Module: Misc
- Defined in:
- lib/rbbt/util/tar.rb,
lib/rbbt/util/misc.rb,
lib/rbbt/util/misc/lock.rb,
lib/rbbt/util/misc/math.rb,
lib/rbbt/util/misc/omics.rb,
lib/rbbt/util/misc/pipes.rb,
lib/rbbt/util/misc/format.rb,
lib/rbbt/util/misc/system.rb,
lib/rbbt/util/misc/inspect.rb,
lib/rbbt/util/misc/objects.rb,
lib/rbbt/util/misc/options.rb,
lib/rbbt/util/misc/development.rb,
lib/rbbt/util/misc/manipulation.rb
Overview
SOURCE: gist.github.com/sinisterchipmunk/1335041 Adapted for Rbbt
Constant Summary collapse
- LOCK_MUTEX =
Mutex.new
- LOCK_REPO_SERIALIZER =
Marshal
- Log2Multiplier =
1.0 / Math.log(2.0)
- Log10Multiplier =
1.0 / Math.log(10.0)
- IUPAC2BASE =
{ "A" => ["A"], "C" => ["C"], "G" => ["G"], "T" => ["T"], "U" => ["U"], "R" => "A or G".split(" or "), "Y" => "C or T".split(" or "), "S" => "G or C".split(" or "), "W" => "A or T".split(" or "), "K" => "G or T".split(" or "), "M" => "A or C".split(" or "), "B" => "C or G or T".split(" or "), "D" => "A or G or T".split(" or "), "H" => "A or C or T".split(" or "), "V" => "A or C or G".split(" or "), "N" => %w(A C T G), }
- BASE2COMPLEMENT =
{ "A" => "T", "C" => "G", "G" => "C", "T" => "A", "U" => "A", }
- THREE_TO_ONE_AA_CODE =
{ "ala" => "A", "arg" => "R", "asn" => "N", "asp" => "D", "cys" => "C", "glu" => "E", "gln" => "Q", "gly" => "G", "his" => "H", "ile" => "I", "leu" => "L", "lys" => "K", "met" => "M", "phe" => "F", "pro" => "P", "ser" => "S", "thr" => "T", "trp" => "W", "tyr" => "Y", "val" => "V" }
- CODON_TABLE =
{ "ATT" => "I", "ATC" => "I", "ATA" => "I", "CTT" => "L", "CTC" => "L", "CTA" => "L", "CTG" => "L", "TTA" => "L", "TTG" => "L", "GTT" => "V", "GTC" => "V", "GTA" => "V", "GTG" => "V", "TTT" => "F", "TTC" => "F", "ATG" => "M", "TGT" => "C", "TGC" => "C", "GCT" => "A", "GCC" => "A", "GCA" => "A", "GCG" => "A", "GGT" => "G", "GGC" => "G", "GGA" => "G", "GGG" => "G", "CCT" => "P", "CCC" => "P", "CCA" => "P", "CCG" => "P", "ACT" => "T", "ACC" => "T", "ACA" => "T", "ACG" => "T", "TCT" => "S", "TCC" => "S", "TCA" => "S", "TCG" => "S", "AGT" => "S", "AGC" => "S", "TAT" => "Y", "TAC" => "Y", "TGG" => "W", "CAA" => "Q", "CAG" => "Q", "AAT" => "N", "AAC" => "N", "CAT" => "H", "CAC" => "H", "GAA" => "E", "GAG" => "E", "GAT" => "D", "GAC" => "D", "AAA" => "K", "AAG" => "K", "CGT" => "R", "CGC" => "R", "CGA" => "R", "CGG" => "R", "AGA" => "R", "AGG" => "R", "TAA" => "*", "TAG" => "*", "TGA" => "*", }
- BLOCK_SIZE =
1024 * 8
- PIPE_MUTEX =
Mutex.new
- OPEN_PIPE_IN =
[]
- COLOR_LIST =
%w(#BC80BD #CCEBC5 #FFED6F #8DD3C7 #FFFFB3 #BEBADA #FB8072 #80B1D3 #FDB462 #B3DE69 #FCCDE5 #D9D9D9)
- ARRAY_MAX_LENGTH =
1000
- STRING_MAX_LENGTH =
ARRAY_MAX_LENGTH * 100
- HASH2MD5_MAX_STRING_LENGTH =
1000
- HASH2MD5_MAX_ARRAY_LENGTH =
100
- MUTEX_FOR_THREAD_EXCLUSIVE =
Mutex.new
- PUSHBULLET_KEY =
begin if ENV["PUSHBULLET_KEY"] ENV["PUSHBULLET_KEY"] else config_api = File.join(ENV['HOME'], 'config/apps/pushbullet/apikey') if File.exist? config_api File.read(config_api).strip else nil end end end
Class Attribute Summary collapse
-
.sensiblewrite_dir ⇒ Object
Returns the value of attribute sensiblewrite_dir.
-
.sensiblewrite_lock_dir ⇒ Object
Returns the value of attribute sensiblewrite_lock_dir.
Class Method Summary collapse
- ._convert_match_condition(condition) ⇒ Object
- ._paste_streams(streams, output, lines = nil, sep = "\t", header = nil) ⇒ Object
- ._untar_cmd(io, destination) ⇒ Object
- ._zip_fields(array, max = nil) ⇒ Object
- .add_defaults(options, defaults = {}) ⇒ Object
- .add_GET_param(url, param, value) ⇒ Object
- .add_libdir(dir = nil) ⇒ Object
- .add_stream_filename(io, filename) ⇒ Object
- .append_zipped(current, new) ⇒ Object
- .array2hash(array, default = nil) ⇒ Object
- .benchmark(repeats = 1, message = nil) ⇒ Object
- .binary_include?(array, elem) ⇒ Boolean
- .bootstrap(elems, num = :current, options = {}, &block) ⇒ Object
- .bootstrap_in_threads(elems, num = :current, options = {}, &block) ⇒ Object
- .break_lines(text, char_size = 80) ⇒ Object
- .camel_case(string) ⇒ Object
- .camel_case_lower(string) ⇒ Object
- .choose(array, select) ⇒ Object
- .collapse_ranges(ranges) ⇒ Object
- .collapse_stream(s, line = nil, sep = "\t", header = nil, &block) ⇒ Object
- .colors_for(list) ⇒ Object
- .common_path(dir, file) ⇒ Object
- .compare_lines(stream1, stream2, args, sort = false) ⇒ Object
- .consolidate(list) ⇒ Object
- .consume_stream(io, in_thread = false, into = nil, into_close = true, &block) ⇒ Object
- .correct_icgc_mutation(pos, ref, mut_str) ⇒ Object
- .correct_mutation(pos, ref, mut_str) ⇒ Object
- .correct_vcf_mutation(pos, ref, mut_str) ⇒ Object
- .counts(array) ⇒ Object
- .digest(text) ⇒ Object
-
.divide(array, num) ⇒ Object
Divides the array into
num
chunks of the same size by placing one element in each chunk iteratively. - .do_once(&block) ⇒ Object
- .dup_stream(stream) ⇒ Object
- .dup_stream_multiple(stream, num = 1) ⇒ Object
- .ensembl_server(organism) ⇒ Object
- .env_add(var, value, sep = ":", prepend = true) ⇒ Object
- .field_position(fields, field, quiet = false) ⇒ Object
- .filename?(string) ⇒ Boolean
- .fingerprint(obj) ⇒ Object
- .fixascii(string) ⇒ Object
- .fixutf8(string) ⇒ Object
- .format_definition_list(defs, size = 80, indent = 20, color = :yellow, sep = "\n\n") ⇒ Object
- .format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow) ⇒ Object
- .format_paragraph(text, size = 80, indent = 0, offset = 0) ⇒ Object
- .format_seconds(time, extended = false) ⇒ Object
- .get_filename(obj) ⇒ Object
- .GET_params2hash(string) ⇒ Object
- .google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) ⇒ Object
-
.gzip(tarfile) ⇒ Object
gzips the underlying string in the given StringIO, returning a new StringIO representing the compressed file.
- .hash2GET_params(hash) ⇒ Object
- .hash2md5(hash) ⇒ Object
- .hash2string(hash) ⇒ Object
- .hash_to_html_tag_attributes(hash) ⇒ Object
- .hostname ⇒ Object
- .html_tag(tag, content = nil, params = {}) ⇒ Object
-
.humanize(value, options = {}) ⇒ Object
source: gist.github.com/ekdevdes/2450285 author: Ethan Kramer (github.com/ekdevdes).
- .humanize_list(list) ⇒ Object
- .in_delta?(a, b, delta = 0.0001) ⇒ Boolean
-
.in_dir(dir) ⇒ Object
WARN: probably not thread safe…
- .index_BED(source, destination, sorted = false) ⇒ Object
- .insist(times = 4, sleep = nil, msg = nil) ⇒ Object
- .intercalate_streams(streams) ⇒ Object
- .intersect_sorted_arrays(a1, a2) ⇒ Object
- .intersect_streams(f1, f2, out, sep = ":") ⇒ Object
- .intersect_streams_cmp_chr(chr1, chr2) ⇒ Object
- .intersect_streams_read(io, sep = ":") ⇒ Object
- .is_filename?(string) ⇒ Boolean
- .IUPAC_to_base(iupac) ⇒ Object
- .lock(file, unlock = true, options = {}) ⇒ Object
- .lock_in_repo(repo, key, *args) ⇒ Object
- .log10(x) ⇒ Object
- .log2(x) ⇒ Object
- .match_fields(field1, field2) ⇒ Object
- .match_value(value, condition) ⇒ Object
- .max(list) ⇒ Object
- .mean(list) ⇒ Object
- .median(array) ⇒ Object
- .memory_use(pid = nil) ⇒ Object
- .memprof ⇒ Object
- .merge_sorted_arrays(a1, a2) ⇒ Object
- .min(list) ⇒ Object
- .mtime_str(path) ⇒ Object
- .name2basename(file) ⇒ Object
- .notify(description, event = 'notification', key = nil) ⇒ Object
- .obj2digest(obj) ⇒ Object
- .obj2md5(obj) ⇒ Object
- .obj2str(obj) ⇒ Object
- .object_delta(*args) ⇒ Object
- .open_pipe(do_fork = false, close = true) ⇒ Object
-
.ordered_divide(array, num) ⇒ Object
Divides the array into chunks of
num
same size by placing one element in each chunk iteratively. - .parse_cmd_params(str) ⇒ Object
- .parse_sql_values(txt) ⇒ Object
- .paste_streams(streams, lines = nil, sep = "\t", header = nil) ⇒ Object
- .path_relative_to(basedir, path) ⇒ Object
- .pid_exists?(pid) ⇒ Boolean
- .pipe ⇒ Object
- .positional2hash(keys, *values) ⇒ Object
- .pre_fork ⇒ Object
- .prepare_entity(entity, field, options = {}) ⇒ Object
- .process_options(hash, *keys) ⇒ Object
- .process_stream(s) ⇒ Object
- .process_to_hash(list) ⇒ Object
- .profile(options = {}) ⇒ Object
- .profile_graph(options = {}) ⇒ Object
- .profile_html(options = {}) ⇒ Object
- .proportions(array) ⇒ Object
- .pull_keys(hash, prefix) ⇒ Object
- .purge_pipes(*save) ⇒ Object
- .random_sample_in_range(total, size) ⇒ Object
- .read_full_stream(io) ⇒ Object
- .read_stream(stream, size) ⇒ Object
- .release_pipes(*pipes) ⇒ Object
- .remove_lines(stream1, stream2, sort) ⇒ Object
- .remove_long_items(obj) ⇒ Object
- .remove_quoted_new_line(stream, quote = '"') ⇒ Object
- .reset_do_once ⇒ Object
- .sample(ary, size, replacement = false) ⇒ Object
- .sample_large_obj(obj, max = 100) ⇒ Object
- .sanitize_filename(filename, length = 254) ⇒ Object
- .save_stream(file, stream) ⇒ Object
- .sd(list) ⇒ Object
- .select_lines(stream1, stream2, sort) ⇒ Object
- .select_ranges(stream1, stream2, sep = "\t") ⇒ Object
- .send_email(from, to, subject, message, options = {}) ⇒ Object
- .sensiblewrite(path, content = nil, options = {}, &block) ⇒ Object
- .snake_case(string) ⇒ Object
- .sort_genomic_locations(stream) ⇒ Object
- .sort_mutation_stream(stream, sep = ":") ⇒ Object
- .sort_mutations(mutations) ⇒ Object
- .sort_stream(stream, header_hash = "#", cmd_args = "-u") ⇒ Object
- .sorted_array_hits(a1, a2) ⇒ Object
- .std_num_vector(v, min, max) ⇒ Object
- .string2const(string) ⇒ Object
-
.string2hash(string) ⇒ Object
options end.
