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/serialize.rb,
lib/rbbt/util/misc/development.rb,
lib/rbbt/util/misc/manipulation.rb,
lib/rbbt/util/misc/communication.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

SKIP_TAG =

"[SKIP TAG]"

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 =

STRING_MAX_LENGTH =

ARRAY_MAX_LENGTH * 100

TSV_MAX_FIELDS =

TSV_MAX_ROWS =

HASH2MD5_MAX_STRING_LENGTH =

HASH2MD5_MAX_ARRAY_LENGTH =

RBBT_IDENTIFY_PATH =

ENV["RBBT_IDENTIFY_PATH"] != 'false'

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

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`

# File 'lib/rbbt/util/misc.rb', line 32

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, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 553

def self._paste_streams(streams, output, lines = nil, sep = "\t", header = nil, &block)
  output.puts header if header
  streams = streams.collect do |stream|
    if defined? Step and Step === stream
      io = stream.get_stream 
      if io
        buffer_stream(io)
      else
        stream.join.path.open
      end
    else
      stream
    end
  end

  begin

    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?
      if block_given?
        min = keys.compact.sort(&block).first
      else
        min = keys.compact.sort.first
      end
      str = []
      threads = []
      keys.each_with_index do |key,i|
        case key
        when min
          if parts[i] == [SKIP_TAG]
            str << [sep * (sizes[i]-1)] if sizes[i] > 0
          else
            str << [parts[i] * sep]
          end

          line = lines[i] = streams[i].gets

          if line.nil? 
            keys[i] = nil
            parts[i] = nil
            streams[i].close unless streams[i].closed?
            streams[i].join if streams[i].respond_to?(:join) 
          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.flatten*sep] * sep
    end

    streams.each do |stream|
      stream.close unless stream.closed?
      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`

# File 'lib/rbbt/util/tar.rb', line 86

def self._untar_cmd(io, destination)
  FileUtils.mkdir_p destination unless File.exist? destination
  CMD.cmd_log("tar xvf - -C '#{destination}'", :in => io)
  nil
end

._zip_fields(array, max = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/objects.rb', line 67

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`

# File 'lib/rbbt/util/misc/options.rb', line 120

def self.add_defaults(options, defaults = {})
  options ||= {}
  case
  when Hash === options
    new_options = options.dup
  when String === options
    new_options = string2hash options
  else
    raise "Format of '#{options.inspect}' not understood. It should be a hash"
  end

  defaults.each do |key, value|
    next if options.include? key

    new_options[key] = value 
  end

  new_options

  options.replace new_options
end

.add_GET_param(url, param, value) ⇒ `Object`

# 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`

# 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`

# File 'lib/rbbt/util/misc/pipes.rb', line 718

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`

# File 'lib/rbbt/util/misc/objects.rb', line 51

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`

# 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`

# File 'lib/rbbt/util/misc/development.rb', line 32

def self.benchmark(repeats = 1, message = nil)
  require 'benchmark'
  res = nil
  begin
    measure = Benchmark.measure do
      repeats.times do
        res = yield
      end
    end
    if message
      STDERR.pust "#{message }: #{ repeats } repeats"
    else
      STDERR.puts "Benchmark for #{ repeats } repeats"
    end
    STDERR.puts measure
  rescue Exception
    STDERR.puts "Benchmark aborted"
    raise $!
  end
  res
end

.binary_include?(array, elem) ⇒ `Boolean`

Returns:

(Boolean)

# 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 = nil, options = {}, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 310

def self.bootstrap(elems, num = nil, options = {}, &block)
  IndiferentHash.setup options

  num = Rbbt::Config.get :cpus, :default_bootstrap_cpus, :bootstrap_cpus if num == :current || num == nil if defined?(Rbbt::Config)
  num = :current if num.nil?
  cpus = case num
         when :current
           n = Etc.nprocessors
           n = elems.length / 2 if n > elems.length/2

           if $BOOTSTRAPPED_CURRENT && $BOOTSTRAPPED_CURRENT + n > Etc.nprocessors
             1
           else
             n
           end
         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


