Class: Bioroebe::Taxonomy::Interactive
Overview
Bioroebe::Taxonomy::Interactive
Constant Summary
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- FASTA_SQL =
#
FASTA_SQL
This constant will point towards a location such as “/home/Temp/bioroebe/autogenerated_sql_files/fasta.sql”.
#
AUTOGENERATED_SQL_FILES_DIR+'fasta.sql'
- BE_VERBOSE =
#
BE_VERBOSE
Constants for this class here.
#
true
- USE_COLOURS =
#
USE_COLOURS
Whether to have colourized output or not.
#
true
- NO_HELP =
false
PROJECT_YAML_DIR
Constants included
from Constants
Constants::AA_DIR, Constants::ARRAY_PROJECT_FILES, Constants::Archaea_Taxonomy_ID, Constants::BASE, Constants::BASE_URL, Constants::Bacteria_Taxonomy_ID, Constants::CITATIONS, Constants::CURATED_DIR, Constants::DATA_DIR, Constants::DELNODES, Constants::DIVISION, Constants::Eukaryota_Taxonomy_ID, Constants::FILE_USE_THIS_DATABASE, Constants::GEM_DIR, Constants::GENCODE, Constants::INCOMING_DIR, Constants::INFO_DIR, Constants::LAST_INTERACTIVE_COMMAND, Constants::LOCALOME_DIR, Constants::LOCAL_MIRROR, Constants::MERGED, Constants::MODULE_PATH, Constants::NAMES, Constants::NAMES_SQL, Constants::NCBI_BASE, Constants::NODES, Constants::NODES_SQL, Constants::NT_DIR, Constants::POSTGRESQL_QUERY_SIZE, Constants::POSTGRE_LOGIN_COMMAND, Constants::PROJECT_DOC_DIR, Constants::SEQUENCES_DIR, Constants::SHARED_HOME, Constants::TAXONOMY_BROWSER, Constants::TEMP_DIR, Constants::TEST_DIR, Constants::TMP_DIR, Constants::URL1
Constants included
from Bioroebe
ALLOWED_RNA_NUCLEOTIDES, AMINOACIDS_DIRECTORY, AMINOACID_FAMILIES, AMINO_ACIDS, AMINO_ACIDS_AVERAGE_MASS_TABLE, AMINO_ACIDS_AVERAGE_MONOISOTOPIC_TABLE, AMINO_ACIDS_ENGLISH, AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER, AMINO_ACIDS_MASS_TABLE, AMINO_ACIDS_MOLECULAR_FORMULA, AMINO_ACIDS_RESTE, AMINO_ACIDS_THREE_TO_ONE, ARRAY_AMINOACIDS_THAT_CAN_BE_PHOSPHORYLATED, ARRAY_AMINO_ACIDS_ALPHABET, ARRAY_NLS_SEQUENCES, ARRAY_REGISTERED_ACTIONS, ARRAY_VALID_DNA_SEQUENCES, AUTOGENERATED_SQL_FILES_DIR, Aminoacids, BIOROEBE_AT_HOME, BIOROEBE_YAML_AMINOACIDS_DIRECTORY, BLOSUM_DIRECTORY, CALCULATE_DIRECTORY, CLEAVE_AND_DIGEST_DIRECTORY, CODONS_DIRECTORY, CODON_TABLES_DIRECTORY, CODON_TABLES_DIRECTORY_FREQUENCY, CONFIGURATION_DIRECTORY, COUNT_DIRECTORY, DEFAULT_DNA_SEQUENCE, DEFAULT_LENGTH_FOR_DNA, DIRECTORY_CODON_TABLES_FREQUENCIES, DNA_NUCLEOTIDES, DOTPLOTS_DIRECTORY, ELECTRON_MICROSCOPY_DIRECTORY, EMAIL, ENGLISH_LONG_NAMES_FOR_THE_AMINO_ACIDS, ENZYMES_DIRECTORY, FASTA_AND_FASTQ_DIRECTORY, FASTA_ENTRIES, FIELD_TERMINATOR, FILE_AMINOACIDS_MOLECULAR_FORMULA, FILE_AMINOACIDS_THREE_TO_ONE, FILE_AMINO_ACIDS, FILE_AMINO_ACIDS_ABBREVIATIONS, FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE, FILE_AMINO_ACIDS_ENGLISH, FILE_AMINO_ACIDS_FREQUENCY, FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER, FILE_AMINO_ACIDS_MASS_TABLE, FILE_AMINO_ACIDS_MOLECULAR_FORMULA, FILE_AMINO_ACIDS_RESTE_YAML, FILE_AMINO_ACIDS_THREE_TO_ONE, FILE_BIO_LANG, FILE_BLOSUM45, FILE_BLOSUM50, FILE_BLOSUM62, FILE_BLOSUM80, FILE_BLOSUM90, FILE_BLOSUM_MATRIX, FILE_BROWSER, FILE_CHROMOSOME_NUMBERS, FILE_COLOURIZE_FASTA_SEQUENCES, FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS, FILE_EXPAND_CD_ALIASES, FILE_GFP_SEQUENCE, FILE_HYDROPATHY_TABLE, FILE_NUCLEAR_LOCALIZATION_SEQUENCES, FILE_NUCLEOTIDES, FILE_NUCLEOTIDES_WEIGHT, FILE_RESTRICTION_ENZYMES, FILE_WEIGHT_OF_COMMON_PROTEINS, FTP_NCBI_TAXONOMY_DATABASE, Fasta, HASH_DNA_NUCLEOTIDES, HOME_DIRECTORY_OF_USER_X, HYDROPATHY_TABLE, LAST_UPDATE, LOCALHOST, LOCAL_DIRECTORY_FOR_UNIPROT, MAIN_DELIMITER, N, NAMES_ENTRIES, NAME_OF_BIO_SHELL, NCBI_GENE, NCBI_NUCCORE, NODES_ENTRIES, NUCLEAR_LOCALIZATION_SEQUENCES, NUCLEOTIDES, NUCLEOTIDES_DIRECTORY, PALINDROMES_DIRECTORY, PARSERS_DIRECTORY, PATHWAYS_DIRECTORY, PATH_TO_THE_RELION_BINARY, PATTERN_DIRECTORY, PDB_DIRECTORY, POSSIBLE_AMINO_ACIDS, POSSIBLE_DNA_NUCLEOTIDES, POSSIBLE_RNA_NUCLEOTIDES, ProteinToDNA, R, REGEX_FOR_N_GLYCOSYLATION_PATTERN, REGEX_PROSITE_FOR_ANY_AMINOACID, RNA_NUCLEOTIDES, ROW_TERMINATOR, RUBY_SRC, SEQUENCE_DIRECTORY, SHALL_WE_LOG_LAST_UPDATE, STOP_CODONS, STRING_MATCHING_DIRECTORY, Seq, Bioroebe::TABULATOR, Bioroebe::TOKEN, Bioroebe::TOPLEVEL_METHODS_DIRECTORY, Bioroebe::TWENTY_CANONICAL_AMINOACIDS, UNICODE_HORIZONTAL_BAR, URL_TO_TAXONOMY_ARCHIVE, URL_TO_THE_DOCUMENTATION, USERS_X, USE_THIS_BROWSER, USE_THIS_COLOUR_FOR_DNA, USE_THIS_ENCODING, UTF_ENCODING, VALID_WAYS_TO_EXIT, VERSION, VERTICAL_UNICODE_BAR
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
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Instance Method Summary
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#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 Shared
be_quiet, 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 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
#all_aminoacids?, #append_what_into, #at_home?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into
Methods included from BaseModule
#absolute_path, #default_file_read, #file_readlines
#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens
#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #ecomment, #efancy, #egold, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours_within_the_bioroebe_namespace?
Methods inherited from Base
#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into
#internal_hash?, #reset_the_internal_hash
#infer_the_namespace, #namespace?