- .sum(list) ⇒ Object
- .swap_quoted_character(stream, charout = "\n", charin = " ", quote = '"') ⇒ Object
-
.tar(path, tarfile = nil) ⇒ Object
Creates a tar file in memory recursively from the given path.
- .tarize(path) ⇒ Object
- .tee_stream_thread(stream) ⇒ Object
-
.tee_stream_thread_multiple(stream, num = 2) ⇒ Object
(also: tee_stream)
- stream_out1, stream_out2
-
end.
- .time_tick ⇒ Object
- .to_utf8(string) ⇒ Object
- .tokenize(str) ⇒ Object
- .total_length(ranges) ⇒ Object
- .translate_dna_mutation_hgvs2rbbt(cds) ⇒ Object
- .translate_prot_mutation_hgvs2rbbt(mutation) ⇒ Object
- .try3times(&block) ⇒ Object
- .txt_digest_str(txt) ⇒ Object
-
.ungzip(tarfile) ⇒ Object
un-gzips the given IO, returning the decompressed version as a StringIO.
-
.untar(io, destination) ⇒ Object
untars the given IO into the specified directory.
- .unzip_in_dir(file, dir) ⇒ Object
- .use_lock_id=(use = true) ⇒ Object
- .variance(list) ⇒ Object
- .with_fifo(path = nil, &block) ⇒ Object
- .zip2hash(list1, list2) ⇒ Object
- .zip_fields(array) ⇒ Object
- .zscore(e, list) ⇒ Object
Class Attribute Details
.sensiblewrite_dir ⇒ Object
Returns the value of attribute sensiblewrite_dir.
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# File 'lib/rbbt/util/misc/pipes.rb', line 13 def sensiblewrite_dir @sensiblewrite_dir end |
.sensiblewrite_lock_dir ⇒ Object
Returns the value of attribute sensiblewrite_lock_dir.
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# File 'lib/rbbt/util/misc/pipes.rb', line 5 def sensiblewrite_lock_dir @sensiblewrite_lock_dir end |
Class Method Details
._convert_match_condition(condition) ⇒ Object
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# File 'lib/rbbt/util/misc.rb', line 28 def self._convert_match_condition(condition) return true if condition == 'true' return false if condition == 'false' return condition.to_regexp if condition[0] == "/" return [:cmp, $1, $2.to_f] if condition =~ /^([<>]=?)(.*)/ return [:invert, _convert_match_condition(condition[1..-1].strip)] if condition[0] == "!" #return {$1 => $2.to_f} if condition =~ /^([<>]=?)(.*)/ #return {false => _convert_match_condition(condition[1..-1].strip)} if condition[0] == "!" return condition end |
._paste_streams(streams, output, lines = nil, sep = "\t", header = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 517 def self._paste_streams(streams, output, lines = nil, sep = "\t", header = nil) output.puts header if header streams = streams.collect do |stream| if defined? Step and Step === stream stream.get_stream || stream.join.path.open else stream end end begin done_streams = [] lines ||= streams.collect{|s| s.gets } keys = [] parts = [] lines.each_with_index do |line,i| if line.nil? keys[i] = nil parts[i] = [] else key, *p = line.chomp.split(sep, -1) keys[i] = key parts[i] = p end end sizes = parts.collect{|p| p.nil? ? 0 : p.length } last_min = nil while lines.compact.any? min = keys.compact.sort.first str = [] keys.each_with_index do |key,i| case key when min str << [parts[i] * sep] line = lines[i] = streams[i].gets if line.nil? keys[i] = nil parts[i] = nil else k, *p = line.chomp.split(sep, -1) keys[i] = k parts[i] = p end else str << [sep * (sizes[i]-1)] if sizes[i] > 0 end end output.puts [min, str*sep] * sep end streams.each do |stream| stream.join if stream.respond_to? :join end rescue Log.exception $! streams.each do |stream| stream.abort if stream.respond_to? :abort end raise $! end end |
._untar_cmd(io, destination) ⇒ Object
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# File 'lib/rbbt/util/tar.rb', line 86 def self._untar_cmd(io, destination) FileUtils.mkdir_p destination unless File.exist? destination CMD.cmd("tar xvf - -C '#{destination}'", :in => io) nil end |
._zip_fields(array, max = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 66 def self._zip_fields(array, max = nil) return [] if array.nil? or array.empty? or (first = array.first).nil? max = array.collect{|l| l.length}.max if max.nil? rest = array[1..-1].collect{|v| v.length == 1 & max > 1 ? v * max : v } first = first * max if first.length == 1 and max > 1 first.zip(*rest) end |
.add_defaults(options, defaults = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 120 def self.add_defaults(, defaults = {}) ||= {} case when Hash === = .dup when String === = string2hash else raise "Format of '#{.inspect}' not understood. It should be a hash" end defaults.each do |key, value| next if .include? key [key] = value end end |
.add_GET_param(url, param, value) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 78 def self.add_GET_param(url, param, value) clean_url, param_str = url.split("?") hash = param_str.nil? ? {} : self.GET_params2hash(param_str) IndiferentHash.setup hash hash[param] = value clean_url << "?" << hash2GET_params(hash) end |
.add_libdir(dir = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 3 def self.add_libdir(dir=nil) dir ||= File.join(Path.caller_lib_dir(caller.first), 'lib') $LOAD_PATH.unshift(dir) unless $LOAD_PATH.include? dir end |
.add_stream_filename(io, filename) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 661 def self.add_stream_filename(io, filename) if ! io.respond_to? :filename class << io attr_accessor :filename end io.filename = filename end end |
.append_zipped(current, new) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 50 def self.append_zipped(current, new) if current.empty? current.replace new.collect{|e| [e]} else current.each do |v| n = new.shift if Array === n v.concat new else v << n end end end current end |
.array2hash(array, default = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 24 def self.array2hash(array, default = nil) hash = {} array.each do |key, value| value = default.dup if value.nil? and not default.nil? hash[key] = value end hash end |
.benchmark(repeats = 1, message = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 32 def self.benchmark(repeats = 1, = nil) require 'benchmark' res = nil begin measure = Benchmark.measure do repeats.times do res = yield end end if puts "#{ }: #{ repeats } repeats" else puts "Benchmark for #{ repeats } repeats" end puts measure rescue Exception puts "Benchmark aborted" raise $! end res end |
.binary_include?(array, elem) ⇒ Boolean
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# File 'lib/rbbt/util/misc/manipulation.rb', line 111 def self.binary_include?(array, elem) upper = array.size - 1 lower = 0 return -1 if upper < lower while(upper >= lower) do idx = lower + (upper - lower) / 2 value = array[idx] case elem <=> value when 0 return true when -1 upper = idx - 1 when 1 lower = idx + 1 else raise "Cannot compare #{[elem.inspect, value.inspect] * " with "}" end end return false end |
.bootstrap(elems, num = :current, options = {}, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 294 def self.bootstrap(elems, num = :current, = {}, &block) IndiferentHash.setup num = :current if num.nil? cpus = case num when :current n = 10 n = elems.length / 2 if n > elems.length/2 n when String num.to_i when Integer if num < 100 num else 32000 / num end else raise "Parameter 'num' not understood: #{Misc.fingerprint num}" end = Misc.add_defaults , :respawn => true, :cpus => cpus = Misc.add_defaults , :bar => "Bootstrap in #{ [:cpus] } cpus: #{ Misc.fingerprint Annotated.purge(elems) }" respawn = [:respawn] and [:cpus] and [:cpus].to_i > 1 index = (0..elems.length-1).to_a.collect{|v| v.to_s } TSV.traverse index, do |pos| elem = elems[pos.to_i] elems.annotate elem if elems.respond_to? :annotate res = begin yield elem rescue Interrupt Log.warn "Process #{Process.pid} was aborted" raise $! end res = nil unless [:into] raise RbbtProcessQueue::RbbtProcessQueueWorker::Respawn, res if respawn == :always and cpus > 1 res end end |
.bootstrap_in_threads(elems, num = :current, options = {}, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 335 def self.bootstrap_in_threads(elems, num = :current, = {}, &block) IndiferentHash.setup num = :current if num.nil? threads = case num when :current 10 when String num.to_i when Integer if num < 100 num else 32000 / num end else raise "Parameter 'num' not understood: #{Misc.fingerprint num}" end = Misc.add_defaults , :respawn => true, :threads => threads = Misc.add_defaults , :bar => "Bootstrap in #{ [:threads] } threads: #{ Misc.fingerprint Annotated.purge(elems) }" index = (0..elems.length-1).to_a.collect{|v| v.to_s } TSV.traverse index, do |pos| elem = elems[pos.to_i] elems.annotate elem if elems.respond_to? :annotate begin res = yield elem rescue Interrupt Log.warn "Process #{Process.pid} was aborted" raise $! end res = nil unless [:into] res end end |
