Top Level Namespace

Includes:: Bioroebe, Bioroebe::EmbeddableInterface, Bioroebe::InternalHashModule, Bioroebe::Postgresql, Bioroebe::RestrictionEnzymes::Statistics, Bioroebe::Taxonomy

Defined Under Namespace

Modules: Bioroebe

Constant Summary

Constants included from Bioroebe::EmbeddableInterface

Bioroebe::EmbeddableInterface::ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE, Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY, Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES, Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION, Bioroebe::EmbeddableInterface::BODY_CSS_STYLE, Bioroebe::EmbeddableInterface::CSS_STYLE_FOR_THE_FORMS, Bioroebe::EmbeddableInterface::INPUT_TYPE_TEXT_AND_BR_TAG, Bioroebe::EmbeddableInterface::TITLE, Bioroebe::EmbeddableInterface::TOP_LOGO_IMAGE, Bioroebe::EmbeddableInterface::USE_THESE_CSS_RULES_FOR_THE_WHOLE_WEBPAGE, Bioroebe::EmbeddableInterface::USE_THIS_PORT

Constants included from Bioroebe::Taxonomy

Bioroebe::Taxonomy::PROJECT_YAML_DIR

Constants included from Bioroebe::Taxonomy::Constants

Bioroebe::Taxonomy::Constants::AA_DIR, Bioroebe::Taxonomy::Constants::ARRAY_PROJECT_FILES, Bioroebe::Taxonomy::Constants::Archaea_Taxonomy_ID, Bioroebe::Taxonomy::Constants::BASE, Bioroebe::Taxonomy::Constants::BASE_URL, Bioroebe::Taxonomy::Constants::BE_VERBOSE, Bioroebe::Taxonomy::Constants::Bacteria_Taxonomy_ID, Bioroebe::Taxonomy::Constants::CITATIONS, Bioroebe::Taxonomy::Constants::CURATED_DIR, Bioroebe::Taxonomy::Constants::DATA_DIR, Bioroebe::Taxonomy::Constants::DELNODES, Bioroebe::Taxonomy::Constants::DIVISION, Bioroebe::Taxonomy::Constants::Eukaryota_Taxonomy_ID, Bioroebe::Taxonomy::Constants::FILE_USE_THIS_DATABASE, Bioroebe::Taxonomy::Constants::GEM_DIR, Bioroebe::Taxonomy::Constants::GENCODE, Bioroebe::Taxonomy::Constants::INCOMING_DIR, Bioroebe::Taxonomy::Constants::INFO_DIR, Bioroebe::Taxonomy::Constants::LAST_INTERACTIVE_COMMAND, Bioroebe::Taxonomy::Constants::LOCALOME_DIR, Bioroebe::Taxonomy::Constants::LOCAL_MIRROR, Bioroebe::Taxonomy::Constants::MERGED, Bioroebe::Taxonomy::Constants::MODULE_PATH, Bioroebe::Taxonomy::Constants::NAMES, Bioroebe::Taxonomy::Constants::NAMES_SQL, Bioroebe::Taxonomy::Constants::NCBI_BASE, Bioroebe::Taxonomy::Constants::NODES, Bioroebe::Taxonomy::Constants::NODES_SQL, Bioroebe::Taxonomy::Constants::NT_DIR, Bioroebe::Taxonomy::Constants::POSTGRESQL_QUERY_SIZE, Bioroebe::Taxonomy::Constants::POSTGRE_LOGIN_COMMAND, Bioroebe::Taxonomy::Constants::PROJECT_DOC_DIR, Bioroebe::Taxonomy::Constants::SEQUENCES_DIR, Bioroebe::Taxonomy::Constants::SHARED_HOME, Bioroebe::Taxonomy::Constants::TAXONOMY_BROWSER, Bioroebe::Taxonomy::Constants::TEMP_DIR, Bioroebe::Taxonomy::Constants::TEST_DIR, Bioroebe::Taxonomy::Constants::TMP_DIR, Bioroebe::Taxonomy::Constants::URL1