  options = Misc.add_defaults options, :respawn => true, :cpus => cpus
  options = Misc.add_defaults options, :bar => "Bootstrap in #{ options[:cpus] } cpus: #{ Misc.fingerprint Annotated.purge(elems) }"
  respawn = options[:respawn] and options[:cpus] and options[:cpus].to_i > 1

  index = (0..elems.length-1).to_a.collect{|v| v.to_s }

  TSV.traverse index, options do |pos|
    if num == :current
      $BOOTSTRAPPED_CURRENT ||= n 
      $BOOTSTRAPPED_CURRENT += 0 
    end
    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 options[:into]
    raise RbbtProcessQueue::RbbtProcessQueueWorker::Respawn, res if respawn == :always and cpus > 1
    res
  end
end

.bootstrap_in_threads(elems, num = :current, options = {}, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 363

def self.bootstrap_in_threads(elems, num = :current, options = {}, &block)
  IndiferentHash.setup options
  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


  options = Misc.add_defaults options, :respawn => true, :threads => threads
  options = Misc.add_defaults options, :bar => "Bootstrap in #{ options[:threads] } threads: #{ Misc.fingerprint Annotated.purge(elems) }"

  index = (0..elems.length-1).to_a.collect{|v| v.to_s }
  TSV.traverse index, options 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 options[:into]
    res
  end
end

.break_lines(text, char_size = 80) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 7

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

.buffer_stream(stream) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 547

def self.buffer_stream(stream)
  sout, sin = Misc.pipe
  Misc.consume_stream(stream, true, sin)
  sout
end

.camel_case(string) ⇒ `Object`

# File 'lib/rbbt/util/misc/format.rb', line 88

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`

# File 'lib/rbbt/util/misc/format.rb', line 95

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 97

def self.choose(array, select)
  array.zip(select).select{|e,s| s }.collect{|e,s| e }
end

.chr_cmp_contigs(chr1, chr2, contigs) ⇒ `Object`



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# File 'lib/rbbt/util/misc/omics.rb', line 386

def self.chr_cmp_contigs(chr1, chr2, contigs)
  contigs.index(chr1) <=> contigs.index(chr2)
end

.chr_cmp_strict(chr1, chr2) ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 372

def self.chr_cmp_strict(chr1, chr2)
  chr1 = chr1.sub(/^chr/, '')
  chr2 = chr2.sub(/^chr/, '')
  if (m1 = chr1.match(/(\d+)$/)) && (m2 = chr2.match(/(\d+)$/))
    m1[1].to_i <=> m2[1].to_i
  elsif chr1 =~ /\d+$/
    -1
  elsif chr2 =~ /\d+$/
    1
  else
    chr1 <=> chr2
  end
end

.chunk(array, num) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 196

def self.chunk(array, num)
  total = array.length
  current = 0
  while current < total
    last = current + num - 1
    yield array[current..last]
    current = last + 1
  end
end

.collapse_ranges(ranges) ⇒ `Object`

# 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`

# File 'lib/rbbt/util/misc/pipes.rb', line 494

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`

# 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`

# File 'lib/rbbt/util/misc/system.rb', line 54

def self.common_path(dir, file)
  file = File.expand_path file
  dir = File.expand_path 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`

# File 'lib/rbbt/util/misc/pipes.rb', line 681

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`

# File 'lib/rbbt/util/misc/objects.rb', line 40

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 290

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)
        Open.mkdir 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?

      #Log.medium "Done consuming stream #{Misc.fingerprint io}"
    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.exist? into_path
    rescue Exception
      Log.medium "Exception consuming stream: #{Misc.fingerprint io}: #{$!.message}"
      io.abort $! if io.respond_to? :abort
      FileUtils.rm into_path if into_path and File.exist? into_path
      raise $!
    end
  end
end