.break_lines(text, char_size = 80) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 5 def self.break_lines(text, char_size=80) text = text.gsub("\n", " ") lines = [] line = [] text.split(/([\s\-]+)/).each do |part| if line.join("").length + part.length > char_size lines << line * "" line = [] end line << part end lines << line * "" lines.flatten.collect{|l| l.strip} * "\n" end |
.camel_case(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 83 def self.camel_case(string) return string if string !~ /_/ && string =~ /[A-Z]+.*/ string.split(/_|(\d+)/).map{|e| (e =~ /^[A-Z]{2,}$/ ? e : e.capitalize) }.join end |
.camel_case_lower(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 90 def self.camel_case_lower(string) string.split('_').inject([]){ |buffer,e| buffer.push(buffer.empty? ? e.downcase : (e =~ /^[A-Z]{2,}$/ ? e : e.capitalize)) }.join end |
.choose(array, select) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 96 def self.choose(array, select) array.zip(select).select{|e,s| s }.collect{|e,s| e } end |
.collapse_ranges(ranges) ⇒ Object
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# File 'lib/rbbt/util/misc/manipulation.rb', line 2 def self.collapse_ranges(ranges) processed = [] last = nil final = [] ranges.sort_by{|range| range.begin }.each do |range| rbegin = range.begin rend = range.end if last.nil? or rbegin > last processed << [rbegin, rend] last = rend else new_processed = [] processed.each do |pbegin,pend| if pend < rbegin final << [pbegin, pend] else eend = [rend, pend].max new_processed << [pbegin, eend] break end end processed = new_processed last = rend if rend > last end end final.concat processed final.collect{|b,e| (b..e)} end |
.collapse_stream(s, line = nil, sep = "\t", header = nil, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 464 def self.collapse_stream(s, line = nil, sep = "\t", header = nil, &block) sep ||= "\t" Misc.open_pipe do |sin| sin.puts header if header process_stream(s) do |s| line ||= s.gets current_parts = [] while line key, *parts = line.chomp.split(sep, -1) case when key.nil? when current_parts.nil? current_parts = parts current_key = key when current_key == key parts.each_with_index do |part,i| if current_parts[i].nil? current_parts[i] = "|" << part else current_parts[i] = current_parts[i] << "|" << part end end (parts.length..current_parts.length-1).to_a.each do |pos| current_parts[pos] = current_parts[pos] << "|" << "" end when current_key.nil? current_key = key current_parts = parts when current_key != key if block_given? res = block.call(current_parts) sin.puts [current_key, res] * sep else sin.puts [current_key, current_parts].flatten * sep end current_key = key current_parts = parts end line = s.gets end if block_given? res = block.call(current_parts) sin.puts [current_key, res] * sep else sin.puts [current_key, current_parts].flatten * sep end unless current_key.nil? end end end |
.colors_for(list) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 4 def self.colors_for(list) unused = COLOR_LIST.dup used = {} colors = list.collect do |elem| if used.include? elem used[elem] else color = unused.shift used[elem]=color color end end [colors, used] end |
.common_path(dir, file) ⇒ Object
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# File 'lib/rbbt/util/misc/system.rb', line 63 def self.common_path(dir, file) file = File. file dir = File. dir return true if file == dir while File.dirname(file) != file file = File.dirname(file) return true if file == dir end return false end |
.compare_lines(stream1, stream2, args, sort = false) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 624 def self.compare_lines(stream1, stream2, args, sort = false) if sort stream1 = Misc.sort_stream stream1 stream2 = Misc.sort_stream stream2 compare_lines(stream1, stream2, args, false) else erase = [] if Path === stream1 or (String === stream1 and File.exist? stream1) file1 = stream1 else file1 = TmpFile.tmp_file erase << file1 Misc.consume_stream(TSV.get_stream(stream1), false, file1) end if Path === stream2 or (String === stream2 and File.exist? stream2) file2 = stream2 else file2 = TmpFile.tmp_file erase << file2 Misc.consume_stream(TSV.get_stream(stream2), false, file2) end CMD.cmd("env LC_ALL=C comm #{args} '#{file1}' '#{file2}'", :pipe => true, :post => Proc.new{ erase.each{|f| FileUtils.rm f } }) end end |
.consolidate(list) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 39 def self.consolidate(list) list.inject(nil){|acc,e| if acc.nil? acc = e else acc.concat e acc end } end |
.consume_stream(io, in_thread = false, into = nil, into_close = true, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 270 def self.consume_stream(io, in_thread = false, into = nil, into_close = true, &block) return if Path === io return unless io.respond_to? :read if io.respond_to? :closed? and io.closed? io.join if io.respond_to? :join return end if in_thread Thread.new(Thread.current) do |parent| begin consume_stream(io, false, into, into_close) rescue Exception parent.raise $! end end else if into Log.medium "Consuming stream #{Misc.fingerprint io} -> #{Misc.fingerprint into}" else Log.medium "Consuming stream #{Misc.fingerprint io}" end begin into = into.find if Path === into if String === into dir = File.dirname(into) FileUtils.mkdir_p dir unless Open.exists?(dir) into_path, into = into, Open.open(into, :mode => 'w') end into.sync = true if IO === into into_close = false unless into.respond_to? :close io.sync = true begin while c = io.readpartial(BLOCK_SIZE) into << c if into end rescue EOFError end io.join if io.respond_to? :join io.close unless io.closed? into.close if into and into_close and not into.closed? into.join if into and into_close and into.respond_to?(:joined?) and not into.joined? block.call if block_given? rescue Aborted Log.medium "Consume stream aborted #{Misc.fingerprint io}" io.abort if io.respond_to? :abort #io.close unless io.closed? FileUtils.rm into_path if into_path and File.exists? into_path rescue Exception Log.medium "Exception consuming stream: #{Misc.fingerprint io}: #{$!.}" io.abort $! if io.respond_to? :abort FileUtils.rm into_path if into_path and File.exists? into_path raise $! end end end |
.correct_icgc_mutation(pos, ref, mut_str) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 119 def self.correct_icgc_mutation(pos, ref, mut_str) mut = mut_str mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/ mut = "+" << mut if ref == '-' [pos, [mut]] end |
.correct_mutation(pos, ref, mut_str) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 126 def self.correct_mutation(pos, ref, mut_str) muts = mut_str.nil? ? [] : mut_str.split(',') muts.collect!{|m| m == '<DEL>' ? '-' : m } ref = '' if ref == '-' while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty? ref = ref[1..-1] raise "REF nil" if ref.nil? pos = pos + 1 muts = muts.collect{|m| m[1..-1]} end muts = muts.collect do |m| m = '' if m == '-' case when ref.empty? "+" << m when (m.length < ref.length and (m.empty? or ref.index(m))) "-" * (ref.length - m.length) when (ref.length == 1 and m.length == 1) m else if ref == '-' res = '+' + m else res = '-' * ref.length res << m unless m == '-' end Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"} res end end [pos, muts] end |
.correct_vcf_mutation(pos, ref, mut_str) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 163 def self.correct_vcf_mutation(pos, ref, mut_str) muts = mut_str.nil? ? [] : mut_str.split(',') muts.collect!{|m| m == '<DEL>' ? '-' : m } while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty? ref = ref[1..-1] raise "REF nil" if ref.nil? pos = pos + 1 unless ref.empty? muts = muts.collect{|m| m[1..-1]} end muts = muts.collect do |m| case when ref.empty? "+" << m when (m.length < ref.length and (m.empty? or ref.index(m))) "-" * (ref.length - m.length) when (ref.length == 1 and m.length == 1) m else if ref == '-' res = '+' + m else res = '-' * ref.length res << m unless m == '-' end Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"} res end end [pos, muts] end |
.counts(array) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 78 def self.counts(array) counts = {} array.each do |e| counts[e] ||= 0 counts[e] += 1 end counts end |
.digest(text) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 135 def self.digest(text) Digest::MD5.hexdigest(text) end |
.divide(array, num) ⇒ Object
Divides the array into num
chunks of the same size by placing one element in each chunk iteratively.