Constants included from Bioroebe::Postgresql

Bioroebe::Postgresql::DROP_TABLE_FASTA, Bioroebe::Postgresql::POSTGRE_DBNAME, Bioroebe::Postgresql::POSTGRE_DROP_FASTA_COMMAND, Bioroebe::Postgresql::POSTGRE_DROP_NAMES_COMMAND, Bioroebe::Postgresql::POSTGRE_DROP_NODES_COMMAND, Bioroebe::Postgresql::POSTGRE_EXTRA_FLAGS, Bioroebe::Postgresql::POSTGRE_HOST, Bioroebe::Postgresql::POSTGRE_LOGIN_COMMAND, Bioroebe::Postgresql::POSTGRE_LOGIN_COMMAND_HOME, Bioroebe::Postgresql::POSTGRE_LOGIN_COMMAND_NO_HEADERS, Bioroebe::Postgresql::POSTGRE_PASSWORD, Bioroebe::Postgresql::POSTGRE_PORT, Bioroebe::Postgresql::POSTGRE_USERNAME

Constants included from Bioroebe

Bioroebe::ALLOWED_RNA_NUCLEOTIDES, Bioroebe::AMINOACIDS_DIRECTORY, Bioroebe::AMINOACID_FAMILIES, Bioroebe::AMINO_ACIDS, Bioroebe::AMINO_ACIDS_AVERAGE_MASS_TABLE, Bioroebe::AMINO_ACIDS_AVERAGE_MONOISOTOPIC_TABLE, Bioroebe::AMINO_ACIDS_ENGLISH, Bioroebe::AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER, Bioroebe::AMINO_ACIDS_MASS_TABLE, Bioroebe::AMINO_ACIDS_MOLECULAR_FORMULA, Bioroebe::AMINO_ACIDS_RESTE, Bioroebe::AMINO_ACIDS_THREE_TO_ONE, Bioroebe::ARRAY_AMINOACIDS_THAT_CAN_BE_PHOSPHORYLATED, Bioroebe::ARRAY_AMINO_ACIDS_ALPHABET, Bioroebe::ARRAY_NLS_SEQUENCES, Bioroebe::ARRAY_REGISTERED_ACTIONS, Bioroebe::ARRAY_VALID_DNA_SEQUENCES, Bioroebe::AUTOGENERATED_SQL_FILES_DIR, Bioroebe::Aminoacids, Bioroebe::BE_VERBOSE, Bioroebe::BIOROEBE_AT_HOME, Bioroebe::BIOROEBE_YAML_AMINOACIDS_DIRECTORY, Bioroebe::BLOSUM_DIRECTORY, Bioroebe::CALCULATE_DIRECTORY, Bioroebe::CLEAVE_AND_DIGEST_DIRECTORY, Bioroebe::CODONS_DIRECTORY, Bioroebe::CODON_TABLES_DIRECTORY, Bioroebe::CODON_TABLES_DIRECTORY_FREQUENCY, Bioroebe::CONFIGURATION_DIRECTORY, Bioroebe::COUNT_DIRECTORY, Bioroebe::DEFAULT_DNA_SEQUENCE, Bioroebe::DEFAULT_LENGTH_FOR_DNA, Bioroebe::DIRECTORY_CODON_TABLES_FREQUENCIES, Bioroebe::DNA_NUCLEOTIDES, Bioroebe::DOTPLOTS_DIRECTORY, Bioroebe::ELECTRON_MICROSCOPY_DIRECTORY, Bioroebe::EMAIL, Bioroebe::ENGLISH_LONG_NAMES_FOR_THE_AMINO_ACIDS, Bioroebe::ENZYMES_DIRECTORY, Bioroebe::FASTA_AND_FASTQ_DIRECTORY, Bioroebe::FASTA_ENTRIES, Bioroebe::FIELD_TERMINATOR, Bioroebe::FILE_AMINOACIDS_MOLECULAR_FORMULA, Bioroebe::FILE_AMINOACIDS_THREE_TO_ONE, Bioroebe::FILE_AMINO_ACIDS, Bioroebe::FILE_AMINO_ACIDS_ABBREVIATIONS, Bioroebe::FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE, Bioroebe::FILE_AMINO_ACIDS_ENGLISH, Bioroebe::FILE_AMINO_ACIDS_FREQUENCY, Bioroebe::FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER, Bioroebe::FILE_AMINO_ACIDS_MASS_TABLE, Bioroebe::FILE_AMINO_ACIDS_MOLECULAR_FORMULA, Bioroebe::FILE_AMINO_ACIDS_RESTE_YAML, Bioroebe::FILE_AMINO_ACIDS_THREE_TO_ONE, Bioroebe::FILE_BIO_LANG, Bioroebe::FILE_BLOSUM45, Bioroebe::FILE_BLOSUM50, Bioroebe::FILE_BLOSUM62, Bioroebe::FILE_BLOSUM80, Bioroebe::FILE_BLOSUM90, Bioroebe::FILE_BLOSUM_MATRIX, Bioroebe::FILE_BROWSER, Bioroebe::FILE_CHROMOSOME_NUMBERS, Bioroebe::FILE_COLOURIZE_FASTA_SEQUENCES, Bioroebe::FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS, Bioroebe::FILE_EXPAND_CD_ALIASES, Bioroebe::FILE_GFP_SEQUENCE, Bioroebe::FILE_HYDROPATHY_TABLE, Bioroebe::FILE_NUCLEAR_LOCALIZATION_SEQUENCES, Bioroebe::FILE_NUCLEOTIDES, Bioroebe::FILE_NUCLEOTIDES_WEIGHT, Bioroebe::FILE_RESTRICTION_ENZYMES, Bioroebe::FILE_WEIGHT_OF_COMMON_PROTEINS, Bioroebe::FTP_NCBI_TAXONOMY_DATABASE, Bioroebe::Fasta, Bioroebe::HASH_DNA_NUCLEOTIDES, Bioroebe::HOME_DIRECTORY_OF_USER_X, Bioroebe::HYDROPATHY_TABLE, Bioroebe::LAST_UPDATE, Bioroebe::LOCALHOST, Bioroebe::LOCAL_DIRECTORY_FOR_UNIPROT, Bioroebe::MAIN_DELIMITER, Bioroebe::N, Bioroebe::NAMES_ENTRIES, Bioroebe::NAME_OF_BIO_SHELL, Bioroebe::NCBI_GENE, Bioroebe::NCBI_NUCCORE, Bioroebe::NODES_ENTRIES, Bioroebe::NUCLEAR_LOCALIZATION_SEQUENCES, Bioroebe::NUCLEOTIDES, Bioroebe::NUCLEOTIDES_DIRECTORY, Bioroebe::PALINDROMES_DIRECTORY, Bioroebe::PARSERS_DIRECTORY, Bioroebe::PATHWAYS_DIRECTORY, Bioroebe::PATH_TO_THE_RELION_BINARY, Bioroebe::PATTERN_DIRECTORY, Bioroebe::PDB_DIRECTORY, Bioroebe::POSSIBLE_AMINO_ACIDS, Bioroebe::POSSIBLE_DNA_NUCLEOTIDES, Bioroebe::POSSIBLE_RNA_NUCLEOTIDES, Bioroebe::ProteinToDNA, Bioroebe::R, Bioroebe::REGEX_FOR_N_GLYCOSYLATION_PATTERN, Bioroebe::REGEX_PROSITE_FOR_ANY_AMINOACID, Bioroebe::RNA_NUCLEOTIDES, Bioroebe::ROW_TERMINATOR, Bioroebe::RUBY_SRC, Bioroebe::SEQUENCE_DIRECTORY, Bioroebe::SHALL_WE_LOG_LAST_UPDATE, Bioroebe::STOP_CODONS, Bioroebe::STRING_MATCHING_DIRECTORY, Bioroebe::Seq, Bioroebe::TABULATOR, Bioroebe::TOKEN, Bioroebe::TOPLEVEL_METHODS_DIRECTORY, Bioroebe::TWENTY_CANONICAL_AMINOACIDS, Bioroebe::UNICODE_HORIZONTAL_BAR, Bioroebe::URL_TO_TAXONOMY_ARCHIVE, Bioroebe::URL_TO_THE_DOCUMENTATION, Bioroebe::USERS_X, Bioroebe::USE_THIS_BROWSER, Bioroebe::USE_THIS_COLOUR_FOR_DNA, Bioroebe::USE_THIS_ENCODING, Bioroebe::UTF_ENCODING, Bioroebe::VALID_WAYS_TO_EXIT, Bioroebe::VERSION, Bioroebe::VERTICAL_UNICODE_BAR

Instance Method Summary collapse

#Bioroebe(i, &block) ⇒ Object

# === Bioroebe().

Methods included from Bioroebe::InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from Bioroebe::RestrictionEnzymes::Statistics