Constructor Details
#initialize(optional_commandline_arguments = nil, run_already = true) ⇒ Interactive
#
initialize
The first argument are the commandline arguments.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 87
def initialize(
optional_commandline_arguments = nil,
run_already = true
)
reset
set_commandline_arguments(
optional_commandline_arguments
)
run if run_already
end
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Class Method Details
.run(i = nil) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1438
def self.run(i = nil)
Taxonomy::Interactive.new(i)
end
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.run_interactive(i = nil) ⇒ Object
#
Taxonomy.run_interactive
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1445
def self.run_interactive(i = nil)
Interactive.run(i) end
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Instance Method Details
#
Use this method to add a comment to the localome table.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1933
def (taxid)
if has? taxid
e 'Please input the comment you wish to add to the '+
'Taxonomy ID '+simp(taxid.to_s)+' now:'
add_this = $stdin.gets.chomp
_ = "UPDATE fasta SET comment_field='"+add_this+"' WHERE taxid='"+taxid.to_s+"'"
run_sql(_)
else
erev "We could not find any entry with the Taxonomy "\
"ID #{taxid.to_s}."
end
end
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#be(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1216
def be(i)
case i.to_sym
when :verbose
be_verbose
when :silent
be_silent
end
end
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#be_silent ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1152
def be_silent
if @be_verbose == false
e 'We are already silent.'
else
@be_verbose = false
e 'We will now be silent.'
end
end
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#be_verbose ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1241
def be_verbose
if @be_verbose == true
e 'We are already verbose.'
else
@be_verbose = true
e 'We will now be verbose.'
end
end
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#be_verbose? ⇒ Boolean
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1198
def be_verbose?
@be_verbose
end
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#check_commandline_arguments ⇒ Object
#
check_commandline_arguments
We check the commandline.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1766
def check_commandline_arguments
@commandline_arguments.each {|entry|
case entry
when :run_connected
do_run_connected end
}
end
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#create_and_save_table(i, be_verbose = false) ⇒ Object
#
create_and_save_table
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 143
def create_and_save_table(
i, be_verbose = false
)
case i
when :default_fasta
i = FASTA_SQL
end
require 'roebe/sql_paradise/commands.rb'
Roebe::SqlParadise::Commands.create_and_save_table(i, be_verbose)
end
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#create_database ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1894
def create_database
case which_database_to_use?
when 'sqlite'
one = 'CREATE TABLE names ( taxid int, name_txt varchar(155), unique_name varchar(100), name_class varchar(25) );'
two = 'CREATE TABLE nodes ( taxid int, parent_taxid int, rank varchar(25) );'
three = 'CREATE TABLE fasta ( name varchar(80), taxid integer, type smallint, lineage_ids varchar(500), lineage_scientific_name varchar(2500), comment_field varchar(8000), filesize integer, modification_time varchar(25), n_accession_numbers integer, path varchar(120) );'
e one
e two
e three
_ = 'sqlite3 '+working_dir?+'names.db "'+one+'"'
esystem _
_ = 'sqlite3 '+working_dir?+'nodes.db "'+two+'"'
esystem _
_ = 'sqlite3 '+working_dir?+'fasta.db "'+three+'"'
esystem _
File.read(Taxonomy::Constants::NAMES_SQL).each_line {|line|
line = line.chomp
if line.include? '"'
line.gsub!(/"/,'\"')
end
_ = 'sqlite3 '+working_dir?+'names.db "'+line+'"'
Esystem.esystem _
}
else end
end
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#create_default_directories ⇒ Object
#
create_default_directories
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 702
def create_default_directories
e 'Creating some directories now.'
array_create_these_directores = %w(
/data/ncbi/taxonomy/
/tmp/robert/autogenerated_sql_files/
/data/curated/sequences/localome/
/data/curated/sequences/aa/
/data/curated/sequences/nt/
/data/curated/sequences/INFO/
/data/curated/sequences/localome/incoming/
); pp array_create_these_directores
mkdir(array)
end
|
#create_dirs(be_verbose = false) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 726
def create_dirs(
be_verbose = false
)
case be_verbose
when :be_verbose
be_verbose = true
end
if be_verbose
opne 'We will create the temp directory and the download directory next.'
end
ensure_that_temp_dir_exists
ensure_that_download_dir_exists
end
|
#create_fasta_table ⇒ Object
#
create_fasta_table
This method generates the fasta table into either postgresql or whatever else you stored things into.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 128
def create_fasta_table
remove(FASTA_SQL)
create_and_save_table(:default_fasta, true) cat FASTA_SQL e 'Trying to drop the fasta table next.'
drop_table :fasta
read_sql :fasta
end
|
#create_sql_file_from_local_fasta_entry(i) ⇒ Object
#
create_sql_file_from_local_fasta_entry
This method will create a .sql file, based on the information obtained from the local fasta entries.
The first argument to it should be an .INFO file, not a fasta file!
#
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|
# File 'lib/bioroebe/taxonomy/interactive.rb', line 1559
def create_sql_file_from_local_fasta_entry(i)
ensure_that_temp_dir_exists
info = Info.new(i, :be_verbose => false)
info.try_to_find_likely_fasta_file if info.taxid
obtain_full_lineage_for(info.taxid) else
if be_verbose?
e 'We did not find a Tax ID for `'+sfile(i)+'`.'
e 'This is considered a fatal error for now - we will thus exit.'
end
exit
end
mkdir(AUTOGENERATED_SQL_FILES_DIR) unless Dir.exist?(AUTOGENERATED_SQL_FILES_DIR)
sql_filename = AUTOGENERATED_SQL_FILES_DIR+
File.basename(i).gsub(/#{File.extname(i)}/,'')+'.sql'
remove(sql_filename) if File.exist? sql_filename string = ''.dup scientific_name = get_scientific_name(info.taxid).strip
if scientific_name.empty? if be_verbose?
ewarn 'The scientific name for '+simp(info.taxid.to_s)+' was empty.'
ewarn 'This we consider to be a runtime error for now, thus '+
'we will exit.'
end
exit
end
string << pad_with_single_quotes(
scientific_name
)+', '
fasta = ParseFasta.new(info.corresponding_datafile)
string << info.taxid.to_s+', '
type = fasta.type? if type == 'DNA'
type = 0
elsif type == 'Protein'
type = 1
end
string << type.to_s+', '
string << pad_with_single_quotes(@lineage_ids)+', '
string << pad_with_single_quotes(@lineage_scientific_name)+', '
string << pad_with_single_quotes(0)+', '
string << fasta.filesize.to_s+', '
string << pad_with_single_quotes(fasta.modification_time.to_s)+', '
string << fasta.n_entries.to_s+', '
string << pad_with_single_quotes(info.corresponding_datafile)
string = InsertInto[
'fasta',
'name, taxid, type, lineage_ids, lineage_scientific_name, comment_field, filesize, modification_time, n_accession_numbers, path', string
]
e 'Now storing into '+sfile(sql_filename) if be_verbose?
write_what_into(string, sql_filename)
if be_verbose?
e 'Next, we will attempt to read in this file into the '
'Postgresql localome (fasta) table.'
end
cmd = POSTGRE_LOGIN_COMMAND+' -f '+sql_filename
esystem(cmd)
if be_verbose?
e 'Done! All should have been well by now. '+
'The Taxonomic ID was '+info.taxid
end
end
|
#create_table(i) ⇒ Object
#
create_table
A wrapper over class CreateTable.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1840
def create_table(i)
i = i.to_s
case i
when 'fasta'
create_fasta_table
else
i << '.sql' result = ::SqlParadise::Commands.create_table(i)
store_here = AUTOGENERATED_SQL_FILES_DIR+'create_table_'+i
e 'Next creating a table for '+simp(i)+'. Will '+
'store into '+sfile(store_here)
save_what_into(result, store_here)
e result
end
end
|
#disable(i) ⇒ Object
#
disable (disable tag)
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 495
def disable(i)
case i.to_sym
when :colours
disable_colours
end
end
|
#disable_colours ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 349
def disable_colours
@use_colours = false
end
|
#do_run_connected ⇒ Object
Also known as:
run_connected
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 688
def do_run_connected
@run_standalone = false
end
|
#do_startup_actions ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1749
def do_startup_actions
if be_verbose?
e Colours.rev+'Welcome to interactive Taxonomy.'+N+N
e 'We will show the help menu now (on startup).'+N+N
show_help
e 'Please input your command(s). ("help" for help, '+
'"quit", "exit" or "q" to exit.)'
nohelp if at_home? end
check_commandline_arguments
end
|
#download(i = f?)