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# File 'lib/rbbt/util/misc/development.rb', line 192 def self.divide(array, num) num = 1 if num == 0 chunks = [] num.to_i.times do chunks << [] end array.each_with_index{|e, i| c = i % num chunks[c] << e } chunks end |
.do_once(&block) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 126 def self.do_once(&block) return nil if $__did_once $__did_once = true yield nil end |
.dup_stream(stream) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 249 def Misc.dup_stream (stream) dup_stream_multiple(stream, 1).first end |
.dup_stream_multiple(stream, num = 1) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 238 def self.dup_stream_multiple(stream, num = 1) stream_dup = stream.dup if stream.respond_to? :annotate stream.annotate stream_dup stream.clear end tee1, *rest = Misc.tee_stream stream_dup, num + 1 stream.reopen(tee1) rest end |
.ensembl_server(organism) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 296 def self.ensembl_server(organism) date = organism.split("/")[1] if date.nil? "www.ensembl.org" else "#{ date }.archive.ensembl.org" end end |
.env_add(var, value, sep = ":", prepend = true) ⇒ Object
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# File 'lib/rbbt/util/misc/system.rb', line 38 def self.env_add(var, value, sep = ":", prepend = true) ENV[var] ||= "" return if ENV[var] =~ /(#{sep}|^)#{Regexp.quote value}(#{sep}|$)/ if prepend ENV[var] = value + sep + ENV[var] else ENV[var] += sep + ENV[var] end end |
.field_position(fields, field, quiet = false) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 100 def self.field_position(fields, field, quiet = false) return field if Integer === field or Range === field raise FieldNotFoundError, "Field information missing" if fields.nil? && ! quiet fields.each_with_index{|f,i| return i if f == field} field_re = Regexp.new /^#{field}$/i fields.each_with_index{|f,i| return i if f =~ field_re} raise FieldNotFoundError, "Field #{ field.inspect } was not found" unless quiet end |
.filename?(string) ⇒ Boolean
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# File 'lib/rbbt/util/misc/system.rb', line 90 def self.filename?(string) String === string and string.length > 0 and string.length < 250 and File.exist?(string) end |
.fingerprint(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 43 def self.fingerprint(obj) case obj when nil "nil" when (defined? Step and Step) "<Step:" << (obj.path || Misc.fingerprint([obj.task.name, obj.inputs])) << ">" when TrueClass "true" when FalseClass "false" when Symbol ":" << obj.to_s when String if obj.length > 100 "'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30)<< "'" else "'" << obj << "'" end when (defined? AnnotatedArray and AnnotatedArray) "<A: #{fingerprint Annotated.purge(obj)} #{fingerprint obj.info}>" when (defined? TSV and TSV::Parser) filename = obj.filename filename = "STDIN(#{rand})" if filename == '-' "<TSVStream:" + (filename || "NOFILENAME") + "--" << Misc.fingerprint(obj.) << ">" when IO (obj.respond_to?(:filename) and obj.filename ) ? "<IO:" + (obj.filename || obj.inspect + rand(100000)) + ">" : obj.inspect when File "<File:" + obj.path + ">" when NamedArray "[<NamedArray: fields=#{fingerprint obj.fields} -- values=#{fingerprint obj[0..-1]}]" when Array if (length = obj.length) > 10 "[#{length}--" << (obj.values_at(0,1, length / 2, -2, -1).collect{|e| fingerprint(e)} * ",") << "]" else "[" << (obj.collect{|e| fingerprint(e) } * ", ") << "]" end when (defined? TSV and TSV) obj.with_unnamed do "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << ";" << fingerprint(obj.keys).inspect << "}" end when Hash if obj.length > 10 "H:{"<< fingerprint(obj.keys) << ";" << fingerprint(obj.values) << "}" else new = "{" obj.each do |k,v| new << fingerprint(k) << '=>' << fingerprint(v) << ' ' end if new.length > 1 new[-1] = "}" else new << '}' end new end else obj.to_s end end |
.fixascii(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 150 def self.fixascii(string) if string.respond_to?(:encode) self.fixutf8(string).encode("ASCII-8BIT") else string end end |
.fixutf8(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 162 def self.fixutf8(string) return nil if string.nil? return string if (string.respond_to? :valid_encoding? and string.valid_encoding?) or (string.respond_to? :valid_encoding and string.valid_encoding) if string.respond_to?(:encode) #string.encode("UTF-16BE", :invalid => :replace, :undef => :replace, :replace => "?").encode('UTF-8') string.encode('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '') else require 'iconv' @@ic ||= Iconv.new('UTF-8//IGNORE', 'UTF-8') @@ic.iconv(string) end end |
.format_definition_list(defs, size = 80, indent = 20, color = :yellow, sep = "\n\n") ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 74 def self.format_definition_list(defs, size = 80, indent = 20, color = :yellow, sep = "\n\n") entries = [] defs.each do |dt,dd| text = format_definition_list_item(dt,dd,size,indent,color) entries << text end entries * sep end |
.format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 56 def self.format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow) dd = "" if dd.nil? dt = Log.color color, dt if color dt = dt.to_s unless dd.empty? len = Log.uncolor(dt).length if indent < 0 text = format_paragraph(dd, size, indent.abs-1, 0) text = dt << "\n" << text else offset = len - indent offset = 0 if offset < 0 text = format_paragraph(dd, size, indent.abs+1, offset) text[0..len-1] = dt end text end |
.format_paragraph(text, size = 80, indent = 0, offset = 0) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 28 def self.format_paragraph(text, size = 80, indent = 0, offset = 0) i = 0 re = /((?:\n\s*\n\s*)|(?:\n\s*(?=\*)))/ text.split(re).collect do |paragraph| i += 1 str = if i % 2 == 1 words = paragraph.gsub(/\s+/, "\s").split(" ") lines = [] line = " "*offset word = words.shift while word word = word[0..size-indent-offset-4] + '...' if word.length >= size - indent - offset while word and Log.uncolor(line).length + Log.uncolor(word).length <= size - indent line << word << " " word = words.shift end lines << ((" " * indent) << line[0..-2]) line = "" end (lines * "\n") else paragraph end offset = 0 str end*"" end |
.format_seconds(time, extended = false) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 21 def self.format_seconds(time, extended = false) seconds = time.to_i str = [seconds/3600, seconds/60 % 60, seconds % 60].map{|t| "%02i" % t }.join(':') str << ".%02i" % ((time - seconds) * 100) if extended str end |
.get_filename(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 330 def self.get_filename(obj) if obj.respond_to? :filename obj.filename elsif obj.respond_to? :path obj.path elsif (Path === obj || (String === obj && Misc.is_filename?(obj))) obj else nil end end |
.GET_params2hash(string) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 54 def self.GET_params2hash(string) hash = {} string.split('&').collect{|item| key, value = item.split("=").values_at 0, 1 hash[key] = value.nil? ? "" : CGI.unescape(value) } hash end |
.google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 106 def self.google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) name1 ||= "list 1" name2 ||= "list 2" name3 ||= "list 3" sizes = [list1, list2, list3, list1 & list2, list1 & list3, list2 & list3, list1 & list2 & list3].collect{|l| l.length} total = total.length if Array === total label = "#{name1}: #{sizes[0]} (#{name2}: #{sizes[3]}, #{name3}: #{sizes[4]})" label << "|#{name2}: #{sizes[1]} (#{name1}: #{sizes[3]}, #{name3}: #{sizes[5]})" label << "|#{name3}: #{sizes[2]} (#{name1}: #{sizes[4]}, #{name2}: #{sizes[5]})" if total label << "| INTERSECTION: #{sizes[6]} TOTAL: #{total}" else label << "| INTERSECTION: #{sizes[6]}" end max = total || sizes.max sizes = sizes.collect{|v| (v.to_f/max * 100).to_i.to_f / 100} url = "https://chart.googleapis.com/chart?cht=v&chs=500x300&chd=t:#{sizes * ","}&chco=FF6342,ADDE63,63C6DE,FFFFFF&chdl=#{label}" end |
.gzip(tarfile) ⇒ Object
gzips the underlying string in the given StringIO, returning a new StringIO representing the compressed file.
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# File 'lib/rbbt/util/tar.rb', line 66 def self.gzip(tarfile) gz = StringIO.new("") z = Zlib::GzipWriter.new(gz) z.write tarfile.string z.close # this is necessary! # z was closed to write the gzip footer, so # now we need a new StringIO StringIO.new gz.string end |
.hash2GET_params(hash) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 63 def self.hash2GET_params(hash) hash.sort_by{|k,v| k.to_s}.collect{|k,v| next unless %w(Symbol String Float Fixnum Integer Numeric TrueClass FalseClass Module Class Object Array).include? v.class.to_s v = case when Symbol === v v.to_s when Array === v v * "," else CGI.escape(v.to_s).gsub('%2F','/') end [ Symbol === k ? k.to_s : k, v] * "=" }.compact * "&" end |
.hash2md5(hash) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 153 def self.hash2md5(hash) return "" if hash.nil? or hash.empty? str = "" keys = hash.keys keys = keys.clean_annotations if keys.respond_to? :clean_annotations keys = keys.sort_by{|k| k.to_s} if hash.respond_to? :unnamed unnamed = hash.unnamed hash.unnamed = true end keys.each do |k| next if k == :monitor or k == "monitor" or k == :in_situ_persistence or k == "in_situ_persistence" _v = hash[k] _k = k v = Annotated.purge(_v) k = Annotated.purge(k) case when TrueClass === v str << k.to_s << "=>true" when FalseClass === v str << k.to_s << "=>false" when Hash === v str << k.to_s << "=>" << hash2md5(v) when Symbol === v str << k.to_s << "=>" << v.to_s when (String === v and v.length > HASH2MD5_MAX_STRING_LENGTH) #str << k.to_s << "=>" << v[0..HASH2MD5_MAX_STRING_LENGTH] << v[v.length-3..v.length+3] << v[-3..-1] << "; #{ v.length }" str << k.to_s << "=>" << v[0..HASH2MD5_MAX_STRING_LENGTH] << "; #{ v.length }" when String === v str << k.to_s << "=>" << v when (Array === v and v.length > HASH2MD5_MAX_ARRAY_LENGTH) #str << k.to_s << "=>[" << (v[0..HASH2MD5_MAX_ARRAY_LENGTH] + v[v.length-3..v.length+3] + v[-3..-1]) * "," << "; #{ v.length }]" str << k.to_s << "=>[" << v[0..HASH2MD5_MAX_ARRAY_LENGTH] * "," << "; #{ v.length }]" when TSV::Parser === v str << remove_long_items(v) when Array === v str << k.to_s << "=>[" << v * "," << "]" when File === v str << k.to_s << "=>[File:" << v.path << "]" else begin v_ins = v.inspect rescue v_ins = "#Object:" << v.object_id.to_s end case when v_ins =~ /:0x0/ str << k.to_s << "=>" << v_ins.sub(/:0x[a-f0-9]+@/,'') else str << k.to_s << "=>" << v_ins end end if _v and defined? Annotated and Annotated === _v and not (defined? AssociationItem and AssociationItem === _v) info = _v.info info = Annotated.purge(info) str << "_" << hash2md5(info) end end hash.unnamed = unnamed if hash.respond_to? :unnamed if str.empty? "" else digest(str) end end |
.hash2string(hash) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 46 def self.hash2string(hash) hash.sort_by{|k,v| k.to_s}.collect{|k,v| next unless %w(Symbol String Float Fixnum Integer Numeric TrueClass FalseClass Module Class Object).include? v.class.to_s [ Symbol === k ? ":" << k.to_s : k, Symbol === v ? ":" << v.to_s : v] * "=" }.compact * "#" end |
.hash_to_html_tag_attributes(hash) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 86 def self.hash_to_html_tag_attributes(hash) return "" if hash.nil? or hash.empty? hash.collect{|k,v| case when (k.nil? or v.nil? or (String === v and v.empty?)) nil when Array === v [k,"'" << v * " " << "'"] * "=" when String === v [k,"'" << v << "'"] * "=" when Symbol === v [k,"'" << v.to_s << "'"] * "=" when TrueClass === v [k,"'" << v.to_s << "'"] * "=" when Numeric === v [k,"'" << v.to_s << "'"] * "=" else nil end }.compact * " " end |
.hostname ⇒ Object
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# File 'lib/rbbt/util/misc/system.rb', line 5 def self.hostname @hostanem ||= `hostname`.strip end |