.correct_icgc_mutation(pos, ref, mut_str) ⇒ `Object`

# 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`

# 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`

# 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? or ref == '-')
      "+" << 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
    when (ref == m)
      nil
    else
      if ref == '-'
        res = '+' + m
      else
        if ref[0] == m[0]
          res = '+' << m[1..-1]
        else
          res = '-' * ref.length
          res << m unless m == '-'
        end
      end
      Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}

      res
    end
  end.compact

  [pos, muts]
end

.counts(array) ⇒ `Object`

# File 'lib/rbbt/util/misc/math.rb', line 77

def self.counts(array)
  counts = {}
  array.each do |e|
    counts[e] ||= 0
    counts[e] += 1
  end

  counts
end

.digest(text) ⇒ `Object`



169
170
171

# File 'lib/rbbt/util/misc/inspect.rb', line 169

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.

# File 'lib/rbbt/util/misc/development.rb', line 208

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`

# 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`



269
270
271

# File 'lib/rbbt/util/misc/pipes.rb', line 269

def self.dup_stream(stream)
  dup_stream_multiple(stream, 1).first
end

.dup_stream_multiple(stream, num = 1) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 252

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)

  #ToDo: I can't explain why the @threads variable appears with the value of
  # @filename
  stream.instance_variable_set(:@threads, nil) if stream.instance_variables.include?(:@threads)

  tee1.annotate(stream)
  rest
end

.ensembl_server(organism) ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 330

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`

# File 'lib/rbbt/util/misc/system.rb', line 17

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`

Raises:

(FieldNotFoundError)

# File 'lib/rbbt/util/misc/objects.rb', line 101

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

.file2md5(file) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 432

def self.file2md5(file)
  if File.exist?(file + '.md5')
    Open.read(file + '.md5')
  else
    md5 = CMD.cmd("md5sum '#{file}'").read.strip.split(" ").first
    begin
      Open.write(file + '.md5', md5)
    rescue
    end
    md5
  end
end

.fingerprint(obj) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 45

def self.fingerprint(obj)
  case obj
  when nil
    "nil"
  when (defined? Step and Step)
    "<Step:"  << (obj.short_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
      digest = Misc.digest(obj)
      "'" << obj.slice(0,30) << "<...#{obj.length} - #{digest[0..4]}...>" << 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.options) << ">"
  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
    fields = obj.fields
    fields = fields.collect if NamedArray === fields
    "[<NamedArray: fields=#{fingerprint 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|| []) << ";" << fingerprint(obj.keys) << "}"
    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
  when Float
    if obj.abs > 10
      "%.1f" % obj
    elsif obj.abs > 1
      "%.3f" % obj
    else
      "%.6f" % obj
    end
  else
    obj.to_s
  end
end

.fixascii(string) ⇒ `Object`

# File 'lib/rbbt/util/misc/format.rb', line 155

def self.fixascii(string)
  if string.respond_to?(:encode)
    self.fixutf8(string).encode("ASCII-8BIT") 
  else
    string
  end
end

.fixutf8(string) ⇒ `Object`

# File 'lib/rbbt/util/misc/format.rb', line 167

def self.fixutf8(string)
  return nil if string.nil?
  return string if string.respond_to?(:encoding) && string.encoding.to_s == "UTF-8" && (string.respond_to?(:valid_encoding?) && string.valid_encoding?) ||
                   (string.respond_to?(:valid_encoding) && string.valid_encoding)

  if string.respond_to?(:encode)
    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`

# File 'lib/rbbt/util/misc/format.rb', line 79

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`

# File 'lib/rbbt/util/misc/format.rb', line 61

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`

# File 'lib/rbbt/util/misc/format.rb', line 28

def self.format_paragraph(text, size = 80, indent = 0, offset = 0)
  i = 0
  offset = 0 if offset.nil?
  indent = 0 if indent.nil?
  size = 80 if size.nil?
  size = size + offset + indent
  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
              offset = 0
              lines << ((" " * indent) << line[0..-2])
              line = ""
            end
            (lines * "\n")
          else
            paragraph
          end
    offset = 0
    str
    end*""
end

