bioroebe 0.10.80 → 0.11.24
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- checksums.yaml +4 -4
- data/README.md +1204 -772
- data/bioroebe.gemspec +3 -3
- data/doc/README.gen +1203 -771
- data/doc/todo/bioroebe_todo.md +391 -365
- 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 +20 -1
- 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/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 +3451 -3366
- data/lib/bioroebe/shell/misc.rb +51 -4311
- data/lib/bioroebe/shell/readline/readline.rb +1 -1
- data/lib/bioroebe/shell/shell.rb +11192 -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 +32 -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
@@ -47,16 +47,25 @@ class Sinatra < ::Sinatra::Base
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Cyberweb.try_to_open_this_URL_via_the_browser(target, use_this_port) { :be_quiet }
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end
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# ========================================================================= #
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# === p
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# ========================================================================= #
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def p(
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i, hash = {}
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)
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return HtmlTags.p(i, hash)
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end
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# ========================================================================= #
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# === Convert into DNA (2 tag, second entry, reverse_complement tag)
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#
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# This method will convert RNA into DNA.
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#
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# http://localhost:
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# http://localhost:4568/reverse_complement
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#
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# Example:
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#
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# http://localhost:
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# http://localhost:4568/reverse_complement/ATGCUUUUUUUUUU
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#
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# ========================================================================= #
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get('/reverse_complement/*') {
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the_params = params['user_input']
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end
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the_params = the_params.strip.upcase if the_params
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if the_params.is_a? Array
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the_params = the_params.flatten.first
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end
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the_reverse_complement = ::Bioroebe.reverse_complement(the_params)
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if the_reverse_complement.is_a? Array
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the_reverse_complement = the_reverse_complement.first.to_s
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end
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the_result = ''.dup
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if the_params.empty?
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the_result
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the_result << return_intro_for_reverse_complement_conversion+
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p(
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'<b> Please input a DNA sequence which will be '\
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'reverse-complemented into DNA.</b>'
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)+
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return_paragraph_of_hyperlinks
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the_result << _+p(
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"The reverse complement of <b>5'-#{the_params.to_s}</b> is:"
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)
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the_result << p(
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"<b>5'-#{the_reverse_complement}</b>",
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css_style: 'margin:1em; font-size: larger; color: blueviolet'
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)
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end
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}
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# ========================================================================= #
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# ========================================================================= #
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get([
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'/to_aa_source'
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delete('/').to_sym
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file, line_number = ::Bioroebe.method(sanitized_URL_part).source_location
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if File.exist? file
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readlines = File.readlines(file)
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# =========================================================================== #
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# Example:
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#
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# =========================================================================== #
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get('/shuffleseq'){
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# ========================================================================= #
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# === /shuffleseq
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# ========================================================================= #
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['/shuffleseq'].each {|target|
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get(target) {
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Cyberweb::HtmlTemplate[
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title: 'Shuffleseq - Shuffle a sequence',
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body: '<pre>'+
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::Bioroebe.shuffleseq(method(:
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::Bioroebe.shuffleseq(method(:reverse_complement))+
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'</pre>'+
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footer
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].to_s
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# ========================================================================= #
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# ========================================================================= #
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get(target) {
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embeddable_interface?.method_random_aminoacids
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}
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}
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# ========================================================================= #
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# http://localhost:4568/reverse_complement_source
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# ========================================================================= #
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['/reverse_complement_source'].each {|target|
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get(target) {
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body = HtmlTags.p('The source is:')+
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'<pre>'+
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::Bioroebe.return_source_code_of_this_method(method(:reverse_complement))+
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'</pre>'+
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footer
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Cyberweb::HtmlTemplate[
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# Example:
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# =========================================================================== #
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get('/reverse_complement'){
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method_reverse_complement
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embeddable_interface?.method_reverse_complement
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# http://localhost:4568/n_stop_codons_in_this_sequence
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# http://localhost:4568/n_stop
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# =========================================================================== #
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%w(
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# ========================================================================= #
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# === /palindromes
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# http://localhost:4568/palindromes
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# ========================================================================= #
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get(target) {
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# ========================================================================= #
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# === view
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# ========================================================================= #
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get('/view') { # view tag
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# ========================================================================= #
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['/random_aminoacids_source'].each {|target|
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body = HtmlTags.p('The source is:')+
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'</pre>'+
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footer
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# ========================================================================= #
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# http://localhost:4568/random_aminoacids/33
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# ========================================================================= #
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['/random_aminoacids/*'].each {|target|
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get(target) {
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#
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# This method will try to discover palindromes.