) ⇒ Object
#
download
This method can be used to download the ncbi database.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 378
def download(i = f?)
i = i.to_s
case i when 'HELP','?','--help'
e 'Currently we can download only the NCBI database.'
e
e 'To do so, do:'
e ' download ncbi'
when /^-?-?ncbi/i,
'database','1','' download_ncbi_database
if be_verbose?
e
e 'If all went well then you could now try to update the '+
'database, by issuing:'
e
efancy ' update databases'
e
end
else
e 'In the method download(), we do not know the given '+
'input `'+simp(i.to_s)+'`.'
end
end
|
#download_ncbi_database ⇒ Object
#
download_ncbi_database
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1924
def download_ncbi_database
Taxonomy.download_ncbi_database end
|
#drop_names_table(be_verbose = true) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 427
def drop_names_table(be_verbose = true)
run_sql POSTGRE_DROP_NAMES_COMMAND, be_verbose
end
|
#drop_nodes_and_names_database_tables(be_verbose = true) ⇒ Object
#
drop_nodes_and_names_database_tables
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 535
def drop_nodes_and_names_database_tables(be_verbose = true)
drop_nodes_table(be_verbose)
drop_names_table(be_verbose)
end
|
#drop_nodes_table(be_verbose = true) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 420
def drop_nodes_table(be_verbose = true)
run_sql POSTGRE_DROP_NODES_COMMAND, be_verbose
end
|
#drop_table(i = Bioroebe::Postgresql::DROP_FASTA_TABLE) ⇒ Object
#
drop_table (drop tag)
Use this method when you wish to drop a table.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1070
def drop_table(
i = Bioroebe::Postgresql::DROP_FASTA_TABLE
)
case i.to_s
when 'nodes'
when 'fasta',
'localomes',
'localome'
i = Bioroebe::Postgresql::DROP_FASTA_TABLE
end
::Bioroebe.run_sql_query(i)
end
|
#enable(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1859
def enable(i)
i = i.to_s
if i.start_with? 'enable'
i.gsub!(/^enable/,'')
end
i.strip!
case i
when 'colours'
enable_colours
end
end
|
#exit_program ⇒ Object
#
exit_program
Use this method when exiting.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1813
def exit_program
exit if run_standalone?
end
|
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1778
def fetch_user_input_via_loop
loop {
begin
obtain_user_input rescue Interrupt
if be_verbose?
e 'Sigint occurred by user interrupt, exiting gracefully now.'
end
exit_program
end
if run_connected?
break if VALID_WAYS_TO_EXIT.include? @user_input
end
}
end
|
#finished(optional_extra_message = '') ⇒ Object
#
finished
Here we simply report to the user that we have finished.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1255
def finished( = '')
unless .empty?
<< '.' unless .end_with? '.'
end
e 'Done! '+
end
|
#first_argument? ⇒ Boolean
Also known as:
f?, f
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1302
def first_argument?
@first_argument
end
|
#generate(i) ⇒ Object
Also known as:
create
#
generate (generate tag)
This method can be used to generate nodes or names .sql files. These .sql files will be generated in the TEMP_DIR, which at the time of writing this documentation is at /tmp/robert.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 287
def generate(i)
i = i.to_s
case i when 'nodes','names','nodes.sql','names.sql'
i.gsub!(/\.sql/,'')
(i) end
end
|
#get(i, use_this_id = nil) ⇒ Object
#
get (get tag)
Get something from the localome table with this method.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 190
def get(
i,
use_this_id = nil
)
i = i.to_s
_ = "SELECT #{i} from fasta".dup
_ << " where taxid='"+use_this_id.to_s+"';" if use_this_id
if i.include? 'taxid' _ << ' ORDER BY taxid'
end
_ << ';'
result = run_sql(_, :silent, :tuples)
return result
end
|
#get_all_info_entries_with_tax_id ⇒ Object
#
get_all_info_entries_with_tax_id
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1110
def get_all_info_entries_with_tax_id
result = []
if be_verbose?
e 'We will now attempt to find all .INFO files that do have a'
e 'proper Taxonomy ID entry.'
end
Dir[INFO_DIR+'*.INFO'].each {|file|
_ = Info.new(file, :be_verbose => false)
if _.has_taxonomy_id?
e sfile(file)+' has a Taxonomy ID.' if be_verbose?
result << file
end
}
return result
end
|
#
Get user input via this method. We prefer to use Readline if it is available, otherwise we will simply use a $stdin.gets() call.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1455
def get_user_input
if Object.const_defined? :Readline
_ = Readline.readline('', true)
Readline::HISTORY.pop if _ =~ /^\s*$/
@user_input = _
else
@user_input = $stdin.gets.chomp
end
sanitize_user_input
process_user_input
return @user_input
end
|
#has_id?(i) ⇒ Boolean
Also known as:
has?
#
has_id?
We ask the localome if an ID is registered. run_sql is defined in the file shared.rb
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1268
def has_id?(i)
i = i.to_s
_ = "SELECT taxid from fasta where taxid='"+i+"'"
if run_sql(_, false, :tuples).strip.empty?
return false
else
return true
end
end
|
#insert_into(i = :nodes) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1671
def insert_into(i = :nodes)
i = i.to_s
case i
when 'fasta'
create_fasta_table
when 'nodes'
populate_nodes_table(:be_verbose)
when 'names'
populate_names_table(:be_verbose)
end
end
|
#load_from_info(i) ⇒ Object
#
load_from_info
This method shall attempt to load from an .NFO file, right into the localome/ directory at /data/curated/sequences/localome/incoming/.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1363
def load_from_info(i)
e 'We will now attempt to load an .INFO file.'
info = Info.new(i)
info.report_id
taxid = info.taxid?
e 'We will try to load a fasta file, if it is nearby.'
_ = info.fasta?
e _
ParseFasta.new(_).report
if has_id? taxid e 'We already have an entry with the Taxonomic ID taxid '+taxid+'.'
e 'You would have to remove it first before you can load a new one.'
e '(Removing is as simple as: remove_id TAXONOMIC_ID_GOES_HERE)'
else
e 'No entry was yet found in the localome table, thus we will '+
'attempt to add this dataset now.'
create_sql_file_from_local_fasta_entry(i)
e 'You can update the path in the Postgresql database via:'
e ' set_path TAXONOMY_ID path_goes_here'
end
end
|
#lupdate(i = :ncbi) ⇒ Object
#
lupdate (update tag)
This is the general way to update something. “update everything’ is the most important component - it will update everything, including the localomes entry.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 453
def lupdate(i = :ncbi)
i = i.to_s case i
when 'localomes',
'local','loc','localome','2',
'fasta',
'database',
'databases'
update_local_localomes when /^ncbi(-|_| )?database$/,
'ncbi',
'1',
'update_ncbi'
update_ncbi_database
when 'all',
'everything',
'both'
update_ncbi_database
update_local_localomes
update_lineage
when 'lineage','lin','li'
update_lineage
else
e 'Not sure what to update - the input was '+sfancy(i.to_s)
end
end
|
#make_taxonomy_gem ⇒ Object
#
make_taxonomy_gem
This is the code that creates the taxonomy .gem.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 859
def make_taxonomy_gem
unless Dir[TAXONOMY_HOME_DIR+'*.gemspec'].empty? cd TAXONOMY_HOME_DIR
end
e
e 'We will now attempt to build the taxonomy .gem (from '+
'directory '+(Dir.pwd+'/').squeeze('/')+')'
e
if File.exist? 'taxonomy.gemspec'
esystem 'gem build taxonomy.gemspec', :use_colours
e
e 'Done. There should now be a .gem file here.'
location = Dir['*.gem']
if location
e 'We assume the full file path to be at:'
e ' '+sfile(location.first)
cp(location.first, TEMP_DIR)
e 'All done - the .gem should be ready now.'
end
else
e 'Could not find a file called taxonomy.gemspec, thus aborting now.'
end
end
|
#
The first argument to this method is the action we wish to check against the menu.
It constitutes the main menu interface of the Taxonomy project. The taxonomy commandline program calls this method here simply menu().
#
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|
# File 'lib/bioroebe/taxonomy/menu.rb', line 34
def (
instruction = user_input?,
optional_this_file = nil
)
i = instruction.to_s.chomp
ensure_that_temp_dir_exists
ensure_that_download_dir_exists
record_last_command(i, first_argument?) case i when 'update',
'lupdate',
'upd'
lupdate(f)
when 'download'
download(f)
when 'status?',
'status',
'stat',
'stats',
'data?',
'try_to_display_the_status'
try_to_display_the_status(f)
when 'disable_colours',
'nocolours',
'nocols',
'nocolour',
'nocol',
'nocolorus'
disable_colours
when 'extract',
'ext'
(File.basename(URL_TO_TAXONOMY_ARCHIVE))
when /^download(_|-)?database$/i,'ncbi_down'
download_ncbi_database
when *VALID_WAYS_TO_EXIT
exit_program
when /^set(-|_| )?be(-|_| )?verbose$/,
'verbose',
'be_verbose'
@be_verbose = true
e 'We will now be verbose.'
when 'last?',
'show_last_command'
show_last_command
when 'query_localome',
'querylocalome',
'qlocalome',
'available?',
'available',
'query?',
'localomes?',
'loc?'