Methods included from Bioroebe::EmbeddableInterface

#erev, localhost_to_use?, #method_codon_frequency_of_this_string, #method_codon_frequency_per_thousand, #method_random_aminoacids, #method_reverse_complement, #method_shuffleseq, #not_yet_implemented, #return_default_submit_button, #return_explanation_of_how_to_use_the_aminoacid_conversion, #return_form_for_blosum_action, #return_form_for_codon_frequency_of_this_string, #return_form_for_compseq_action, #return_form_for_is_a_palindrome_action, #return_form_for_mirror_repeat_action, #return_form_for_n_stop_codons_in_this_sequence, #return_form_for_palindromes_action, #return_form_for_reverse_complement_action, #return_form_for_shuffleseq_action, #return_form_for_to_aa_action, #return_form_for_to_dna_action, #return_header_codon_frequency_of_this_string, #return_header_for_palindromes, #return_header_random_aminoacids, #return_header_to_aminoacid_conversion, #return_header_to_chunked_display, #return_index_of_hyperlinks, #return_intro_for_blosum, #return_intro_for_compseq, #return_intro_for_mirror_repeat_conversion, #return_intro_for_n_stop_codons_in_this_sequence, #return_intro_for_reverse_complement_conversion, #return_intro_for_shuffleseq, #return_intro_for_to_dna_conversion, #return_paragraph_of_hyperlinks, #return_sinatra_method_for_compseq, #return_sinatra_to_chunked, #return_sinatra_to_chunked_with_arguments, #return_sinatra_to_dna, #return_sinatra_to_dna_with_arguments, #return_sinatra_to_rna_with_arguments, #return_view_string, routes?, #title?

Methods included from Bioroebe::Taxonomy

#array_size?, be_verbose?, cd, #citations?, #clean, cleanup, #delnodes?, #division?, download_directory?, e, #edit, #edit_gemspec, #edit_instructions, #edit_password, #edit_shared_code_file, #edit_taxonomy, enable_colours, ensure_that_temp_dir_exists, #find_highest_entries_in_sql, #gencode?, #generate_html_links_for, #get_id_of, #get_parent_id_of, #get_scientific_name_of, interactive, load, #merged?, #names?, #nodes?, #pad, #pad_properly, #pad_sql, project_base_dir?, #project_base_dir?, project_yaml_dir?, #remove_delimiter, report_n_species, #return_current_hours_minutes_seconds, #return_full_lineage_of, save_into_which_file?, save_when_we_last_updated_the_database, #search_id, show_current_time_and_date, #show_current_time_and_date, #show_help, show_remote_urls_to_the_NCBI_taxonomy_webpage, #split, status, status?, taxonomy_download_directory?, #test, #to_utf, update, use_colours?, #verify_proper_sql_structures

Methods included from Bioroebe::Taxonomy::Shared

be_quiet, #be_verbose?, be_verbose?, #cd, #edit_login_file, #eliminate_tabulator, #ensure_that_download_dir_exists, #ensure_that_temp_dir_exists, #mkdir, #readlines, #set_pgpassword, #show_password, #show_time_now, #split_at, #split_at_tabulator, #tokenize

Methods included from Bioroebe::Taxonomy::Constants

#info_dir?, #work_directory?