.html_tag(tag, content = nil, params = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 108 def self.html_tag(tag, content = nil, params = {}) attr_str = hash_to_html_tag_attributes(params) attr_str = " " << attr_str if String === attr_str and attr_str != "" html = if content.nil? "<#{ tag }#{attr_str}/>" else "<#{ tag }#{attr_str}>#{ content }</#{ tag }>" end html end |
.humanize(value, options = {}) ⇒ Object
source: gist.github.com/ekdevdes/2450285 author: Ethan Kramer (github.com/ekdevdes)
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# File 'lib/rbbt/util/misc/format.rb', line 108 def self.humanize(value, = {}) if .empty? [:format] = :sentence end values = value.to_s.split('_') values.each_index do |index| # lower case each item in array # Miguel Vazquez edit: Except for acronyms values[index].downcase! unless values[index].match(/[a-zA-Z][A-Z]/) end if [:format] == :allcaps values.each do |value| value.capitalize! end if .empty? [:seperator] = " " end return values.join " " end if [:format] == :class values.each do |value| value.capitalize! end return values.join "" end if [:format] == :sentence values[0].capitalize! unless values[0].match(/[a-zA-Z][A-Z]/) return values.join " " end if [:format] == :nocaps return values.join " " end end |
.humanize_list(list) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 177 def self.humanize_list(list) return "" if list.empty? if list.length == 1 list.first else list[0..-2].collect{|e| e.to_s} * ", " << " and " << list[-1].to_s end end |
.in_delta?(a, b, delta = 0.0001) ⇒ Boolean
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# File 'lib/rbbt/util/misc/math.rb', line 129 def self.in_delta?(a, b, delta = 0.0001) (a.to_f - b.to_f).abs < delta end |
.in_dir(dir) ⇒ Object
WARN: probably not thread safe…
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# File 'lib/rbbt/util/misc/system.rb', line 77 def self.in_dir(dir) old_pwd = FileUtils.pwd res = nil begin FileUtils.mkdir_p dir unless File.exist?(dir) FileUtils.cd dir res = yield ensure FileUtils.cd old_pwd end res end |
.index_BED(source, destination, sorted = false) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 392 def self.index_BED(source, destination, sorted = false) pos_function = Proc.new do |k| k.split(":").values_at(1, 2).collect{|i| i.to_i} end if Open.exists? destination Persist::Sharder.new destination, false, "fwt", :pos_function => pos_function do |key| key.split(":")[0] end else io = IO === io ? io : Open.open(source) max_size = 0 nio = Misc.open_pipe do |sin| while line = io.gets chr, start, eend, id, *rest = line.split("\t") l = id.length max_size = l if max_size < l chr = chr.sub('chr','') sin << [chr, start, eend, id] * "\t" << "\n" end end TmpFile.with_file do |tmpfile| Misc.consume_stream(nio, false, tmpfile) value_size = max_size destination = destination.find if Path === destination sharder = Persist::Sharder.new destination, true, "fwt", :value_size => value_size, :range => true, :pos_function => pos_function do |key| key.split(":")[0] end TSV.traverse tmpfile, :type => :array, :bar => "Creating BED index for #{Misc.fingerprint source}" do |line| chr, start, eend, id, *rest = line.split("\t") key = [chr, start, eend] * ":" sharder[key] = id end sharder.read sharder end end end |
.insist(times = 4, sleep = nil, msg = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 137 def self.insist(times = 4, sleep = nil, msg = nil) if Array === times sleep_array = times times = sleep_array.length sleep = sleep_array.shift end try = 0 if sleep.nil? sleep_array = ([0] + [0.001, 0.01, 0.1] * (times / 3)).sort[0..times-1] sleep = sleep_array.shift end begin yield rescue TryAgain sleep sleep retry rescue StopInsist raise $!.exception rescue Aborted, Interrupt if msg Log.warn("Not Insisting after Aborted: #{$!.} -- #{msg}") else Log.warn("Not Insisting after Aborted: #{$!.}") end raise $! rescue Exception if msg Log.warn("Insisting after exception: #{$!.class} #{$!.} -- #{msg}") elsif FalseClass === msg nil else Log.warn("Insisting after exception: #{$!.class} #{$!.}") end if sleep and try > 0 sleep sleep sleep = sleep_array.shift || sleep if sleep_array else Thread.pass end try += 1 retry if try < times raise $! end end |
.intercalate_streams(streams) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 607 def self.intercalate_streams(streams) Misc.open_pipe do |sin| continue = true while continue lines = streams.collect{|stream| stream.eof? ? nil : stream.gets }.compact lines.each do |line| sin.puts line end continue = false if lines.empty? end streams.each do |stream| stream.join if stream.respond_to? :join stream.close if stream.respond_to? :close and not stream.closed? end end end |
.intersect_sorted_arrays(a1, a2) ⇒ Object
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# File 'lib/rbbt/util/misc/manipulation.rb', line 60 def self.intersect_sorted_arrays(a1, a2) e1, e2 = a1.shift, a2.shift intersect = [] while true break if e1.nil? or e2.nil? case e1 <=> e2 when 0 intersect << e1 e1, e2 = a1.shift, a2.shift when -1 e1 = a1.shift while not e1.nil? and e1 < e2 when 1 e2 = a2.shift e2 = a2.shift while not e2.nil? and e2 < e1 end end intersect end |
.intersect_streams(f1, f2, out, sep = ":") ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 334 def self.intersect_streams(f1, f2, out, sep=":") finish = false return if f1.eof? or f2.eof? line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep) line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep) while not finish cmp = intersect_streams_cmp_chr(chr1,chr2) case cmp when -1 move = 1 when 1 move = 2 else if eend1 < start2 move = 1 elsif eend2 < start1 move = 2 else pos2 = f2.pos sline2, schr2, sstart2, seend2, srest2 = line2, chr2, start2, eend2, rest2 while chr1 == chr2 and eend1 >= start2 out.puts line1 + "\t" + line2 if start1 <= eend2 if f2.eof? chr2 = 'next2' else line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep) end end line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2 f2.seek(pos2) move = 1 end end case move when 1 if f1.eof? finish = true else line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep) end when 2 if f2.eof? finish = true else line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep) end end end end |
.intersect_streams_cmp_chr(chr1, chr2) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 322 def self.intersect_streams_cmp_chr(chr1, chr2) if chr1 =~ /^\d+$/ and chr2 =~ /^\d+$/ chr1 <=> chr2 elsif chr1 =~ /^\d+$/ -1 elsif chr2 =~ /^\d+$/ 1 else chr1 <=> chr2 end end |
.intersect_streams_read(io, sep = ":") ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 309 def self.intersect_streams_read(io, sep=":") line = io.gets.chomp parts = line.split(sep, -1) chr, start, eend, *rest = parts start = start.to_i if eend =~ /^\d+(\t.*)?$/ eend = eend.to_i else eend = start.to_i end [line,chr, start, eend, rest] end |
.is_filename?(string) ⇒ Boolean
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# File 'lib/rbbt/util/misc/system.rb', line 94 def self.is_filename?(string) return true if defined? PATH and Path === string return true if string.respond_to? :exists return true if String === string and string.length < 265 and File.exist? string return false end |
.IUPAC_to_base(iupac) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 264 def self.IUPAC_to_base(iupac) IUPAC2BASE[iupac] end |
.lock(file, unlock = true, options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/lock.rb', line 21 def self.lock(file, unlock = true, = {}) unlock, = true, unlock if Hash === unlock return yield if file.nil? and not Lockfile === [:lock] file = file.find if Path === file FileUtils.mkdir_p File.dirname(File.(file)) unless File.exist? File.dirname(File.(file)) case [:lock] when Lockfile lockfile = [:lock] lockfile.lock unless lockfile.locked? when FalseClass lockfile = nil unlock = false when Path, String lock_path = [:lock].find lockfile = Lockfile.new(lock_path, ) lockfile.lock else lock_path = File.(file + '.lock') lockfile = Lockfile.new(lock_path, ) lockfile.lock end res = nil begin res = yield lockfile rescue KeepLocked unlock = false res = $!.payload ensure if unlock begin if lockfile.locked? lockfile.unlock else end rescue Exception Log.warn "Exception unlocking: #{lockfile.path}" Log.exception $! end end end res end |
.lock_in_repo(repo, key, *args) ⇒ Object
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# File 'lib/rbbt/util/misc/lock.rb', line 72 def self.lock_in_repo(repo, key, *args) return yield file, *args if repo.nil? or key.nil? lock_key = "lock-" << key begin if repo[lock_key] and Misc.hostname == (info = LOCK_REPO_SERIALIZER.load(repo[lock_key]))["host"] and info["pid"] and not Misc.pid_exists?(info["pid"]) Log.info("Removing lockfile: #{lock_key}. This pid #{Process.pid}. Content: #{info.inspect}") repo.out lock_key end rescue Log.warn("Error checking lockfile #{lock_key}: #{$!.}. Removing. Content: #{begin repo[lock_key] rescue "Could not open file" end}") repo.out lock_key if repo.include? lock_key end while repo[lock_key] sleep 1 end repo[lock_key] = LOCK_REPO_SERIALIZER.dump({:hostname => Misc.hostname, :pid => Process.pid}) res = yield lock_key, *args repo.delete lock_key res end |
.log10(x) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 10 def self.log10(x) Math.log(x) * Log10Multiplier end |
.log2(x) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 6 def self.log2(x) Math.log(x) * Log2Multiplier end |
.match_fields(field1, field2) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 3 def self.match_fields(field1, field2) return true if field1 == field2 if m = field1.match(/\((.*)\)/) field1 = m[1] end if m = field2.match(/\((.*)\)/) field2 = m[1] end field1 == field2 end |
.match_value(value, condition) ⇒ Object
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# File 'lib/rbbt/util/misc.rb', line 39 def self.match_value(value, condition) condition = _convert_match_condition(condition.strip) if String === condition case condition when Regexp !! value.match(condition) when NilClass, TrueClass value === TrueClass or (String === value and value.downcase == 'true') when FalseClass value === FalseClass or (String === value and value.downcase == 'false') when String Numeric === value ? value.to_f == condition.to_f : value == condition when Numeric value.to_f == condition.to_f when Array case condition.first when :cmp value.to_f.send(condition[1], condition[2]) when :invert ! match_value(value, condition[1] ) else condition.inject(false){|acc,e| acc = acc ? true : match_value(value, e) } end else raise "Condition not understood: #{Misc.fingerprint condition}" end end |
.max(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 14 def self.max(list) max = nil list.each do |v| next if v.nil? max = v if max.nil? or v > max end max end |
.mean(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 45 def self.mean(list) sum(list).to_f / list.compact.length end |
.median(array) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 49 def self.median(array) sorted = array.sort len = sorted.length (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0 end |
.memory_use(pid = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 371 def self.memory_use(pid=nil) `ps -o rss -p #{pid || $$}`.strip.split.last.to_i end |
.memprof ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 110 def self.memprof require 'memprof' Memprof.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure Memprof.stop print Memprof.stats end res end |
.merge_sorted_arrays(a1, a2) ⇒ Object
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# File 'lib/rbbt/util/misc/manipulation.rb', line 79 def self.merge_sorted_arrays(a1, a2) e1, e2 = a1.shift, a2.shift new = [] while true case when (e1 and e2) case e1 <=> e2 when 0 new << e1 e1, e2 = a1.shift, a2.shift when -1 new << e1 e1 = a1.shift when 1 new << e2 e2 = a2.shift end when e2 new << e2 new.concat a2 break when e1 new << e1 new.concat a1 break else break end end new end |
.min(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 23 def self.min(list) min = nil list.each do |v| next if v.nil? min = v if min.nil? or v < min end min end |