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# This method will determine how many stop codons are in the given
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# sequence.
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#
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#
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# ========================================================================= #
|
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%w(
|
@@ -490,7 +498,7 @@ class Sinatra < ::Sinatra::Base
|
|
490
498
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}
|
491
499
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|
492
500
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# ========================================================================= #
|
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-
# http://localhost:
|
501
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+
# http://localhost:4568/is_palindrome
|
494
502
|
# ========================================================================= #
|
495
503
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get('/is_palindrome') {
|
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return_header_for_palindromes('Is palindrome')+
|
@@ -507,7 +515,7 @@ class Sinatra < ::Sinatra::Base
|
|
507
515
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#
|
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516
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# Example:
|
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517
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#
|
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-
# http://localhost:
|
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+
# http://localhost:4568/is_palindromes/ATTA
|
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519
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#
|
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520
|
# ========================================================================= #
|
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get('/is_palindrome/*') {
|
@@ -543,7 +551,7 @@ class Sinatra < ::Sinatra::Base
|
|
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551
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# ========================================================================= #
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# === /mirror_source
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#
|
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-
# http://localhost:
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+
# http://localhost:4568/mirror_source
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# ========================================================================= #
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get('/mirror_source'){
|
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file, line_number = ::Bioroebe.method(:mirror_repeat).source_location
|
@@ -564,9 +572,9 @@ class Sinatra < ::Sinatra::Base
|
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}
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# ========================================================================= #
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-
# http://localhost:
|
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-
# http://localhost:
|
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-
# http://localhost:
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+
# http://localhost:4568/chunked_display
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+
# http://localhost:4568/chunked
|
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+
# http://localhost:4568/upcase
|
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578
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# ========================================================================= #
|
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Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
|
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get(target) {
|
@@ -580,11 +588,11 @@ class Sinatra < ::Sinatra::Base
|
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#
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# Visit:
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#
|
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-
# http://localhost:
|
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+
# http://localhost:4568/compseq
|
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#
|
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# Example:
|
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#
|
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-
# http://localhost:
|
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+
# http://localhost:4568/compseq/ATGCUUUUUUUUUU
|
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|
#
|
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597
|
# ========================================================================= #
|
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get('/compseq/*') {
|
@@ -619,8 +627,8 @@ class Sinatra < ::Sinatra::Base
|
|
619
627
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}
|
620
628
|
|
621
629
|
# ========================================================================= #
|
622
|
-
# http://localhost:
|
623
|
-
# http://localhost:
|
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|
+
# http://localhost:4568/to_aa
|
631
|
+
# http://localhost:4568/to_aminoacids
|
624
632
|
# ========================================================================= #
|
625
633
|
Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.each {|target|
|
626
634
|
get(target) {
|
@@ -639,7 +647,7 @@ class Sinatra < ::Sinatra::Base
|
|
639
647
|
#
|
640
648
|
# Example:
|
641
649
|
#
|
642
|
-
# http://localhost:
|
650
|
+
# http://localhost:4568/mirror
|
643
651
|
# =========================================================================== #
|
644
652
|
get('/mirror'){
|
645
653
|
body = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
|
@@ -663,8 +671,8 @@ class Sinatra < ::Sinatra::Base
|
|
663
671
|
#
|
664
672
|
# Usage Examples:
|
665
673
|
#
|
666
|
-
# http://localhost:
|
667
|
-
# http://localhost:
|
674
|
+
# http://localhost:4568/to_dna
|
675
|
+
# http://localhost:4568/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
|
668
676
|
#
|
669
677
|
# =========================================================================== #
|
670
678
|
get('/to_dna'){
|
@@ -676,11 +684,11 @@ class Sinatra < ::Sinatra::Base
|
|
676
684
|
#
|
677
685
|
# This method will convert RNA into DNA.
|
678
686
|
#
|
679
|
-
# http://localhost:
|
687
|
+
# http://localhost:4568/to_dna
|
680
688
|
#
|
681
689
|
# Example:
|
682
690
|
#
|
683
|
-
# http://localhost:
|
691
|
+
# http://localhost:4568/to_dna/ATGCUUUUUUUUUU
|
684
692
|
#
|
685
693
|
# ========================================================================= #
|
686
694
|
get('/to_dna/*') {
|
@@ -722,11 +730,11 @@ class Sinatra < ::Sinatra::Base
|
|
722
730
|
#
|
723
731
|
# This method will convert RNA into DNA.
|
724
732
|
#
|
725
|
-
# http://localhost:
|
733
|
+
# http://localhost:4568/chunked
|
726
734
|
#
|
727
735
|
# Example:
|
728
736
|
#
|
729
|
-
# http://localhost:
|
737
|
+
# http://localhost:4568/chunked/ATGCUUUUUUUUUU
|
730
738
|
#
|
731
739
|
# ========================================================================= #
|
732
740
|
Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
|
@@ -765,7 +773,7 @@ class Sinatra < ::Sinatra::Base
|
|
765
773
|
#
|
766
774
|
# Example:
|
767
775
|
#
|
768
|
-
# http://localhost:
|
776
|
+
# http://localhost:4568/compseq
|
769
777
|
#
|
770
778
|
# =========================================================================== #
|
771
779
|
get('/compseq'){
|
@@ -820,8 +828,8 @@ class Sinatra < ::Sinatra::Base
|
|
820
828
|
#
|
821
829
|
# Examples:
|
822
830
|
#
|
823
|
-
# http://localhost:
|
824
|
-
# http://localhost:
|
831
|
+
# http://localhost:4568/to_aa/ATGGGGCCCGCGCCA
|
832
|
+
# http://localhost:4568/to_aa/GGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTG
|
825
833
|
#
|
826
834
|
# ========================================================================= #
|
827
835
|
Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.map {|entry| "#{entry}/*" }.each {|target|