query_localome_including_path
when 'lineageid',
'lineage_id',
'lineage_ids',
'lineageids', 'show_lineage_from_localome_table',
'slocalome'
show_lineage_from_localome_table(f)
when 'query','qu'
query(f)
when 'name_path',
'namepath'
e run_sql('select name,path from fasta;',false, :tuples)
when 'sql',
'seql'
sql(f)
when 'projectbasedir',
'basedir?',
'project_base_dir'
e PROJECT_BASE_DIR
when 'grep'
esystem 'grep -r '+f.to_s+' '+MODULE_PATH+'*'
when 'set_database','setdatabase','database'
set_database(f) when /^enable/
enable(i) when 'password?',
'password',
'show_password',
'spassword',
'spass',
'showpassword'
show_password
when 'show_sql_commands_only',
'showsqlcommandsonly',
'show2'
show_sql_commands_only
when 'commands?',
'commands',
'show_sql_commands',
'sql?',
'sqlinfo',
'tables?',
'stored?',
'databases?',
'database?',
'sql_commands?'
show_sql_commands
when 'AUTOGENERATED_SQL_FILES_DIR','autogenerated_sql_files_dir'
e AUTOGENERATED_SQL_FILES_DIR
when 'use_which_database?',
'which_database?',
'd??',
'datenbank?',
'usewhichdatabase?',
'usewhichdatabase',
'whichdatabase?'
e File.read(FILE_USE_THIS_DATABASE)
when /^populate(_|-)?nodes(_|-)?table$/i,
'nodestable',
'nodes.sql'
nodes_sql
when 'populate_names_table','populatenamestable','namestable',
'names.sql'
names_sql
when /^create(_|-)?database/,
'cdata'
create_database
when 'make_sql',
'makesql',
'msql',
'do_sql',
'dosql',
'generatesql'
nodes_sql
names_sql
when 'config?'
show_configuration
when 'dirs?','feedback','d?','dir?','home?'
show_important_directories when 'last_update',
'last_update?',
'lup',
'lup?',
'lupd',
'lupdate?',
'lastupdate',
'lupd?',
'lastupdate?',
'lastupdated?',
'last_upd?'
try_to_show_when_the_last_update_has_happened
when 'create_fasta_table',
'ftable',
'fff',
'cfasta',
'createfastatable'
create_fasta_table
when 'names',
'nodes',
'fasta2',
'names_db',
'nodes_db',
'fasta_db'
cd SHARED_HOME unless f
i = i.gsub(/_db/,'') this_file = i+'.sql'
remove(i+'.sql', true) if File.exist? this_file
if be_verbose?
e 'In '+sdir(Dir.pwd+'/')+', we will now generate the '+
sfile(this_file)+' file anew. This may take'
e 'a while, please be patient.'
end
create_and_save_table(i)
populate(i, false, this_file) finished 'Generated '+i.to_s+'.' if File.exist? this_file
when 'cat'
cat(f)
when 'cd'
cd(f, :be_verbose)
when 'colours?'
e 'Will we use colours: '+@use_colours.to_s
when 'BASE?','base'
cd working_directory?
when 'url?'
e NCBI_URL
when 'date',
'time',
'date?',
'time?',
'show_current_time_and_date'
show_current_time_and_date
when 'populate',
'pop',
'loadup', 'create_sql_file_from_local_fasta_entry'
create_sql_file_from_local_fasta_entry(f)
when 'create?'
e 'We can create:'
e ' names'
e ' nodes'
when 'create_table','ctable','createtable','create'
create_table(first_argument?)
when 'create_dirs','cdirs'
create_dirs(:be_verbose)
when 'verify?','verify','ver','v','debug','debug?'
verify_proper_sql_structures
when 'help','hlep',
'subhelp',
'shelp',
'helps',
'?',
'hlp',
'--help',
'-help'
show_help
when 'instructions?','instruction','ins','ins?',
'inst?','instruction?'
try_to_show_instructions
when 'test','batch','batch_process','batch_read_info_files',
'batch?','batchprocess'
ParseFasta.batch_process when 'parent_id','pid','parentid','pid?','parentof',
'get_parent_id_of','parent'
e 'The parent id of Tax ID '+sfancy(f)+' is: '+simp(
get_parent_id_of(f)
)
when 'get_scientific_name_of','getscientificnameof', 'science','sciname','sci','sciid','scif',
'show_scientific_name_of','scientific_name_of',
'name_of',
'scientific_name',
'scientificname'
show_scientific_name_of(f)
when 'insert_into','insertinto','iinto'
insert_into(f)
when 'postgres_size?','show_postgres_size','showpostgressize',
'showsize','size?','table_size?','tablesize?'
show_postgres_size
when 'fasta_table?','fastatable?'
result = run_sql(
'select * from fasta limit 0;',
false).strip.gsub(/\(0 rows\)/,'')
e 'The fasta table has these entries: '+N+' '+result
when 'search_by_name','search_in_database_for_name','sname',
'search','name','searchfor','sfor','search_for'
result = search_in_database_for_name(f).strip.split(N)
result.each {|entry|
entry = entry.split('|'); e entry[0]+' '+entry[1]
}
when 'find_highest',
'latest','current','akt'
find_highest_entries_in_sql
when 'fullhelp','fhelp'
begin
require 'case_parser'
CaseParser.parse(__FILE__).each {|entry|
e " - #{entry}"
}
rescue LoadError
end
when 'enable_colours','enablecolours','yescolours',
'ecolours'
enable_colours
when 'be'
be(f)
when 'dropper'
drop_nodes_and_names_database_tables
when 'read_in_names_and_nodes_sql_files','readinnamesandnodessqlfiles'
read_in_names_and_nodes_sql_files
when 'verbose?'
e be_verbose?.to_s
when 'open','open_project_files'
open_project_files
when 'set_path','setpath','spath','path','update_path'
set_path(f)
when 'info?','i?','info','info2','inf','nfo',
'parse_info','parseinfo','pinfo'
if f cliner {
_ = Info.new(f)
_.show_info(false) _.show_likely_fasta_file_if_it_can_be_found
if _.location.include? 'incoming/'
e 'We found the string incoming/ as being part of the location of the .INFO file.'
e '(The full location is: '+sfile(_.location?)+')'
e 'We thus assume that you wish to automatically load this dataset into '
e 'the localome table, and we will do so now.'
create_sql_file_from_local_fasta_entry(f)
end
}
else
cliner {
report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
}
end
when 'obtain_full_lineage_for','obtainfulllineagefor'
pp obtain_full_lineage_for(f)
e 'This has also built the two lineage IDs:'+N+N
efancy ' '+@lineage_ids.to_s
efancy ' '+@lineage_scientific_name.to_s
when 'search_in_localomes','searchinlocalomes','sin',
'searchlocalomes','slocal','slocalomes'
search_in_localomes(f)
when 'query_localomes_by_modtime','mod_time','modtime',
'modtime?'
query_localomes_by_modtime
when 'get_all_info_entries_with_tax_id','getallinfoentrieswithtaxid',
'ginfo','get_all_info_entries_with_taxid'
get_all_info_entries_with_tax_id
when 'fasta?','table?'
e 'We use these values for the fasta table:'
e ' '+FASTA_ENTRIES
when 'type','types','type?','types?',
'show_type_of_all_info_files','showtypeofallinfofiles'
show_type_of_all_info_files(f)
when 'name,taxid','names,taxid'
run_sql 'select name,taxid from fasta ORDER BY taxid;'
when 'get_id','id','id?','getid','idof?','gid','getidof',
'get_id_of','showid'
get_id_of(f)
when 'edit','edit_login'
edit(f)
when 'lineage','get_lineage','getlineage','get_parent_ids',
'getparentids','gpids','pids','pids_of','pidsof',
'allids','linage'
return_full_lineage_of(f)
report_lineage_of(f)
when 'login?','login_information?','linfo?','login',
'show_login_information','showlogininformation'
show_login_information
when 'nodes?','show_nodes_table','shownodestable'
show_nodes_table
when 'store_where?','storewhere?'
e 'We will store at '+sdir(TEMP_DIR)
when 'generate'
generate(f)
when 'remove','remove_taxid_from_localome_table',
'remove_id'
remove_taxid_from_localome_table(f)
when 'drop_table','droptable','drop','dropt'
drop_table(f)
when 'disable'
disable(f)
when 'where','where?'
e TAXONOMY_DIR+'names.dmp'
e TAXONOMY_DIR+'nodes.dmp'
when 'taxtree','taxtree?','tree','treetax','tax_tree'
taxtree(f)
when 'query_whether_we_have_this_id','has_id?','hasid','hasid?'
query_whether_we_have_this_id(f)
when 'update_lineage','updatelineage','ulineage'
update_lineage when 'll','LL','l',
'lll',
'show_directory_content',
'directory_paradise'
show_directory_content
when 'load_from_info','linfo','loadinfo'
load_from_info(f)
when 'lafo','loadup_localomes','loaduplocalomes','goloc',
'localomes_go','localomesgo','golocal','goloco',
'localgo',
'update_local_localomes',
'update2',
'default'
update_local_localomes
when 'show_all_eukarya','eukarya?','eukarya','eucarya?','eucarya',
'eukaryota','seu','euk'
show_all_eukarya(f)
when 'repeat_last','last_command','lastcommand','last' repeat_last_command
when 'deepfasta' _ = Taxonomy::ParseFasta.new(f)
e 'The (at least one) sequence is: '+sfancy(_.sequence.first)
e 'The status for '+sfile(_.location)+' is as follows:'
_.report_status
pp _.hash
when 'isdna','is_dna','isdna?'
Taxonomy::IsDNA.new(f).report
when 'nohelp','nhelp','nh','silence'
nohelp
when 'silent','be_silent','besilent'
be_silent
nohelp
when 'taxid','t','taxid?','tid'
get_id_of(f)
e 'http://www.ncbi.nlm.nih.gov/taxonomy/?term='+f.to_s
when 'silently_update_ncbi_database'
silently_update_ncbi_database
when 'n_info?','ninfo'
report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
when 'taxid,name,path'
run_sql 'SELECT taxid,name,path from fasta ORDER BY taxid;'
when 'name,path,taxid'
run_sql 'SELECT name,path,taxid from fasta ORDER BY taxid;'
when 'taxid,name,path,filesize'
run_sql 'SELECT taxid,name,path,filesize from fasta ORDER BY taxid;'
when 'dependencies?','deps?','dep?'
try_to_show_dependencies
when 'taxid,path'
run_sql 'SELECT taxid,path from fasta ORDER BY taxid;'
when 'name,path'
run_sql 'SELECT name,path from fasta ORDER BY name;'
when 'name,taxid,path'
run_sql 'SELECT name,taxid,path from fasta ORDER BY taxid;'
when 'taxid,name'
run_sql 'SELECT taxid,name from fasta ORDER BY taxid;'
when 'edit_instructions'
edit_instructions
when 'make_taxonomy_gem','make_gem','gem','makegem',
'make','gemmer'
make_taxonomy_gem
when 'check_available','checkavailable','cavail',
'cavailable','cava'
Taxonomy::CheckAvailable.new
when 'www?','www','cgi?','cgi'
e 'http://localomics.imp.univie.ac.at:8666/'
when 'sdc'
begin
require 'show_directory_content'
ShowDirectoryContent.new
rescue; end when 'all_info_files','all_info','allinfo','fa?'
pp Dir[AA_DIR+'*.fa']
when 'localome?'
localome?
when 'add_comment','comment','addcomment'
(f)
when 'comments?'
'taxid,comment_field'
when 'update_database','ud','updatedatabases','update_databases',
'update_ncbi_database',
'updatencbidatabase','update_ncbi',
'main' update_ncbi_database
when 'finished'
finished
when '',nil
show_short_help
when 'ftp','start_ftp'
begin
require 'ftp_paradise'
FtpParadise::InteractiveFtp.new
rescue LoadError
e 'ftp is not available, it would depend on the ftp_paradise gem.'
end
when 'prokarya?','prokarya','procarya?','procarya',
'show_all_prokarya','spu'
show_all_prokarya
when 'parse','parse_fasta','parsefasta','par','pa','paste',
'papa','pp','fasta','fas','-','pfasta'
_ = ParseFasta.new(f)
_.report_one_sequence
e 'The status for '+sfile(_.location)+' is as follows:'
_.report_status
when 'port?','port','show_port','showport','sport?','sport',
'--port','-port','p?'
show_port
when 'show_changelog','changes?','showchangelog','changelog?'
show_changelog
when 'shared_code?','sharedcode?','show_shared_code_location',
'showsharedcodelocation','sshared','scode?'
show_shared_code_location
when 'pwd','pwd?'
e sdir( ( Dir.pwd+'/' ).squeeze('/') )
when 'edit_gemspec','gemspec','gemspec?','gspec'
edit_gemspec
when 'show_table_names','table_names?','tablenames','tnames',
'table_names','tablenames?','tnames?','1'
show_table_names
when 'paths?'
'taxid,name,path'
when 'create_default_directories','cdd','simulate'
create_default_directories
else if i.include? '.INFO'
'parse_info',i
elsif i.include? '.fa' 'parse_fasta',i
elsif i.include? AA_DIR
'parse_fasta',i
elsif i.include?(',') query_from_localome_table(i)
elsif ::Rcfiles::DirectoryAliases.does_include?(i)
e sdir(rds(Dir.pwd+'/'))
else
e 'In the method menu(), file '+__FILE__.to_s+':'
e 'We did not find the input: `'+sfancy(i.to_s)+'`'
end
end end
|
#names_sql ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1700
def names_sql
store_here = AUTOGENERATED_SQL_FILES_DIR+'names.sql'
File.delete(store_here) if File.exist? store_here
e 'We will populate the names-table next. This will take a while.'
populate_names_table :be_verbose, store_here
end
|
#nodes_sql ⇒ Object
#
nodes_sql
Use this method to generate the nodes.sql file.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1712
def nodes_sql
store_here = AUTOGENERATED_SQL_FILES_DIR+'nodes.sql'
File.delete(store_here) if File.exist? store_here
e 'We will populate the nodes-table next. This will take a while.'
populate_nodes_table :be_verbose, store_here
end
|
#nohelp ⇒ Object
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|
# File 'lib/bioroebe/taxonomy/interactive.rb', line 1002
def nohelp
@no_help = true
end
|
#obtain_full_lineage_for(f) ⇒ Object
Also known as:
get_lineage_ids_and_lineage_scientific_name
#
obtain_full_lineage_for
The input to this method should be an existing TaxID.
#
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|
# File 'lib/bioroebe/taxonomy/interactive.rb', line 1042
def obtain_full_lineage_for(f)
result = return_full_lineage_of(f) if result
@lineage_ids = ''.dup
@lineage_scientific_name = ''.dup
hash = Hash[result]
hash.each {|taxid, scientific_name|
@lineage_ids << taxid.to_s+' -> '
@lineage_scientific_name << scientific_name.chomp+' (Tax id: '+taxid.to_s+'), '
}
@lineage_scientific_name = @lineage_scientific_name.strip
@lineage_scientific_name.chop! if @lineage_scientific_name.end_with? ','
@lineage_ids.strip!
if @lineage_ids.end_with? '->'
@lineage_ids[-2,2] = ''.dup
@lineage_ids.strip!
end
@lineage_scientific_name.chomp!
end
return result
end
|
#open_project_files ⇒ Object
#
open_project_files (open tag)
This method will open the various project files in the editor.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 678
def open_project_files
ARRAY_PROJECT_FILES.each {|entry|
_ = (editor?+' '+PROJECT_BASE_DIR+'lib/taxonomy/'+entry.to_s).squeeze '/'
esystem _
}
end
|
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1484
def process_user_input(i = @user_input)
if i.is_a? Array
i.each {|entry| process_user_input(entry) }
else if i.include? ';'
process_user_input(i.split(';'))
else
(@cmd, @first_argument)
end
end
end
|
#query(i) ⇒ Object
#
query
Formulate a query against the database.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1096
def query(i)
case i.to_s
when 'localome','extended','main'
query_localome_including_path
when 'modtime'
query_localomes_by_modtime
when 'ncbi'
e 'https://www.ncbi.nlm.nih.gov/taxonomy'
end
end
|
#query_from_localome_table(i) ⇒ Object
#
query_from_localome_table
This will display the result as well.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 342
def query_from_localome_table(i)
e get(i)
end
|
#query_localome ⇒ Object
#
query_localome
Query the localome table.
#
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|
# File 'lib/bioroebe/taxonomy/interactive.rb', line 545
def query_localome
e 'These organisms are available locally:'
result = run_query(
'select name,taxid from fasta ORDER BY taxid;',
false, :tuples)
splitted = result.split(N)
splitted.each_with_index {|entry, index|
index += 1
inner_splitted = entry.split('|')
name = inner_splitted[0].strip.ljust(30)
e ' ('+index.to_s+') '+name+' -> TaxID: '+
simp(inner_splitted[1].strip)
}
report_n_registered_organisms_in_localome(splitted.size)
end
|
#query_localome_including_path ⇒ Object
Also known as:
localome?