.mtime_str(path) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 231 def self.mtime_str(path) path = path.find if Path === path if File.exists? path "mtime: " << File.mtime(path).to_s else "mtime: not present" end end |
.name2basename(file) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 22 def self.name2basename(file) sanitize_filename(file.gsub("/",'>').gsub("~", '-')) end |
.notify(description, event = 'notification', key = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 388 def self.notify(description, event='notification', key = nil) if PUSHBULLET_KEY.nil? and key.nil? Log.warn "Could not notify, no PUSHBULLET_KEY" return end Thread.new do application = 'rbbt' event ||= 'notification' key ||= PUSHBULLET_KEY `curl -s --header "Authorization: Bearer #{key}" -X POST https://api.pushbullet.com/v2/pushes --header 'Content-Type: application/json' --data-binary '{"type": "note", "title": "#{event}", "body": "#{description}"}'` end end |
.obj2digest(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 316 def self.obj2digest(obj) str = obj2str(obj) if str.empty? "" else digest(str) end end |
.obj2md5(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 326 def self.obj2md5(obj) obj2digest(obj) end |
.obj2str(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 241 def self.obj2str(obj) _obj = obj obj = Annotated.purge(obj) if Annotated === obj str = case obj when TrueClass 'true' when FalseClass 'false' when Hash "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}" when Symbol obj.to_s when (defined? Path and Path) if obj.exists? if obj.directory? "directory: #{obj.glob("**/*")}" else "file: " << obj << "--" << mtime_str(obj) end else obj + " (file missing)" end when String obj = obj.chomp if String === obj if obj.length > HASH2MD5_MAX_STRING_LENGTH sample_large_obj(obj, HASH2MD5_MAX_STRING_LENGTH) << "--" << txt_digest_str(obj) else obj end when Array if obj.length > HASH2MD5_MAX_ARRAY_LENGTH "[" << sample_large_obj(obj, HASH2MD5_MAX_ARRAY_LENGTH).collect{|v| obj2str(v)} * "," << "]" else "[" << obj.collect{|v| obj2str(v)} * "," << "]" end when TSV::Parser remove_long_items(obj) when File if obj.respond_to? :filename and obj.filename "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">" else "<IO:" << obj.path << "--" << mtime_str(obj.path) << ">" end when (defined? Step and Step) "<IO:" << obj.path << ">" when IO if obj.respond_to? :filename and obj.filename "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">" else obj.inspect + rand(1000000).to_s end else if obj.respond_to? :filename and obj.filename "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">" else obj_ins = obj.inspect obj_str = if obj_ins =~ /:0x0/ obj_ins.gsub(/:0x[a-f0-9]+/,'') else obj_ins end end end if defined? Annotated and Annotated === _obj and not (defined? AssociationItem and AssociationItem === _obj) info = Annotated.purge(_obj.info) str << "_" << obj2str(info) end str end |
.object_delta(*args) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 260 def self.object_delta(*args) res, delta = nil, nil MUTEX_FOR_THREAD_EXCLUSIVE.synchronize do pre = Set.new delta = Set.new GC.start ObjectSpace.each_object(*args) do |o| pre.add o end res = yield GC.start ObjectSpace.each_object(*args) do |o| delta.add o unless pre.include? o end end Log.info "Delta: #{delta.inspect}" res end |
.open_pipe(do_fork = false, close = true) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 64 def self.open_pipe(do_fork = false, close = true) raise "No block given" unless block_given? sout, sin = Misc.pipe if do_fork parent_pid = Process.pid pid = Process.fork { purge_pipes(sin) sout.close begin yield sin sin.close if close and not sin.closed? rescue Exception Log.exception $! Process.kill :INT, parent_pid Kernel.exit! -1 end Kernel.exit! 0 } sin.close ConcurrentStream.setup sout, :pids => [pid] else ConcurrentStream.setup sin, :pair => sout thread = Thread.new(Thread.current) do |parent| begin yield sin sin.close if close and not sin.closed? and not sin.aborted? rescue Aborted Log.medium "Aborted open_pipe: #{$!.}" rescue Exception Log.medium "Exception in open_pipe: #{$!.}" Log.exception $! parent.raise $! raise $! end end sin.threads = [thread] ConcurrentStream.setup sout, :threads => [thread], :pair => sin end sout end |
.ordered_divide(array, num) ⇒ Object
Divides the array into chunks of num
same size by placing one element in each chunk iteratively.
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# File 'lib/rbbt/util/misc/development.rb', line 205 def self.ordered_divide(array, num) last = array.length - 1 chunks = [] current = 0 while current <= last next_current = [last, current + num - 1].min chunks << array[current..next_current] current = next_current + 1 end chunks end |
.parse_cmd_params(str) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 3 def self.parse_cmd_params(str) return str if Array === str str.scan(/ (?:["']([^"']*?)["']) | ([^"'\s]+) /x).flatten.compact end |
.parse_sql_values(txt) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 186 def self.parse_sql_values(txt) io = StringIO.new txt.strip values = [] fields = [] current = nil quoted = false while c = io.getc if quoted if c == "'" quoted = false else current << c end else case c when "(" current = "" when ")" fields << current values << fields fields = [] current = nil when ',' if not current.nil? fields << current current = "" end when "'" quoted = true when ";" break else current << c end end end values end |
.paste_streams(streams, lines = nil, sep = "\t", header = nil) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 579 def self.paste_streams(streams, lines = nil, sep = "\t", header = nil) sep ||= "\t" num_streams = streams.length Misc.open_pipe do |sin| self._paste_streams(streams, sin, lines, sep, header) end end |
.path_relative_to(basedir, path) ⇒ Object
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# File 'lib/rbbt/util/misc/system.rb', line 48 def self.path_relative_to(basedir, path) path = File.(path) unless path[0] == "/" basedir = File.(basedir) unless basedir[0] == "/" if path.index(basedir) == 0 if basedir[-1] == "/" return path[basedir.length..-1] else return path[basedir.length+1..-1] end else return nil end end |
.pid_exists?(pid) ⇒ Boolean
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# File 'lib/rbbt/util/misc/system.rb', line 9 def self.pid_exists?(pid) return false if pid.nil? begin Process.getpgid(pid.to_i) true rescue Errno::ESRCH false end end |
.pipe ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 24 def self.pipe OPEN_PIPE_IN.delete_if{|pipe| pipe.closed? } res = PIPE_MUTEX.synchronize do sout, sin = IO.pipe OPEN_PIPE_IN << sin [sout, sin] end Log.debug{"Creating pipe #{[res.last.inspect,res.first.inspect] * " => "}"} res end |
.positional2hash(keys, *values) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 11 def self.positional2hash(keys, *values) if Hash === values.last extra = values.pop inputs = Misc.zip2hash(keys, values) inputs.delete_if{|k,v| v.nil? or (String === v and v.empty?)} inputs = Misc.add_defaults inputs, extra inputs.delete_if{|k,v| not keys.include?(k) and not (Symbol === k ? keys.include?(k.to_s) : keys.include?(k.to_sym))} inputs else Misc.zip2hash(keys, values) end end |
.pre_fork ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 8 def self.pre_fork Persist::CONNECTIONS.values.each do |db| db.close if db.write? end Log::ProgressBar::BARS.clear ObjectSpace.each_object(Mutex) do |m| begin m.unlock rescue ThreadError end if m.locked? end end |
.prepare_entity(entity, field, options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 16 def self.prepare_entity(entity, field, = {}) return entity unless defined? Entity return entity unless String === entity or Array === entity ||= {} dup_array = .delete :dup_array if Entity === field or (Entity.respond_to?(:formats) and (_format = Entity.formats.find(field))) params = .dup params[:format] ||= params.delete "format" params.merge!(:format => _format) unless _format.nil? or (params.include?(:format) and not ((f = params[:format]).nil? or (String === f and f.empty?))) mod = Entity === field ? field : Entity.formats[field] entity = mod.setup( ((entity.frozen? and not entity.nil?) ? entity.dup : ((Array === entity and dup_array) ? entity.collect{|e| e.nil? ? e : e.dup} : entity) ), params ) end entity end |
.process_options(hash, *keys) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 140 def self.(hash, *keys) if keys.length == 1 hash.include?(keys.first.to_sym) ? hash.delete(keys.first.to_sym) : hash.delete(keys.first.to_s) else keys.collect do |key| hash.include?(key.to_sym) ? hash.delete(key.to_sym) : hash.delete(key.to_s) end end end |
.process_stream(s) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 427 def self.process_stream(s) begin yield s s.join if s.respond_to? :join rescue s.abort if s.respond_to? :abort raise $! end end |
.process_to_hash(list) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 41 def self.process_to_hash(list) result = yield list zip2hash(list, result) end |
.profile(options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 93 def self.profile( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop printer = RubyProf::FlatPrinter.new(result) printer.print(STDOUT, ) end res end |
.profile_graph(options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 75 def self.profile_graph( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop #result.eliminate_methods!([/annotated_array_clean_/]) printer = RubyProf::GraphPrinter.new(result) printer.print(STDOUT, ) end res end |
.profile_html(options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 54 def self.profile_html( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop printer = RubyProf::MultiPrinter.new(result) TmpFile.with_file do |dir| FileUtils.mkdir_p dir unless File.exist? dir printer.print(:path => dir, :profile => 'profile') CMD.cmd("firefox -no-remote '#{ dir }'") end end res end |
.proportions(array) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 88 def self.proportions(array) total = array.length proportions = Hash.new 0 array.each do |e| proportions[e] += 1.0 / total end class << proportions; self;end.class_eval do def to_s sort{|a,b| a[1] == b[1] ? a[0] <=> b[0] : a[1] <=> b[1]}.collect{|k,c| "%3d\t%s" % [c, k]} * "\n" end end proportions end |
.pull_keys(hash, prefix) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 148 def self.pull_keys(hash, prefix) new = {} hash.keys.each do |key| if key.to_s =~ /#{ prefix }_(.*)/ case when String === key new[$1] = hash.delete key when Symbol === key new[$1.to_sym] = hash.delete key end else if key.to_s == prefix.to_s new[key] = hash.delete key end end end new end |
.purge_pipes(*save) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 55 def self.purge_pipes(*save) PIPE_MUTEX.synchronize do OPEN_PIPE_IN.each do |pipe| next if save.include? pipe pipe.close unless pipe.closed? end end end |
.random_sample_in_range(total, size) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 217 def self.random_sample_in_range(total, size) p = Set.new if size > total / 10 template = (0..total - 1).to_a size.times do |i| pos = (rand * (total - i)).floor if pos == template.length - 1 v = template.pop else v, n = template[pos], template[-1] template.pop template[pos] = n end p << v end else size.times do pos = nil while pos.nil? pos = (rand * total).floor if p.include? pos pos = nil end end p << pos end end p end |
.read_full_stream(io) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 257 def self.read_full_stream(io) str = "" begin while block = io.read(BLOCK_SIZE) str << block end io.join if io.respond_to? :join rescue io.abort if io.respond_to? :abort end str end |
.read_stream(stream, size) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 331 def self.read_stream(stream, size) str = nil Thread.pass while IO.select([stream],nil,nil,1).nil? while not str = stream.read(size) IO.select([stream],nil,nil,1) Thread.pass raise ClosedStream if stream.eof? end while str.length < size raise ClosedStream if stream.eof? IO.select([stream],nil,nil,1) if new = stream.read(size-str.length) str << new end end str end |