|
@@ -872,7 +880,7 @@ class Sinatra < ::Sinatra::Base
|
|
872
880
|
#
|
873
881
|
# Example:
|
874
882
|
#
|
875
|
-
# http://localhost:
|
883
|
+
# http://localhost:4568/blosum
|
876
884
|
#
|
877
885
|
# =========================================================================== #
|
878
886
|
get('/blosum'){
|
@@ -898,11 +906,11 @@ class Sinatra < ::Sinatra::Base
|
|
898
906
|
#
|
899
907
|
# This method will convert RNA into DNA.
|
900
908
|
#
|
901
|
-
# http://localhost:
|
909
|
+
# http://localhost:4568/mirror
|
902
910
|
#
|
903
911
|
# Example:
|
904
912
|
#
|
905
|
-
# http://localhost:
|
913
|
+
# http://localhost:4568/mirror/ATGCUUUUUUUUUU
|
906
914
|
#
|
907
915
|
# ========================================================================= #
|
908
916
|
get('/mirror/*') {
|
@@ -942,7 +950,7 @@ class Sinatra < ::Sinatra::Base
|
|
942
950
|
# ========================================================================= #
|
943
951
|
# === /blosum_source
|
944
952
|
#
|
945
|
-
# http://localhost:
|
953
|
+
# http://localhost:4568/blosum_source
|
946
954
|
# ========================================================================= #
|
947
955
|
get('/blosum_source'){
|
948
956
|
file, line_number = ::Bioroebe.method(:blosum).source_location
|
@@ -967,11 +975,11 @@ class Sinatra < ::Sinatra::Base
|
|
967
975
|
#
|
968
976
|
# This method will show the blosum matrices.
|
969
977
|
#
|
970
|
-
# http://localhost:
|
978
|
+
# http://localhost:4568/blosum
|
971
979
|
#
|
972
980
|
# Example:
|
973
981
|
#
|
974
|
-
# http://localhost:
|
982
|
+
# http://localhost:4568/blosum/42
|
975
983
|
#
|
976
984
|
# ========================================================================= #
|
977
985
|
get('/blosum/*') {
|
@@ -997,6 +1005,114 @@ class Sinatra < ::Sinatra::Base
|
|
997
1005
|
the_result
|
998
1006
|
}
|
999
1007
|
|
1008
|
+
# ========================================================================= #
|
1009
|
+
# === /random_aminoacids
|
1010
|
+
#
|
1011
|
+
# http://localhost:4568/random_aminoacids
|
1012
|
+
# ========================================================================= #
|
1013
|
+
['/random_aminoacids'].each {|target|
|
1014
|
+
get(target) {
|
1015
|
+
embeddable_interface?.method_random_aminoacids
|
1016
|
+
}
|
1017
|
+
}
|
1018
|
+
|
1019
|
+
# ========================================================================= #
|
1020
|
+
# === /codon_frequency_of_this_string
|
1021
|
+
#
|
1022
|
+
# http://localhost:4568/codon_frequency_of_this_string
|
1023
|
+
# ========================================================================= #
|
1024
|
+
['/codon_frequency_of_this_string'].each {|target|
|
1025
|
+
get(target) {
|
1026
|
+
embeddable_interface?.method_codon_frequency_of_this_string
|
1027
|
+
}
|
1028
|
+
}
|
1029
|
+
|
1030
|
+
# ========================================================================= #
|
1031
|
+
# === Codon Frequencies
|
1032
|
+
#
|
1033
|
+
# Example:
|
1034
|
+
#
|
1035
|
+
# http://localhost:4568/codon_frequency_of_this_string/ATGCUUUUUUUUUU
|
1036
|
+
#
|
1037
|
+
# ========================================================================= #
|
1038
|
+
get('/codon_frequency_of_this_string/*') {
|
1039
|
+
the_params = params[:splat]
|
1040
|
+
if the_params.is_a? Array
|
1041
|
+
the_params = the_params.join(' ')
|
1042
|
+
end
|
1043
|
+
if params.has_key? 'user_input'
|
1044
|
+
the_params = params['user_input']
|
1045
|
+
end
|
1046
|
+
the_params = the_params.strip.upcase if the_params
|
1047
|
+
if the_params.is_a? Array
|
1048
|
+
the_params = the_params.flatten.first
|
1049
|
+
end
|
1050
|
+
the_result = ''.dup
|
1051
|
+
if the_params.empty?
|
1052
|
+
the_result << return_intro_for_reverse_complement_conversion+
|
1053
|
+
p(
|
1054
|
+
'<b> Please input a DNA sequence.'
|
1055
|
+
)+
|
1056
|
+
return_paragraph_of_hyperlinks
|
1057
|
+
else
|
1058
|
+
_ = embeddable_interface?.return_intro_for_reverse_complement_conversion
|
1059
|
+
the_result << p(
|
1060
|
+
Bioroebe.codon_frequency_of_this_string(the_params)
|
1061
|
+
)
|
1062
|
+
end
|
1063
|
+
the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
|
1064
|
+
the_result << embeddable_interface?.hyperlinks_paragraph
|
1065
|
+
the_result
|
1066
|
+
}
|
1067
|
+
# ========================================================================= #
|
1068
|
+
# === /codon_frequency_of_this_string
|
1069
|
+
#
|
1070
|
+
# http://localhost:4568/codon_frequency_of_this_string
|
1071
|
+
# ========================================================================= #
|
1072
|
+
['/codon_frequency_of_this_string'].each {|target|
|
1073
|
+
get(target) {
|
1074
|
+
embeddable_interface?.method_codon_frequency_of_this_string
|
1075
|
+
}
|
1076
|
+
}
|
1077
|
+
|
1078
|
+
# ========================================================================= #
|
1079
|
+
# === Codon Frequencies
|
1080
|
+
#
|
1081
|
+
# Example:
|
1082
|
+
#
|
1083
|
+
# http://localhost:4568/frequency_per_thousand/ATGCUUUUUUUUUU
|
1084
|
+
#
|
1085
|
+
# ========================================================================= #
|
1086
|
+
get('/frequency_per_thousand/*') {
|
1087
|
+
the_params = params[:splat]
|
1088
|
+
if the_params.is_a? Array
|
1089
|
+
the_params = the_params.join(' ')
|
1090
|
+
end
|
1091
|
+
if params.has_key? 'user_input'
|
1092
|
+
the_params = params['user_input']
|
1093
|
+
end
|
1094
|
+
the_params = the_params.strip.upcase if the_params
|
1095
|
+
if the_params.is_a? Array
|
1096
|
+
the_params = the_params.flatten.first
|
1097
|
+
end
|
1098
|
+
the_result = ''.dup
|
1099
|
+
if the_params.empty?