Methods included from Bioroebe

#Sequence, [], ad_hoc_task, align_this_string_via_multiple_sequence_alignment, #all_aminoacids?, all_aminoacids?, allowed_dna_nucleotides?, amino_acid_average_mass, amino_acid_monoisotopic_mass, aminoacid_families?, aminoacid_frequency, aminoacid_substitution, aminoacids?, append_what_into, array_colourize_this_aminoacid, atomic_composition, automatically_rename_this_fasta_file, available_blosum_matrices?, available_codon_tables?, base_composition, batch_create_windows_executables, be_verbose?, bisulfite_treatment, blast_neighborhood, blosum_directory?, blosum_matrix, calculate_exponential_growth, calculate_levensthein_distance, calculate_melting_temperature_for_more_than_thirteen_nucleotides, calculate_n50_value, calculate_original_amount_of_cells_of_exponential_growth, calculate_the_frequencies_of_this_species, calculate_weight_of_the_aminoacids_in_this_fasta_file, can_base_pair_with?, #cat, cat, change_directory, clear_array_colourize_this_aminoacid, clear_stop_codons, cleave, cleave_with_trypsin, cliner, codon_frequencies_of_this_sequence, codon_frequency_of_this_string, codon_table_dataset?, codon_table_in_use?, codon_tables, codons_for_this_aminoacid?, colourize_aa, colourize_this_aminoacid_sequence_for_the_commandline, colourize_this_fasta_dna_sequence, colours, compacter, complement, complementary_dna_strand, complementary_rna_strand, compseq, contains_an_inverted_repeat?, convert_global_env, convert_one_letter_to_full, convert_one_letter_to_three, convert_this_codon_to_that_aminoacid, count_AT, count_GC, count_amount_of_aminoacids, count_amount_of_nucleotides, count_non_DNA_bases_in_this_sequence, create_file, create_jar_archive, create_new_sequence, create_random_aminoacids, create_the_pdf_tutorial, decode_this_aminoacid_sequence, deduce_aminoacid_sequence, deduce_most_likely_aminoacid_sequence, deduce_most_likely_aminoacid_sequence_as_string, #default_colour?, default_colour?, delimiter?, determine_n_glycosylation_matches, determine_start_codons_from_the_codon_table, determine_stop_codons_from_the_codon_table, digest_this_dna, directory_frequencies?, disable_colours, display_all_open_reading_frames_from_this_sequence, dna_sequence, dna_to_aminoacid_sequence, do_not_truncate, do_truncate, dotplot_array, downcase_chunked_display, download, download_directory?, download_fasta, download_human_genome, download_taxonomy_database, download_this_pdb, e, #ecomment, edit_C_to_U, editor?, embeddable_interface, enable_colours, ensure_that_the_base_directories_exist, erev, esystem, every_reverse_palindrome_in_this_string, ewarn, extract, extractseq, fasta_dir?, fasta_directory?, fetch_data_from_uniprot, fetch_fasta_sequence_from_pdb, file_amino_acids, file_amino_acids_abbreviations, file_amino_acids_frequency, file_amino_acids_long_name_to_one_letter, file_fastq_quality_schemes, file_molecular_weight, #file_restriction_enzymes, file_restriction_enzymes, file_statistics?, file_talens, filter_away_invalid_aminoacids, filter_away_invalid_nucleotides, find_substring, format_this_nucleotide_sequence, frequency_per_thousand, gc_content, genbank_to_fasta, generate_nucleotide_sequence_based_on_these_frequencies, generate_pdf_tutorial, generate_random_dna_sequence, generate_random_rna_sequence, guess_format, hamming_distance, has_this_restriction_enzyme?, hash_codon_tables?, index_this_fasta_file, infer_type_from_this_sequence, initialize_codons, initialize_default_stop_codons, input_as_dna, is_a_protein?, is_a_purine?, is_a_pyrimidine?, is_a_stop_codon?, is_an_aminoacid?, is_in_the_three_letter_code?, #is_on_roebe?, is_on_roebe?, is_palindrome?, is_reverse_complement?, is_start_codon?, is_this_a_valid_codon?, is_this_sequence_a_EGF2_pattern?, last_updated?, leading_five_prime, length_modifier, levenshtein_distance, load_and_return_the_restriction_enzymes, load_psych_or_syck, load_the_codon_table_dataset, log_directory?, longest_common_substring, map_ncbi_entry_to_eutils_id, min3, mirror_repeat_of, mkdir, #mkdir, move_file, move_file_to_its_correct_location, mv, n_stop_codons_in_this_sequence?, n_transitions, n_transversions, no_file_exists_at, nucleotide_permutations, number_of_clones, one_to_three, only_nucleotides?, open_in_browser, open_reading_frames_to_aminoacid_sequence, overwrite_fasta_header, palindrome_generator, parse, parse_fasta, parse_fasta_file, parse_fasta_quietly, parse_pdb_file, parse_this_prosite_pattern, partner_nucleotide, partner_nucleotide_hash, pathways, pdb_directory?, percentage_count_non_DNA_bases_in_this_sequence, permanently_disable_opn, permutations, phred_error_probability, plain_palindrome, possible_codons_for_these_aminoacids, possible_codons_for_this_aminoacid, project_base_dir?, project_yaml_directory?, #pwd, pwd, quaternary