.release_pipes(*pipes) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 47 def self.release_pipes(*pipes) PIPE_MUTEX.synchronize do pipes.flatten.each do |pipe| pipe.close unless pipe.closed? end end end |
.remove_lines(stream1, stream2, sort) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 652 def self.remove_lines(stream1, stream2, sort) self.compare_lines(stream1, stream2, '-2 -3', sort) end |
.remove_long_items(obj) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 104 def self.remove_long_items(obj) case when IO === obj remove_long_items("IO: " + (obj.respond_to?(:filename) ? (obj.filename || obj.inspect) : obj.inspect )) when obj.respond_to?(:path) remove_long_items("File: " + obj.path) when TSV::Parser === obj filename = obj.filename filename = "STDIN(rand-#{rand(10000000)})" if filename == '-' remove_long_items("TSV Stream: " + filename + " -- " << Misc.fingerprint(obj.)) when TSV === obj remove_long_items((obj.all_fields || []) + obj.keys.sort) when (Array === obj and obj.length > ARRAY_MAX_LENGTH) remove_long_items(obj[0..ARRAY_MAX_LENGTH-2] << "TRUNCATED at #{ ARRAY_MAX_LENGTH }/#{obj.length}") when (Hash === obj and obj.length > ARRAY_MAX_LENGTH) remove_long_items(obj.collect.compact[0..ARRAY_MAX_LENGTH-2] << ["TRUNCATED", "at #{ ARRAY_MAX_LENGTH }/#{obj.length}"]) when (String === obj and obj.length > STRING_MAX_LENGTH) obj[0..STRING_MAX_LENGTH-1] << " TRUNCATED at #{STRING_MAX_LENGTH}/#{obj.length}" when Hash === obj new = {} obj.each do |k,v| new[k] = remove_long_items(v) end new when Array === obj obj.collect do |e| remove_long_items(e) end else obj end end |
.remove_quoted_new_line(stream, quote = '"') ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 697 def self.remove_quoted_new_line(stream, quote = '"') swap_quoted_character(stream, "\n", " ", quote) end |
.reset_do_once ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 133 def self.reset_do_once $__did_once = false end |
.sample(ary, size, replacement = false) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 248 def self.sample(ary, size, replacement = false) if ary.respond_to? :sample ary.sample size else total = ary.length p = random_sample_in_range(total, size) ary.values_at *p end end |
.sample_large_obj(obj, max = 100) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 139 def self.sample_large_obj(obj, max = 100) length = obj.length head = obj[0..max/2] tail = obj[-max/2..-1] middle = (1..9).to_a.collect{|i| pos = (length / 10) * i + i; obj[pos-1..pos+1]}.flatten if Array === obj head + middle + tail + ["LENGTH: #{obj.length}"] else head << "..." << middle*"," << "..." << tail << "(#{obj.length})" end end |
.sanitize_filename(filename, length = 254) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 26 def self.sanitize_filename(filename, length = 254) if filename.length > length if filename =~ /(\..{2,9})$/ extension = $1 else extension = '' end post_fix = "--#{filename.length}@#{length}_#{Misc.digest(filename)[0..4]}" + extension filename = filename[0..(length - post_fix.length - 1)] << post_fix else filename end filename end |
.save_stream(file, stream) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 587 def self.save_stream(file, stream) out, save = Misc.tee_stream stream out.filename = file save.filename = file Thread.new(Thread.current) do |parent| begin Misc.sensiblewrite(file, save) rescue Exception save.abort if save.respond_to? :abort stream.abort if stream.respond_to? :abort stream.join Log.medium "Exception in save_stream: #{$!.}" raise $! end end out end |
.sd(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 72 def self.sd(list) return nil if list.length < 3 variance = self.variance(list) Math.sqrt(variance) end |
.select_lines(stream1, stream2, sort) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 656 def self.select_lines(stream1, stream2, sort) self.compare_lines(stream1, stream2, '-1 -2', sort) end |
.select_ranges(stream1, stream2, sep = "\t") ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 386 def self.select_ranges(stream1, stream2, sep = "\t") Misc.open_pipe do |sin| intersect_streams(stream1, stream2,sin, sep) end end |
.send_email(from, to, subject, message, options = {}) ⇒ Object
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# File 'lib/rbbt/util/misc/system.rb', line 19 def self.send_email(from, to, subject, , = {}) IndiferentHash.setup() = Misc.add_defaults , :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login server, port, user, pass, from_alias, to_alias, auth = Misc. , :server, :port, :user, :pass, :from_alias, :to_alias, :auth msg = <<-END_OF_MESSAGE From: #{from_alias} <#{from}> To: #{to_alias} <#{to}> Subject: #{subject} #{} END_OF_MESSAGE Net::SMTP.start(server, port, server, user, pass, auth) do |smtp| smtp. msg, from, to end end |
.sensiblewrite(path, content = nil, options = {}, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 350 def self.sensiblewrite(path, content = nil, = {}, &block) force = Misc. , :force if Open.exists? path and not force Misc.consume_stream content return end = Misc.pull_keys .dup, :lock = [:lock] if Hash === [:lock] tmp_path = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_dir}) tmp_path_lock = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_lock_dir}) tmp_path_lock = nil if FalseClass === [:lock] Misc.lock tmp_path_lock, do if Open.exists? path and not force Log.warn "Path exists in sensiblewrite, not forcing update: #{ path }" Misc.consume_stream content else FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory? File.dirname(tmp_path) FileUtils.rm_f tmp_path if File.exist? tmp_path begin case when block_given? File.open(tmp_path, 'wb', &block) when String === content File.open(tmp_path, 'wb') do |f| f.write content end when (IO === content or StringIO === content or File === content) Open.write(tmp_path) do |f| f.sync = true while block = content.read(BLOCK_SIZE) f.write block end end else File.open(tmp_path, 'wb') do |f| end end begin Misc.insist do Open.mv tmp_path, path, end rescue Exception raise $! unless File.exist? path end FileUtils.touch path if File.exist? path content.join if content.respond_to? :join and not (content.respond_to?(:joined?) and content.joined?) if Lockfile === [:lock] and [:lock].locked? [:lock].unlock end Open.notify_write(path) rescue Aborted Log.medium "Aborted sensiblewrite -- #{ Log.reset << Log.color(:blue, path) }" content.abort if content.respond_to? :abort Open.rm path if File.exist? path rescue Exception exception = (AbortedStream === content and content.exception) ? content.exception : $! Log.medium "Exception in sensiblewrite: [#{Process.pid}] #{exception.} -- #{ Log.color :blue, path }" content.abort if content.respond_to? :abort Open.rm path if File.exist? path raise exception rescue Log.exception $! raise $! ensure FileUtils.rm_f tmp_path if File.exist? tmp_path end end end end |
.snake_case(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 96 def self.snake_case(string) return nil if string.nil? string = string.to_s if Symbol === string string. gsub(/([A-Z]{2,})([A-Z][a-z])/,'\1_\2'). gsub(/([a-z])([A-Z])/,'\1_\2'). gsub(/\s/,'_').gsub(/[^\w_]/, ''). split("_").collect{|p| p.match(/[A-Z]{2,}/) ? p : p.downcase } * "_" end |
.sort_genomic_locations(stream) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 305 def self.sort_genomic_locations(stream) sort_stream(stream, '#', '-k1,1 -k2,2n -t:') end |
.sort_mutation_stream(stream, sep = ":") ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 670 def self.sort_mutation_stream(stream, sep=":") CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true) end |
.sort_mutations(mutations) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 269 def self.sort_mutations(mutations) mutations.collect do |mutation| chr,pos,mut = mutation.split ":" chr.sub!(/^chr/i,'') chr = 22 if chr == "Y" chr = 23 if chr == "X" chr = 24 if chr == "MT" or chr == "M" [chr.to_i, pos.to_i, mut, mutation] end.sort do |a,b| case a[0] <=> b[0] when -1 -1 when 1 1 when 0 case a[1] <=> b[1] when -1 -1 when 1 1 when 0 a[2] <=> b[2] end end end.collect{|p| p.last } end |
.sort_stream(stream, header_hash = "#", cmd_args = "-u") ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 437 def self.sort_stream(stream, header_hash = "#", cmd_args = "-u") Misc.open_pipe do |sin| begin stream = TSV.get_stream stream line = stream.gets while line =~ /^#{header_hash}/ do sin.puts line line = stream.gets end line_stream = Misc.open_pipe do |line_stream_in| line_stream_in.puts line Misc.consume_stream(stream, false, line_stream_in) end sorted = CMD.cmd("env LC_ALL=C sort #{cmd_args || ""}", :in => line_stream, :pipe => true) Misc.consume_stream(sorted, false, sin) rescue if defined? step and step step.abort end end end end |
.sorted_array_hits(a1, a2) ⇒ Object
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# File 'lib/rbbt/util/misc/manipulation.rb', line 36 def self.sorted_array_hits(a1, a2) e1, e2 = a1.shift, a2.shift counter = 0 match = [] while true break if e1.nil? or e2.nil? case e1 <=> e2 when 0 match << counter e1, e2 = a1.shift, a2.shift counter += 1 when -1 while not e1.nil? and e1 < e2 e1 = a1.shift counter += 1 end when 1 e2 = a2.shift e2 = a2.shift while not e2.nil? and e2 < e1 end end match end |
.std_num_vector(v, min, max) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 32 def self.std_num_vector(v, min, max) v_min = Misc.min(v) v_max = Misc.max(v) v_range = v_max - v_min range = max.to_f - min.to_f v.collect{|e| min + range * (e.to_f - v_min) / v_range } end |
.string2const(string) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 21 def self.string2const(string) return nil if string.nil? mod = Kernel string.to_s.split('::').each do |str| mod = mod.const_get str end mod end |
.string2hash(string) ⇒ Object
options end
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# File 'lib/rbbt/util/misc/options.rb', line 214 def self.string2hash(string) = {} string.split('#').each do |str| key, sep, value = str.partition "=" key = key[1..-1].to_sym if key[0] == ":" [key] = true and next if value.empty? [key] = value[1..-1].to_sym and next if value[0] == ":" [key] = Regexp.new(/#{value[1..-2]}/) and next if value[0] == "/" and value[-1] == "/" [key] = value[1..-2] and next if value =~ /^['"].*['"]$/ [key] = value.to_i and next if value =~ /^\d+$/ [key] = value.to_f and next if value =~ /^\d*\.\d+$/ [key] = true and next if value == "true" [key] = false and next if value == "false" [key] = value and next [key] = begin saved_safe = $SAFE $SAFE = 0 eval(value) rescue Exception value ensure $SAFE = saved_safe end end return = {} string.split(/#/).each do |str| if str.match(/(.*)=(.*)/) option, value = $1, $2 else option, value = str, true end option = option.sub(":",'').to_sym if option.chars.first == ':' value = value.sub(":",'').to_sym if String === value and value.chars.first == ':' if value == true [option] = option.to_s.chars.first != '!' else [option] = Thread.start do $SAFE = 0; case when value =~ /^(?:true|T)$/i true when value =~ /^(?:false|F)$/i false when Symbol === value value when (String === value and value =~ /^\/(.*)\/$/) Regexp.new /#{$1}/ else begin Kernel.const_get value rescue begin raise if value =~ /[a-z]/ and defined? value eval(value) rescue Exception value end end end end.value end end end |
.sum(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 41 def self.sum(list) list.compact.inject(0.0){|acc,e| acc += e} end |
.swap_quoted_character(stream, charout = "\n", charin = " ", quote = '"') ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 675 def self.swap_quoted_character(stream, charout="\n", charin=" ", quote='"') io = Misc.open_pipe do |sin| begin quoted = false prev = nil while c = stream.getc if c == quote and not prev == "\\" quoted = ! quoted end c = charin if c == charout and quoted sin << c prev = c end rescue stream.abort if stream.respond_to? :abort raise $! ensure stream.join if stream.respond_to? :join end end end |
.tar(path, tarfile = nil) ⇒ Object
Creates a tar file in memory recursively from the given path.