|
1100
|
+
the_result << return_intro_for_reverse_complement_conversion+
|
1101
|
+
p(
|
1102
|
+
'<b>Please input a DNA sequence.</b>'
|
1103
|
+
)+
|
1104
|
+
return_paragraph_of_hyperlinks
|
1105
|
+
else
|
1106
|
+
_ = embeddable_interface?.return_intro_for_reverse_complement_conversion
|
1107
|
+
the_result << HtmlTags.pre(
|
1108
|
+
Bioroebe.frequency_per_thousand(the_params)
|
1109
|
+
)
|
1110
|
+
end
|
1111
|
+
the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
|
1112
|
+
the_result << embeddable_interface?.hyperlinks_paragraph
|
1113
|
+
the_result
|
1114
|
+
}
|
1115
|
+
|
1000
1116
|
end
|
1001
1117
|
|
1002
1118
|
# =========================================================================== #
|
@@ -1,5 +1,5 @@
|
|
1
1
|
# =========================================================================== #
|
2
|
-
#
|
2
|
+
# === amino_acids_long_name_to_one_letter.yml
|
3
3
|
#
|
4
4
|
# In code this will be:
|
5
5
|
#
|
@@ -7,7 +7,7 @@
|
|
7
7
|
#
|
8
8
|
# Note that the file here stores both the english and the german names.
|
9
9
|
# =========================================================================== #
|
10
|
-
#
|
10
|
+
# x = YAML.load_file(Bioroebe.file_amino_acids_long_name_to_one_letter)
|
11
11
|
# =========================================================================== #
|
12
12
|
|
13
13
|
# =========================================================================== #
|
@@ -1 +1 @@
|
|
1
|
-
firefox # palemoon
|
1
|
+
firefox # chromium # palemoon
|
@@ -1,7 +1,6 @@
|
|
1
|
-
This directory is primarily intended to provide some links to
|
2
|
-
|
3
|
-
|
4
|
-
and so forth.
|
1
|
+
This directory is primarily intended to provide some links to external
|
2
|
+
resources - in particular genome information, the latest revisions to
|
3
|
+
a genome, where it can be downloaded, and so forth.
|
5
4
|
|
6
5
|
As such we will focus on model organisms primarily.
|
7
6
|
|
@@ -49,7 +49,7 @@ AccII: CGCG 2
|
|
49
49
|
AccIII: TCCGGA 1
|
50
50
|
Acc16I: TGCGCA 3
|
51
51
|
Acc65I: GGTACC 1
|
52
|
-
Acc113I: AGTACT 3
|
52
|
+
Acc113I: AGTACT 3 # blunt end
|
53
53
|
AccB1I: GGYRCC 1
|
54
54
|
AccB7I: CCANNNNNTGG 7
|
55
55
|
AclI: AACGTT 2
|
@@ -108,11 +108,11 @@ BalI: TGGCCA 3
|
|
108
108
|
BamHI: GGATCC 1
|
109
109
|
BanI: GGYRCC 1
|
110
110
|
BanII: GRGCYC 5
|
111
|
-
BanIII: ATCGAT 2
|
111
|
+
BanIII: ATCGAT 2 # At CG.
|
112
112
|
BbeI: GGCGCC 5
|
113
113
|
BbrPI: CACGTG 3
|
114
114
|
BbuI: GCATGC 5
|
115
|
-
Bbv12I: GWGCWC
|
115
|
+
Bbv12I: GWGCWC 5
|
116
116
|
BclI: TGATCA 1
|
117
117
|
BcnI: CCSGG 2
|
118
118
|
BcoI: CYCGRG 1
|