_file(_) if File.exist? _
|
147
|
-
|
148
|
-
require 'bioroebe/toplevel_methods/log_directory.rb' # ← Required for: Bioroebe.store_here?
|
149
|
-
# ========================================================================= #
|
150
|
-
# === store_here?
|
151
|
-
#
|
152
|
-
# Where to store output generated by BioRoebe. Should point to a
|
153
|
-
# locally existing directory.
|
154
|
-
# ========================================================================= #
|
155
|
-
def store_here?
|
156
|
-
::Bioroebe.store_here?
|
157
|
-
end
|
158
|
-
|
159
|
-
# ========================================================================= #
|
160
|
-
# === show_log_dir
|
161
|
-
# ========================================================================= #
|
162
|
-
def show_log_dir
|
163
|
-
e ::Bioroebe.log_dir?
|
164
|
-
end
|
165
|
-
|
166
|
-
end; end
|