#
query_localome_including_path
We also show the path here.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 507
def query_localome_including_path
e 'These organisms are available locally:'
result = run_query(
'select name,taxid,path from fasta ORDER BY taxid;',
false, :tuples)
splitted = result.split(N)
splitted.each_with_index {|entry, index|
index += 1
inner_splitted = entry.split('|')
name = inner_splitted[0].strip.ljust(40)
path = 'the local path is at '+N+' '+sfancy(inner_splitted[2])
e ' ('+index.to_s+') '+name+' -> TaxID: '+
simp(inner_splitted[1].strip)+', '+path
}
report_n_registered_organisms_in_localome(splitted.size)
end
|
#query_localomes_by_modtime ⇒ Object
#
query_localomes_by_modtime
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1086
def query_localomes_by_modtime
_ = 'SELECT name,modification_time FROM fasta ORDER BY modification_time;'
run_sql_query _
end
|
#query_whether_we_have_this_id(i) ⇒ Object
#
query_whether_we_have_this_id(i)
We query whether we have a specific ID or whether we don’t.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 365
def query_whether_we_have_this_id(i)
if has_id? i
e 'We do have the id '+simp(i.to_s)+'.'
else
e 'We do not have the id '+simp(i.to_s)+'.'
end
end
|
#rds(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/menu.rb', line 910
def rds(i)
i.squeeze('/')
end
|
#read_in_names_and_nodes_sql_files(be_verbose = true) ⇒ Object
#
read_in_names_and_nodes_sql_files
We use two commands for populating names.sql and nodes.sql tables.
#
#read_sql(i = :fasta) ⇒ Object
#
read_sql
Read in sql into the Postgre Database.
#
#record_last_command(consider_storing_this = '', optional = '') ⇒ Object
#
record_last_command
Use this method to record the last command issued.
The constant LAST_INTERACTIVE_COMMAND determines where we store this.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1168
def record_last_command(
consider_storing_this = '',
optional = ''
)
what = consider_storing_this.to_s.dup what << '|'+optional.to_s unless optional.to_s.empty?
unless what.empty?
unless Dir.exist? TEMP_DIR
e 'We will now create the directory '+sdir(TEMP_DIR)+'.'
ensure_that_temp_dir_exists
end
begin
write_what_into(what, LAST_INTERACTIVE_COMMAND)
rescue Exception => error
e "A small error has happened in the method: "\
"#{__method__}()"
p error
e "Could not write into `#{sfile(into)}`."
end
end unless what.include? 'last?' end
|
#remove_taxid_from_localome_table(i) ⇒ Object
#
remove_taxid_from_localome_table
This method will remove a TaxID from the localome table.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 248
def remove_taxid_from_localome_table(i)
i = i.to_s
if has_id? i
run_sql "
DELETE FROM fasta
WHERE taxid='"+i+"';
"
if be_verbose?
e 'Removed entry '+simp(i)+
' (Taxonomy ID) from the localome (fasta) table.'
end
else
e "Could not find TaxID #{simp(i)}." if be_verbose?
end
end
|
#repeat_last_command ⇒ Object
#report_how_long_it_took_us(i = 0, title_of_table = 'NCBI-based taxonomy table') ⇒ Object
#
report_how_long_it_took_us
The input to this method should be the number of seconds, i.e. 60 seconds.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 623
def report_how_long_it_took_us(
i = 0,
title_of_table = 'NCBI-based taxonomy table'
)
n_minutes = (i.to_f / 60.0).to_s
if n_minutes.size > 4
n_minutes = n_minutes[0,4]
end
e 'Updating the '+title_of_table+' took us '+
sfancy(i.to_s)+' seconds (= '+n_minutes.to_s+' minutes).'
end
|
#report_how_many_info_files_exist_and_how_many_lack_taxonomy_id ⇒ Object
#
report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
This will check on at least one directory.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1335
def report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
_ = get_all_info_entries_with_tax_id
e 'We will try to assess the various .INFO files from the '+
sdir(info_dir?)+'.'
n_info_files = Dir[INFO_DIR+'*.INFO'].size
if n_info_files > 0
e 'We did find '+sfancy(_.size)+' .INFO files with Taxonomy ID. '+
'That means that '+sfancy( Dir[INFO_DIR+'*.INFO'].size - _.size )+
' .INFO files do not have '
e 'a Taxonomy ID. In total there are '+sfancy(n_info_files.to_s)+
' .INFO files there.'
info_files_in_incoming_dir = Dir[INCOMING_DIR+'*.INFO']
if info_files_in_incoming_dir.size > 0
e 'We also found at least one .INFO file in '+sdir(INCOMING_DIR)+'.'
e 'We will display them now:'
pp info_files_in_incoming_dir
end
else
e 'We found no .INFO file there.'
end
end
|
#report_lineage_ids_and_lineage_scientific_name(i) ⇒ Object
#
report_lineage_ids_and_lineage_scientific_name
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 412
def report_lineage_ids_and_lineage_scientific_name(i)
e 'The lineage of all parent ids for Tax ID '+sfancy(i)+' is: '+
@lineage_ids+', and in long form '+@lineage_scientific_name
end
|
#report_lineage_of(f) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 610
def report_lineage_of(f)
obtain_full_lineage_for(f)
report_lineage_ids_and_lineage_scientific_name(f)
e
generate_html_links_for( @lineage_ids.split(' -> ') )
end
|
#report_n_registered_organisms_in_localome(i) ⇒ Object
#
report_n_registered_organisms_in_localome
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 527
def report_n_registered_organisms_in_localome(i)
e 'We have a total of '+sfancy(i.to_s)+' organisms '+
'registered in the localome (== fasta) table.'
end
|
#report_total_amount_of_proteomes(i) ⇒ Object
#
report_total_amount_of_proteomes
The input should be an array of Taxonomy IDs.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 923
def report_total_amount_of_proteomes(i)
if i.is_a? Array
n_entries = 0
i.each {|entry|
n_entries += run_query("select n_accession_numbers from fasta WHERE taxid='"+entry+"';",
false,
:tuples).strip.to_i
}
e 'We have found a total of '+sfancy(n_entries.to_s)+' accession '+
'numbers from the above dataset.'
end
end
|
#report_tree_lineage(i) ⇒ Object
#
report_tree_lineage
This method expects an Array as input, which contains all the IDs that we will report in a tree (hence the name tree here).
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 236
def report_tree_lineage(i)
i.each_with_index {|entry, index|
padding = ' ' * (index+1)
e padding+entry.to_s
}
end
|
#reset ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 101
def reset
super()
infer_the_namespace
@be_verbose = BE_VERBOSE
@use_colours = USE_COLOURS
@no_help = false
@run_standalone = true
end
|
#return_dependencies ⇒ Object
#
return_dependencies
We return the dependencies file here.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1531
def return_dependencies
PROJECT_DOC_DIR+'DEPENDENCIES'
end
|
#return_gemspec_file ⇒ Object
#
return_gemspec_file
We return the main taxonomy.gemspec file here.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 781
def return_gemspec_file
return PROJECT_BASE_DIR+'taxonomy.gemspec'
end
|
#return_instructions ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1538
def return_instructions
PROJECT_DOC_DIR+'INSTRUCTIONS'
end
|
#return_login_file ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 788
def return_login_file
return Bioroebe::Taxonomy.project_base_dir?+'postgresql_login_command.rb'
end
|
#return_shared_code ⇒ Object
#return_taxonomy_file ⇒ Object
#
We return the bin/taxonomy file here.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1515
def return_taxonomy_file
return PROJECT_BASE_DIR+'bin/taxonomy'
end
|
#run ⇒ Object
Also known as:
run_in_interactive_mode
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1949
def run
do_startup_actions
fetch_user_input_via_loop
end
|
#run_connected? ⇒ Boolean
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1804
def run_connected?
! run_standalone?
end
|
#run_standalone? ⇒ Boolean
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1797
def run_standalone?
@run_standalone
end
|
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1471
def sanitize_user_input
splitted = @user_input.split(' ')
@cmd = splitted.first
if @user_input.empty?
@first_argument = nil
else
@first_argument = splitted[1..-1].join(' ') end
end
|
#search_in_database_for_name(i = 'Zygosaccharomyces rouxii') ⇒ Object
#
search_in_database_for_name
Use this method to search in a database for a name.
This is something such as the following SQL query:
select taxid FROM names WHERE name_txt LIKE '%Zygosaccharomyces rouxii%' limit 30;
It will return the TaxID of the organism.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 946
def search_in_database_for_name(i = 'Zygosaccharomyces rouxii')
e 'We will now try to search the names table for '+sfancy(i)+'.'
