bioroebe 0.10.80 → 0.11.25
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- checksums.yaml +4 -4
- data/README.md +3117 -2645
- data/bioroebe.gemspec +3 -3
- data/doc/README.gen +3116 -2644
- data/doc/todo/bioroebe_todo.md +418 -387
- 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/colours_for_base/colours_for_base.rb +18 -8
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
- data/lib/bioroebe/base/commandline_application/misc.rb +18 -8
- data/lib/bioroebe/base/misc.rb +16 -0
- data/lib/bioroebe/base/prototype/misc.rb +1 -1
- data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
- data/lib/bioroebe/codons/show_codon_usage.rb +2 -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 +24 -4
- data/lib/bioroebe/constants/misc.rb +20 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -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/{shell/tk.rb → electron_microscopy/electron_microscopy_module.rb} +15 -10
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
- data/lib/bioroebe/genome/README.md +4 -0
- data/lib/bioroebe/genome/genome.rb +67 -0
- data/lib/bioroebe/gui/gtk +1 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
- data/lib/bioroebe/misc/ruler.rb +1 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
- data/lib/bioroebe/parsers/gff.rb +1 -9
- data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
- 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/open_in_browser.py +20 -0
- data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
- data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
- data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +34 -0
- data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
- data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
- data/lib/bioroebe/sequence/protein.rb +105 -3
- data/lib/bioroebe/sequence/sequence.rb +61 -2
- data/lib/bioroebe/shell/menu.rb +3752 -3667
- data/lib/bioroebe/shell/misc.rb +51 -4311
- data/lib/bioroebe/shell/readline/readline.rb +1 -1
- data/lib/bioroebe/shell/shell.rb +11199 -28
- data/lib/bioroebe/siRNA/siRNA.rb +81 -1
- data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
- 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/info/check_available.rb +15 -9
- data/lib/bioroebe/taxonomy/info/info.rb +17 -2
- data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
- data/lib/bioroebe/taxonomy/interactive.rb +139 -95
- 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/databases.rb +1 -1
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +101 -63
- data/lib/bioroebe/toplevel_methods/misc.rb +17 -16
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
- 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.rb +1 -9
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
- 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/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 +101 -52
- data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
- data/lib/bioroebe/yaml/genomes/README.md +3 -4
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
- metadata +33 -35
- data/doc/setup.rb +0 -1655
- data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
- 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/user_input.rb +0 -88
- data/lib/bioroebe/shell/xorg.rb +0 -45
@@ -11,7 +11,6 @@ module Bioroebe
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module EmbeddableInterface
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require 'bioroebe/sequence/reverse_complement.rb'
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require 'bioroebe/toplevel_methods/chunked_display.rb'
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require 'bioroebe/toplevel_methods/is_on_roebe.rb'
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require 'bioroebe/toplevel_methods/nucleotides.rb'
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@@ -126,7 +125,9 @@ module EmbeddableInterface
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ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE = %w(
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/blosum
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/compseq
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/codon_frequency_of_this_string
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/is_palindrome
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/frequency_per_thousand
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/n_stop_codons_in_this_sequence
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/to_aa
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/to_chunked
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)
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end
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# ========================================================================= #
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# === method_reverse_complement
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# ========================================================================= #
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def method_reverse_complement
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return_intro_for_reverse_complement_conversion+
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HtmlTags.p(
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'You can reverse complement a DNA sequence through this API.'
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)+
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HtmlTags.p(
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'Simply input the nucleotide String, such as "ATGCT", '\
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'without the "" quotes.'
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)+
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return_form_for_reverse_complement_action+
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hyperlink_paragraph
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end
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# ========================================================================= #
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# === Bioroebe::EmbeddableInterface.localhost_to_use?