Returns a StringIO whose underlying String is the contents of the tar file.
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# File 'lib/rbbt/util/tar.rb', line 14 def self.tar(path, tarfile = nil) tarfile ||= StringIO.new("") Gem::Package::TarWriter.new(tarfile) do |tar| Dir[File.join(path, "**/*")].each do |file| mode = File.stat(file).mode relative_file = file.sub /^#{Regexp::escape path}\/?/, '' if File.directory?(file) tar.mkdir relative_file, mode else tar.add_file relative_file, mode do |tf| File.open(file, "rb") { |f| tf.write f.read } end end end end tarfile.rewind tarfile end |
.tarize(path) ⇒ Object
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# File 'lib/rbbt/util/tar.rb', line 37 def self.tarize(path, gz = nil) gz ||= StringIO.new('wb') tar = Misc.in_dir(path) do self.tar('.') end tar.rewind string = tar.string z = Zlib::GzipWriter.new(gz) z.write string z.close gz.reopen('read') gz.rewind gz end |
.tee_stream_thread(stream) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 234 def self.tee_stream_thread(stream) tee_stream_thread_multiple(stream, 2) end |
.tee_stream_thread_multiple(stream, num = 2) ⇒ Object Also known as: tee_stream
- stream_out1, stream_out2
-
end
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# File 'lib/rbbt/util/misc/pipes.rb', line 170 def self.tee_stream_thread_multiple(stream, num = 2) in_pipes = [] out_pipes = [] num.times do sout, sin = Misc.pipe in_pipes << sin out_pipes << sout end filename = stream.filename if stream.respond_to? :filename splitter_thread = Thread.new(Thread.current) do |parent| begin skip = [false] * num begin while block = stream.readpartial(BLOCK_SIZE) in_pipes.each_with_index do |sin,i| begin sin.write block rescue IOError Log.error("Tee stream #{i} #{Misc.fingerprint stream} IOError: #{$!.}"); skip[i] = true end unless skip[i] end end rescue IOError end in_pipes.first.close rescue Aborted, Interrupt stream.abort if stream.respond_to? :abort out_pipes.each do |sout| sout.abort if sout.respond_to? :abort end Log.medium "Tee aborting #{Misc.fingerprint stream}" raise $! rescue Exception stream.abort if stream.respond_to? :abort out_pipes.each do |sout| sout.abort if sout.respond_to? :abort end Log.medium "Tee exception #{Misc.fingerprint stream}" raise $! end end out_pipes.each do |sout| ConcurrentStream.setup sout, :threads => splitter_thread, :filename => filename, :_pair => stream end out_pipes.first.autojoin = true out_pipes.first.callback = Proc.new do stream.join in_pipes[1..-1].each do |sin| sin.close unless sin.closed? end end out_pipes end |
.time_tick ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 283 def self.time_tick if $_last_time_tick.nil? $_last_time_tick = Time.now puts "Tick started: #{Time.now}" else ellapsed = Time.now - $_last_time_tick puts "Tick ellapsed: #{ellapsed.to_i} s. #{(ellapsed * 1000).to_i - ellapsed.to_i * 1000} ms" $_last_time_tick = Time.now end end |
.to_utf8(string) ⇒ Object
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# File 'lib/rbbt/util/misc/format.rb', line 158 def self.to_utf8(string) string.encode("UTF-16BE", :invalid => :replace, :undef => :replace, :replace => "?").encode('UTF-8') end |
.tokenize(str) ⇒ Object
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# File 'lib/rbbt/util/misc.rb', line 67 def self.tokenize(str) str.scan(/"[^"]*"|'[^']*'|[^"'\s]+/) end |
.total_length(ranges) ⇒ Object
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# File 'lib/rbbt/util/misc/manipulation.rb', line 32 def self.total_length(ranges) self.collapse_ranges(ranges).inject(0) do |total,range| total += range.end - range.begin + 1 end end |
.translate_dna_mutation_hgvs2rbbt(cds) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 199 def self.translate_dna_mutation_hgvs2rbbt(cds) change = case when cds =~ />/ cds.split(">").last when cds =~ /del/ deletion = cds.split("del").last.chomp case when deletion =~ /^\d+$/ "-" * deletion.to_i when deletion =~ /^[ACTG]+$/i "-" * deletion.length else Log.debug "Unknown deletion: #{ deletion }" deletion end when cds =~ /ins/ insertion = cds.split("ins").last case when insertion =~ /^\d+$/ "+" + "N" * insertion.to_i when insertion =~ /^[NACTG]+$/i "+" + insertion else Log.debug "Unknown insertion: #{insertion }" insertion end else Log.debug "Unknown change: #{cds}" "?(" << cds << ")" end change end |
.translate_prot_mutation_hgvs2rbbt(mutation) ⇒ Object
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# File 'lib/rbbt/util/misc/omics.rb', line 232 def self.translate_prot_mutation_hgvs2rbbt(mutation) one_aa_code = THREE_TO_ONE_AA_CODE.values one_aa_code << "X" << "B" << "Z" << "J" << "*" << "?" one_aa_code_re = one_aa_code*"" subs = Regexp.new("^[#{one_aa_code_re}]\\d+[#{one_aa_code_re}]") f_aa = Regexp.new("^[#{one_aa_code_re}]\\d+") mutation.sub!('p.', '') mutation = case when mutation =~ subs mutation when mutation =~ /fs/ mutation =~ f_aa if Regexp.last_match(0).nil? Log.debug "Unknown Frameshift: #{mutation}" nil else Regexp.last_match(0) + "Frameshift" end when mutation =~ /ins|del|>/ mutation =~ f_aa if Regexp.last_match(0).nil? Log.debug "Unknown Indel" nil else Regexp.last_match(0) + "Indel" end else Log.debug "Unknown change: #{mutation}" nil end end |
.try3times(&block) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 186 def self.try3times(&block) insist(3, &block) end |
.txt_digest_str(txt) ⇒ Object
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# File 'lib/rbbt/util/misc/inspect.rb', line 227 def self.txt_digest_str(txt) "digest: " << digest(txt) end |
.ungzip(tarfile) ⇒ Object
un-gzips the given IO, returning the decompressed version as a StringIO
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# File 'lib/rbbt/util/tar.rb', line 79 def self.ungzip(tarfile) z = Zlib::GzipReader.new(tarfile) unzipped = StringIO.new(z.read) z.close unzipped end |
.untar(io, destination) ⇒ Object
untars the given IO into the specified directory
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# File 'lib/rbbt/util/tar.rb', line 94 def self.untar(io, destination) return _untar_cmd(io, destination) end |
.unzip_in_dir(file, dir) ⇒ Object
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# File 'lib/rbbt/util/misc/development.rb', line 402 def self.unzip_in_dir(file, dir) raise "Target is not a directory: #{file}" if File.exist?(dir) and not File.directory?(dir) if Open.remote? file file = file.find if Path === file Open.open(file) do |stream| TmpFile.with_file(stream.read, true, :extension => 'zip') do |zip_file| CMD.cmd("unzip '#{zip_file}' -d '#{dir}'") end end else file = file.find if Path === file zip_file = file CMD.cmd("unzip '#{zip_file}' -d '#{dir}'") end end |
.use_lock_id=(use = true) ⇒ Object
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# File 'lib/rbbt/util/misc/lock.rb', line 2 def self.use_lock_id=(use = true) if use Log.medium "Activating lockfile ids" Lockfile.dont_use_lock_id = false Lockfile.refresh = 2 Lockfile.max_age = 30 Lockfile.suspend = 4 else Log.medium "De-activating lockfile ids" Lockfile.dont_use_lock_id = true Lockfile.refresh = 4 Lockfile.max_age = 60 Lockfile.suspend = 8 end end |
.variance(list) ⇒ Object
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# File 'lib/rbbt/util/misc/math.rb', line 55 def self.variance(list) return nil if list.length < 3 mean = mean(list) list = list.compact list_length = list.length total_square_distance = 0.0 list.each do |value| distance = value.to_f - mean total_square_distance += distance * distance end variance = total_square_distance / (list_length - 1) end |
.with_fifo(path = nil, &block) ⇒ Object
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# File 'lib/rbbt/util/misc/pipes.rb', line 36 def self.with_fifo(path = nil, &block) begin erase = path.nil? path = TmpFile.tmp_file if path.nil? File.mkfifo path yield path ensure FileUtils.rm path if erase end end |
.zip2hash(list1, list2) ⇒ Object
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# File 'lib/rbbt/util/misc/options.rb', line 33 def self.zip2hash(list1, list2) hash = {} list1.each_with_index do |e,i| hash[e] = list2[i] end hash end |
.zip_fields(array) ⇒ Object
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# File 'lib/rbbt/util/misc/objects.rb', line 77 def self.zip_fields(array) if array.length < 10000 _zip_fields(array) else zipped_slices = [] max = array.collect{|l| l.length}.max array.each_slice(10000) do |slice| zipped_slices << _zip_fields(slice, max) end new = zipped_slices.first zipped_slices[1..-1].each do |rest| rest.each_with_index do |list,i| new[i].concat list end end new end end |