_ = "select taxid,name_txt FROM names WHERE name_txt LIKE '%"+i+"%' LIMIT 3;"
result = run_sql_query(_, false, :tuples)
return result
end
|
#search_in_localomes(i = 'Blastocystis hominis') ⇒ Object
#
search_in_localomes
This will search in localomes.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 664
def search_in_localomes(i = 'Blastocystis hominis')
if be_verbose?
e 'We will now try to search the fasta table for `'+sfancy(i)+'`.'
end
_ = "select name,modification_time FROM fasta WHERE name LIKE '%"+i+"%' LIMIT 3;"
result = run_sql_query(_, true)
return result
end
|
#select_name_and_lineage_ids ⇒ Object
#
select_name_and_lineage_ids
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 900
def select_name_and_lineage_ids
run_query('select name,lineage_ids from fasta;', false, :tuples)
end
|
#select_name_and_tax_id_and_lineage_ids ⇒ Object
#
select_name_and_tax_id_and_lineage_ids
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 907
def select_name_and_tax_id_and_lineage_ids
run_query('select name,taxid,lineage_ids from fasta;', false, :tuples)
end
|
#select_name_and_tax_id_and_lineage_ids_and_path ⇒ Object
#
select_name_and_tax_id_and_lineage_ids_and_path
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 914
def select_name_and_tax_id_and_lineage_ids_and_path
run_query('select name,taxid,lineage_ids,path from fasta;', false, :tuples)
end
|
#set_commandline_arguments(i = nil) ⇒ Object
#
set_commandline_arguments
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1741
def set_commandline_arguments(i = nil)
i = [i] unless i.is_a? Array
@commandline_arguments = i end
|
#set_database(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1722
def set_database(i)
i = i.to_s.chomp.delete('"')
if i.empty?
e 'Please provide the type of the database you wish to '\
'use, such as "postgresql".'
else
case i
when 'postgre'
i = 'postgresql'
end
i = i.downcase
e 'Storing '+i+' into '+sfile(FILE_USE_THIS_DATABASE)+'.'
write_what_into(i, FILE_USE_THIS_DATABASE)
end
end
|
#set_path(i) ⇒ Object
#
set_path
Use this method to update the path to a local fasta entry, inside the localome entry. In order for this to work, the ID must exist.
Complete usage example:
spath 1257118 /resources/seqdata/curated/sequences/localome/proteomes/Acanthamoeba_castellanii_Neff_pep.fa
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 964
def set_path(i)
if i.include? ' '
splitted = i.split(' ')
taxid_to_update = splitted[0].to_s
new_path = splitted[1].to_s
if has_id? taxid_to_update e 'Now updating path for TaxID '+sfancy(taxid_to_update)+'.'
run_sql "UPDATE fasta SET path='"+new_path+"' WHERE taxid='"+taxid_to_update+"'"
else
e 'We could not find a TaxID '+sfancy(taxid_to_update)+
' in the localome table. Thus can not update the path.'
end
else
if File.exist? i
data = File.readlines(i).map(&:chomp).reject {|entry| entry.empty? }
data.each {|entry|
entry = entry.strip
if entry.include? '|'
splitted = entry.split('|')
else splitted = entry.split("\t")
end
set_path(splitted.first+' '+splitted[1])
}
e 'Note: if you wish to see the modified dataset, input: taxid,path'
else
e 'Format was not correct. Please either provide a file as argument,'
e 'or use input such as this here:'
e
e ' spath 1257118 /resources/seqdata/curated/sequences/localome/proteomes/Acanthamoeba_castellanii_Neff_pep.fa'
e
end
end
end
|
#show_all_eukarya(optional_show_path = false) ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 299
def show_all_eukarya(
optional_show_path = false
)
e 'We found these Eukaryota in the localomes Database:'+N+N
if optional_show_path.is_a? String
_ = select_name_and_tax_id_and_lineage_ids_and_path else
_ = select_name_and_tax_id_and_lineage_ids
end
n_entries = _.split(N).size
result = []
counter = 0
_.split(N).each_with_index {|entry|
splitted = entry.split('|')
lineage = splitted[2]
if lineage =~ / #{Eukaryota_Taxonomy_ID} /
scientific_name = splitted.first.strip
counter += 1
result = simp(counter.to_s)+') '+scientific_name+
' ('+sfancy('TaxID')+': '+splitted[1].to_s.strip+')'
if optional_show_path.is_a? String
result << (' Path: '+splitted[3]).ljust(40) end
e result
result << scientific_name
else end
}
e N+N+'Out of '+sfancy(n_entries.to_s)+' registered '\
'entries in total in the localomes database,'
e sfancy(result.size.to_s)+' belong to Eukaryota (the Taxonomy '\
'ID of Eukaryota is '+sfancy(Eukaryota_Taxonomy_ID.to_s)+').'
array = _.split(N).map {|entry| entry.split('|')[1].strip}
report_total_amount_of_proteomes(array)
end
|
#show_all_prokarya ⇒ Object
#
show_all_prokarya (prokarya tag)
This method will show all entries in the database that are from Prokaryotes.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1413
def show_all_prokarya
_ = select_name_and_tax_id_and_lineage_ids
n_entries = _.split(N).size
result = []
counter = 0
_.split(N).each_with_index {|entry|
splitted = entry.split('|')
lineage = splitted[2]
if lineage =~ / #{Bacteria_Taxonomy_ID} /
scientific_name = splitted.first.strip
counter += 1
e simp(counter.to_s)+') '+scientific_name+' ('+
sfancy('TaxID')+': '+splitted[1].to_s.strip+')'
result << scientific_name
end
}
e N+N+'Out of '+sfancy(n_entries.to_s)+' registered entries in '+
'total in the localomes database,'
e sfancy(result.size.to_s)+' belong to Prokarya (the Taxonomy ID of '+
'Prokarya is '+sfancy(Bacteria_Taxonomy_ID.to_s)+').'
end
|
#show_changelog ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1522
def show_changelog
cat PROJECT_DOC_DIR+'CHANGELOG_FROM_0.0.14_TO_0.0.15'
end
|
#show_configuration ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1693
def show_configuration
e which_database_to_use?
end
|
#show_important_directories ⇒ Object
#
show_important_directories
Delegate towards Taxonomy.status? from here.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1295
def show_important_directories
Taxonomy.status?
end
|
#show_last_command ⇒ Object
#show_lineage_from_localome_table(i) ⇒ Object
#
show_lineage_from_localome_table
The TaxID must exist before we can use this.
Usage examples:
show_lineage_from_localome_table 2762
slocalome 2762
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1318
def show_lineage_from_localome_table(i)
result = run_sql(
"select lineage_ids from fasta WHERE taxid='"+i.to_s+"';", false, :tuples
).chomp.strip
if result.empty?
e 'This TaxID was not found in the localome table.'
e 'To find out which entries exist in the localome table, do "localome?".'
else
e result
end
end
|
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 759
def show_login_information
e 'The login information is stored in the file '
e
e ' '+sfile(
Bioroebe::Taxonomy.project_base_dir?+'databases/postgresql_login_command.rb'
)
e
show_port end
|
#show_nodes_table ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 795
def show_nodes_table
e 'We use these values for the nodes table:'
e
efancy ' taxid'
efancy ' parent_taxid'
efancy ' rank'
e
e 'We will also try to show a random selection of 10 entries from '\
'there now:'
run_sql 'SELECT taxid,parent_taxid,rank FROM nodes
ORDER BY RANDOM(), taxid LIMIT 10'
end
|
#show_port ⇒ Object
#
show_port
Use this method to show the port.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 814
def show_port
e "The port we will use is: #{simp('UNKNOWN')}"
end
|
#show_postgres_size ⇒ Object
#
show_postgres_size
This method will show the size of the postgres database.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1019
def show_postgres_size
e 'Next querying the size of the postgresql table:'
sql_query POSTGRESQL_QUERY_SIZE, true
e 'The total disk size for the robert_db is:'
sql_query "SELECT pg_size_pretty(pg_database_size('robert_db'));",true
e 'Size of '+sfancy(:names)+' is: '+
sql_query(
"SELECT pg_size_pretty(pg_total_relation_size('names'));",false, :tuples)
e 'Size of '+sfancy(:nodes)+' is: '+
sql_query(
"SELECT pg_size_pretty(pg_total_relation_size('nodes'));",false, :tuples)
e 'Size of '+sfancy(:fasta)+' is: '+
sql_query(
"SELECT pg_size_pretty(pg_total_relation_size('fasta'));",false, :tuples)
end
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#show_scientific_name_of(i) ⇒ Object
#
show_scientific_name_of
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 434
def show_scientific_name_of(i)
result = get_scientific_name_of(i).to_s
if result.empty?
e 'We tried to find a Tax ID but we got no result.'
e 'Are you able to connect to the postgresql-database?'
e 'Perhaps this Tax ID does not exist.'
else
e 'The scientific name of Tax ID '+lightblue(i.to_s)+
' is: '+simp(result)
end
end
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#show_shared_code_location ⇒ Object
#
show_shared_code_location
To invoke this method, do:
shared_code?