_encoding_DNA_to_numbers, quaternary_encoding_letter_to_number, quaternary_encoding_number_to_letter, quaternary_encoding_numbers_to_DNA, quaternary_encoding_translate_from_alphabet_string_into_the_corresponding_DNA_sequence, random_aminoacid?, rds, readline_is_available?, regex_with_startcodons, remove_file, remove_invalid_aminoacids, remove_numbers, remove_subsequence, report_base_composition, require_all_aminoacids_files, require_all_calculate_files, require_all_cleave_and_digest_files, require_all_codon_files, require_all_count_files, require_all_dotplot_files, require_all_electron_microscopy_files, require_all_enzymes_files, require_all_fasta_and_fastq_files, require_all_nucleotides_files, require_all_palindromes_files, require_all_parser_files, require_all_pattern_files, require_all_pdb_files, require_all_sequence_files, require_all_string_matching_files, require_all_taxonomy_files, require_all_utility_scripts_files, require_the_toplevel_methods, restriction_enzyme, restriction_enzymes, restriction_enzymes?, restriction_enzymes_file, restriction_sites?, return_DNA_composition_hash, return_DNA_nucleotides, return_all_open_reading_frames_from_this_sequence, return_all_positions_of_this_nucleotide, return_all_substring_matches, return_aminoacid_sequence_from_this_pdb_file, return_aminoacid_sequence_from_this_string, return_array_from_tryptic_digest, return_array_of_common_aminoacids, return_array_of_sequence_matches, return_chunked_display, return_composition_from_this_aminoacid_sequence, return_consensus_sequence_of, return_current_day_month_year, return_current_hours_minutes_seconds, return_every_substring_from_this_sequence, return_fasta_entry_with_the_highest_gc_content, return_fasta_sequence_from_this_pdb_file, return_fasta_subsection_of_this_file, return_illumina_offset, return_long_aminoacid_name, return_longest_ORF_from_this_sequence, return_longest_substring_via_LCS_algorithm, return_n_ORFs_in_this_sequence, return_n_repeats, return_new_filename_based_on_fasta_identifier, return_nucleotide_sequence_as_ten_nucleotides_chunks, return_random_aminoacid_from_this_prosite_pattern, return_random_codon_sequence_for_this_aminoacid_sequence, return_random_nucleotide, return_restriction_enzyme_sequence_and_cut_position, return_sanger_offset, return_sequence_from_this_file, return_sequence_that_is_cut_via_restriction_enzyme, return_short_aminoacid_letter_from_long_aminoacid_name, return_sizeseq, return_solexa_offset, return_source_code_of_this_method, return_subsequence_based_on_indices, return_the_most_likely_codon_sequence_for_this_aminoacid_sequence, return_ubiquitin_sequence, rev, #rev, reverse_complement, reverse_sequence, rna_sequence, rna_splicing, rnalfold, ruler, ruler_return_as_string, ruler_return_as_string_without_colours, run_gtk_controller, run_sql_query, salt_adjusted_tm, sanitize_nucleotide_sequence, sanitize_this_fasta_file, scan_for_rgg_motifs, scan_this_input_for_startcodons, sdir, sequence?, sequence_based_on_these_restriction_enzymes, set_codon_table_in_use, set_default_colour, set_log_directory, set_pgpassword, set_start_codon, set_start_codons, set_stop_codons, set_use_this_codon_table, set_use_this_yaml_engine=, sfancy, sfile, shell, show_aminoacids_mass_table, show_atomic_composition, show_codon_tables, show_complementary_dna_strand, show_exon_statistics, show_fasta_header, show_fasta_statistics, show_n_glycosylation_motifs, show_restriction_enzymes, show_time_now, showorf, shuffleseq, simp, simplify_fasta_header, sizeseq, sort_aminoacid_based_on_its_hydrophobicity, start_codon?, start_codons?, start_sinatra_interface, stop_codons?, strict_filter_away_invalid_aminoacids, sum_of_odd_integers, swarn, taxonomy_directory?, taxonomy_download_directory?, taxonomy_ncbi_database_last_update_log_file, this_aminoacid_has_n_codons, this_nucleotide_pairs_with?, thousand_percentage, three_delimiter, three_to_one, to_aminoacids, to_camelcase, to_dna, to_rna, to_utf, trailing_three_prime, transitions_to_transversions_ratio, translate_all_three_frames, truncate?, try_to_pass_through_beautiful_url, try_to_rename_kde_konsole?, two_dimensional_plot, unique_two_paired_permutations, upcase_this_aminoacid_sequence_and_remove_numbers, upload_this_pdf_file, use_colours?, #use_colours_in_general?, use_opn?, use_this_codon_table, use_which_yaml_engine?, user_home_directory?, version?, weight_of_these_aminoacids?, weight_of_this_aminoacid?, wget_download, windows_platform?, write_what_into

Instance Method Details

#Bioroebe(i, &block) ⇒ `Object`

#

Bioroebe()

Usage example for this:

require 'bioroebe'    
seq = Bioroebe('AAAACCCGGT')

#



760
761
762

# File 'lib/bioroebe/sequence/sequence.rb', line 760

def Bioroebe(i, &block)
  ::Bioroebe.create_new_sequence(i, &block)
end