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# ========================================================================= #
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"http://localhost:#{USE_THIS_PORT}/"
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end
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# ========================================================================= #
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# === return_form_for_reverse_complement_action
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# ========================================================================= #
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def return_form_for_reverse_complement_action(
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route_to_this_action = '/reverse_complement/'
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)
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'<form id="reverse_complement" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
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INPUT_TYPE_TEXT_AND_BR_TAG+
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return_default_submit_button+'
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</form>'
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end
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# ========================================================================= #
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# === return_sinatra_to_dna
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</form>'
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end
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# ========================================================================= #
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# === method_random_aminoacids
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# ========================================================================= #
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def method_random_aminoacids
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Cyberweb::HtmlTemplate[
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title: 'Random Aminoacids',
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body: return_header_random_aminoacids+
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HtmlTags.p(
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'This entry point can be used to "create" a random sequence '\
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'of amino acids. Simply input how many aminoacids to '\
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'create, as a <b>number</b>.')+
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footer
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].to_s
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end
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# ========================================================================= #
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# === return_header_random_aminoacids
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# ========================================================================= #
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def return_header_random_aminoacids
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HtmlTags.h1('Random aminoacids',
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css_style: 'margin-left:0.25em;')
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end
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# ========================================================================= #
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# === return_form_for_is_a_palindrome_action
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# ========================================================================= #
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</form>'
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end
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# ========================================================================= #
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# === method_reverse_complement
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# ========================================================================= #
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def method_reverse_complement
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return_intro_for_reverse_complement_conversion+
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HtmlTags.p(
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'You can reverse complement a DNA sequence through this API.'
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)+
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HtmlTags.p(
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'Simply input the nucleotide String, such as "ATGCT", '\
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'without the "" quotes.'
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)+
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return_form_for_reverse_complement_action+
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hyperlink_paragraph
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end
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# ========================================================================= #
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# === method_random_aminoacids
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# ========================================================================= #
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def method_random_aminoacids
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Cyberweb::HtmlTemplate[
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title: 'Random Aminoacids',
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body: return_header_random_aminoacids+
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HtmlTags.p(
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'This entry point can be used to "create" a random sequence '\
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'of amino acids. Simply input how many aminoacids to '\
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'create, as a <b>number</b>.')+
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footer
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].to_s
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end
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# ========================================================================= #
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# === return_header_random_aminoacids
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# ========================================================================= #
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def return_header_random_aminoacids
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HtmlTags.h1('Random aminoacids',
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css_style: 'margin-left:0.25em;')
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end
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# ========================================================================= #
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# === return_header_codon_frequency_of_this_string
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# ========================================================================= #
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def return_header_codon_frequency_of_this_string
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HtmlTags.h1('Codon frequence of this string',
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css_style: 'margin-left:0.25em;')
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end
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# ========================================================================= #
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# === return_form_for_reverse_complement_action
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# ========================================================================= #
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def return_form_for_reverse_complement_action(
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route_to_this_action = '/reverse_complement/'
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)
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'<form id="reverse_complement" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
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INPUT_TYPE_TEXT_AND_BR_TAG+
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return_default_submit_button+'
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</form>'
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end
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# ========================================================================= #
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# === return_form_for_codon_frequency_of_this_string
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# ========================================================================= #
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def return_form_for_codon_frequency_of_this_string(
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route_to_this_action = '/codon_frequency_of_this_string/'
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)
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'<form id="codon_frequency_of_this_string" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
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INPUT_TYPE_TEXT_AND_BR_TAG+
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return_default_submit_button+'
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</form>'
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end
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# ========================================================================= #
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# === method_codon_frequency_of_this_string
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# ========================================================================= #
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def method_codon_frequency_of_this_string
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Cyberweb::HtmlTemplate[
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title: 'Codon Frequence of this string',
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body: return_header_codon_frequency_of_this_string+
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HtmlTags.p(
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'This entry point can be used to show the codon frequency '\
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'of the given string.')+
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footer
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].to_s
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end
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# ========================================================================= #
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# === method_codon_frequency_per_thousand
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# ========================================================================= #
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def method_codon_frequency_per_thousand
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Cyberweb::HtmlTemplate[
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title: 'Codon Frequence per thousand',
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body: return_header_codon_frequency_of_this_string+
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HtmlTags.p(
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'This entry point can be used to show the codon frequency '\
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'of the given string.')+
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footer
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].to_s
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end
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end
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# =========================================================================== #
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