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1284
def show_shared_code_location
e 'You can find the file shared.rb here:'
_ = base_dir?
e ' '+sfile(_+'/shared.rb')
end
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#show_short_help ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1009
def show_short_help
e '(Type "help" or "?" for help, or "nohelp" to disable '\
'this notification here).' unless @no_help
end
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#show_sql_commands ⇒ Object
Also known as:
sql?, table_names?
#
show_sql_commands (sql tag)
This method will feedback the SQL commands to create our postgre table and also show the Insert commands used.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1823
def show_sql_commands
e N+'The three commands to create the '+
simp('PostgreSQL database')+' are:'+N+N
e ' (1) names table:'+N+N
efancy ' '+create_table(:names).to_s
e N+' (2) nodes table:'+N+N
efancy ' '+create_table(:nodes).to_s
e N+' (3) fasta table:'+N+N
efancy ' '+create_table(:fasta).to_s
end
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#show_sql_commands_only ⇒ Object
#
show_sql_commands_only
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1874
def show_sql_commands_only
e Commands.create_table :taxonomy_nodes
e
e Commands.create_table :taxonomy_names
e
e Commands.create_table :taxonomy_fasta
e
end
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#show_table_names ⇒ Object
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1228
def show_table_names
e N+'The SQL table structure is as follows:'+N+N
efancy 'names.sql'
e ' (1) '+NAMES_ENTRIES+N+N
efancy 'nodes.sql'
e ' (2) '+NODES_ENTRIES+N+N
efancy 'fasta.sql'
e ' (3) '+FASTA_ENTRIES+N+N
end
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#show_type_of_all_info_files(i = nil) ⇒ Object
#
show_type_of_all_info_files
We will get all .INFO files and display the type.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1390
def show_type_of_all_info_files(i = nil)
if i
info = Info.new(i, :silent)
info.find_fasta
if info.fasta?
fasta = ParseFasta.new(info.corresponding_datafile)
e sfile(i)+' is DNA or Protein? '+fasta.type.to_s
else
e 'We could not locate a local fasta entry for '+sfile(i)
end
else Dir[INFO_DIR+'*'].each {|entry|
show_type_of_all_info_files(entry)
}
end
end
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#silently_update_ncbi_database ⇒ Object
#
silently_update_ncbi_database
This method is the one that can be used to silently update the NCBI table via a cron job.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 889
def silently_update_ncbi_database
download :ncbi, :be_silent
'names'
'nodes'
drop_nodes_and_names_database_tables(:be_silent)
read_in_names_and_nodes_sql_files(:be_silent)
end
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#taxtree(i) ⇒ Object
#
taxtree
Obtain the taxtree, then display it. Input to this should be the Taxonomy ID. We will first check the localome table, then query from the two ncbi tables.
To test this method, try:
taxtree 106583
taxtree 77166
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 218
def taxtree(i)
i = i.to_s
e 'The lineage for Taxonomy ID '+simp(i)+' is as follows:'
if has? i lineage_ids = get('lineage_ids', i).strip.split('->').map(&:strip)
else
lineage_ids = return_full_lineage_of(i)
lineage_ids.map! {|entry| entry[0]}
end
report_tree_lineage(lineage_ids)
end
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#try_to_display_the_status(i = nil) ⇒ Object
#
try_to_display_the_status
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 268
def try_to_display_the_status(
i = nil
)
if i and !i.empty? StatFile.new(i) if Object.const_defined?(:StatFile)
else
Taxonomy.status?
Info.status
end
end
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#try_to_show_dependencies ⇒ Object
#
try_to_show_dependencies
Show the dependencies of the Taxonomy Module. This will tell us which dependencies we have to satisfy.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 746
def try_to_show_dependencies
_ = return_dependencies
if File.exist? _
e 'The Taxonomy Module depends on these Ruby Gems:'+N+N
cat _
else
e 'We could not find a file at position `'+sfile(_)+'`.'
end
end
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#try_to_show_instructions ⇒ Object
#
try_to_show_instructions
This method will try to show the instructions to the user, based on what the method return_instructions() will give us.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1502
def try_to_show_instructions
_ = return_instructions
if File.exist? _
e 'Now reading in from file `'+sfile(_)+'`.'
cat _
else
e 'We could not find a file at position '+_
end
end
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#try_to_show_when_the_last_update_has_happened ⇒ Object
#
try_to_show_when_the_last_update_has_happened
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 356
def try_to_show_when_the_last_update_has_happened
e cat(SAVE_FILE) if File.exist? SAVE_FILE
end
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#update_lineage ⇒ Object
#
update_lineage
This will update only the lineage part of the localome database, which means the lineageIDs and the lineage scientific names. In order for this to work, we need to obtain the TaxID of the specific organism.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 826
def update_lineage
e 'We will now obtain all TaxIDs in the localome table.' if be_verbose?
obtain_taxids = run_sql('select taxid from fasta;', false, :tuples).split(N).
map(&:strip).map(&:to_i).sort
obtain_taxids.reject! {|entry|
entry.to_i == 0
}
obtain_taxids.each {|taxid|
e 'Now updating entry with the TaxID: '+sfancy(taxid.to_s)
get_lineage_ids_and_lineage_scientific_name(taxid)
report_lineage_ids_and_lineage_scientific_name(taxid)
if has_id?(taxid)
lineage_id = pad_with_single_quotes(@lineage_ids)
lineage_scientific_name = pad_with_single_quotes(@lineage_scientific_name)
_ = "UPDATE fasta SET lineage_ids="+lineage_id+", lineage_scientific_name="+lineage_scientific_name+" WHERE taxid='"+taxid.to_s+"'"
run_sql_query(_)
e 'Updated entry.' if be_verbose?
else
e 'We did not find the TaxID: '+simp(taxid.to_s)
end
}
e 'Finished updating lineage.' if be_verbose?
end
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#update_local_localomes ⇒ Object
#
update_local_localomes
Update the local collection. This will overwrite the old dataset completely, so be careful when using this.
To invoke this method via the interactive menu, do:
update databases
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 168
def update_local_localomes
show_current_time
create_fasta_table _ = get_all_info_entries_with_tax_id
show_current_time
_.each {|entry|
e "Next working on `#{sfile(entry)}`."
create_sql_file_from_local_fasta_entry(entry)
}
report_how_many_info_files_exist_and_how_many_lack_taxonomy_id
old_time = @time
show_time_now new_time = @time
difference = Time.parse(new_time) - Time.parse(old_time)
report_how_long_it_took_us(difference, 'localome table')
end
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#update_ncbi_database ⇒ Object
Also known as:
update_database
#
update_ncbi_database
This method can be used to update the NCBI Taxonomy database.
This includes a download, extracting it, generating the .sql files, and then populating the postgresql database.
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 569
def update_ncbi_database
download :ncbi if be_verbose?
e 'We will update the local postgre NCBI Table '\
'now (this may take about one hour in total):'
end
'names'
'nodes'
if be_verbose?
e 'We will next load this dataset into the Database.'
e 'First, dropping the old table entries in the Postgresql database '
e 'via the DROP TABLE command:'
end
drop_nodes_and_names_database_tables
nodes_size = File.size(NODES_SQL).to_s
names_size = File.size(NAMES_SQL).to_s
e 'Next we will populate the two tables with '+sfancy('names.sql')+
' (Filesize: '+names_size+') and '+sfancy('nodes.sql')+
' (Filesize: '+nodes_size+') file.'
e 'This may take a while, possibly about an hour, so '\
'please remain patient.'
read_in_names_and_nodes_sql_files
e 'Nota bene: the above commands can only work if psql '\
'is in your $PATH.'
e 'If it did not work, please check and see first '\
'whether your $PATH variable is proper.'
e N+'We will display the content of the $PATH variable '\
'now: '+sfancy(ENV['PATH'])
old_time = @time
show_time_now new_time = @time
difference = Time.parse(new_time) - Time.parse(old_time)
report_how_long_it_took_us(difference)
end
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#use_colours? ⇒ Boolean
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 695
def use_colours?
@use_colours
end
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 719
def user_input?
@user_input
end
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#which_database_to_use? ⇒ Boolean
#
which_database_to_use?
#
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# File 'lib/bioroebe/taxonomy/interactive.rb', line 1686
def which_database_to_use?
File.read(PROJECT_YAML_DIR+'use_this_database.yml')
end
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