.format_seconds(time, extended = false) ⇒ `Object`

# 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

.genomic_location_cmp(gpos1, gpos2, sep = ":") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 390

def self.genomic_location_cmp(gpos1, gpos2, sep = ":")
  chr1, _sep, pos1 = gpos1.partition(sep)
  chr2, _sep, pos2 = gpos2.partition(sep)
  cmp = chr1 <=> chr2
  case cmp
  when 0
    pos1.to_i <=> pos2.to_i
  else
    cmp
  end
end

.genomic_location_cmp_contigs(gpos1, gpos2, contigs, sep = ":") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 414

def self.genomic_location_cmp_contigs(gpos1, gpos2, contigs, sep = ":")
  chr1, _sep, pos1 = gpos1.partition(sep)
  chr2, _sep, pos2 = gpos2.partition(sep)
  cmp = chr_cmp_contigs(chr1, chr2, contigs)
  case cmp
  when 0
    pos1.to_i <=> pos2.to_i
  else
    cmp
  end
end

.genomic_location_cmp_strict(gpos1, gpos2, sep = ":") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 402

def self.genomic_location_cmp_strict(gpos1, gpos2, sep = ":")
  chr1, _sep, pos1 = gpos1.partition(sep)
  chr2, _sep, pos2 = gpos2.partition(sep)
  cmp = chr_cmp_strict(chr1, chr2)
  case cmp
  when 0
    pos1.to_i <=> pos2.to_i
  else
    cmp
  end
end

.genomic_mutations_to_BED(mutations, chr_prefix = false, sort_order = :normal) ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 533

def self.genomic_mutations_to_BED(mutations, chr_prefix = false, sort_order = :normal)
  io = if Array === sort_order

         case chr_prefix.to_s.downcase
         when "remove"
           sort_order = sort_order.collect{|chr| chr.sub('chr', '') }  if sort_order.first.include?('chr') 
         when "true", "add"
           sort_order = sort_order.collect{|chr| "chr" + chr }  unless sort_order.first.include?('chr')
         end

         sort_genomic_locations_by_contig(mutations, sort_order)

       else

         case sort_order.to_s
         when 'strict'
           sort_genomic_locations_strict(mutations)
         else
           sort_genomic_locations(mutations)
         end

       end

  TSV.traverse io, :type => :array, :into => :stream do |mutation|
    chr, pos, mut, *rest = mutation.split(":")
    size = case mut
           when nil
             1
           when /^\+(.*)/
             1 + $1.length
           when /^\-(.*)/
             $1.length
           else
             mut.length
           end

    case chr_prefix.to_s.downcase
    when "true", "add"
      chr = "chr" + chr if ! chr.include?('chr')
    when "remove"
      chr = chr.sub("chr", '') if chr.include?('chr')
    end
    [chr, pos.to_i - 1, pos.to_i - 1 + size, mutation] * "\t"
  end
end

.get_filename(obj) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 445

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`

# 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`

# File 'lib/rbbt/util/misc/math.rb', line 105

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.

# 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`

# 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`

# File 'lib/rbbt/util/misc/inspect.rb', line 187

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 = TSV === _v ? _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 TSV === v
      str << k.to_s << "=>" << obj2md5(v)
    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`

# 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.to_s.chomp,
      Symbol === v ? ":" << v.to_s : v.to_s.chomp] * "="
  }.compact * "#"
end

.hash_to_html_tag_attributes(hash) ⇒ `Object`

# 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 3

def self.hostname
  @hostanem ||= `hostname`.strip
end

.html_tag(tag, content = nil, params = {}) ⇒ `Object`

# 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.to_s }</#{ tag }>"
  end

  html
end

.humanize(value, options = {}) ⇒ `Object`

source: gist.github.com/ekdevdes/2450285 author: Ethan Kramer (github.com/ekdevdes)

# File 'lib/rbbt/util/misc/format.rb', line 113

def self.humanize(value, options = {})
  if options.empty?
    options[: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 options[:format] == :allcaps
    values.each do |value|
      value.capitalize!
    end

    if options.empty?
      options[:seperator] = " "
    end

    return values.join " "
  end

  if options[:format] == :class
    values.each do |value|
      value.capitalize!
    end

    return values.join ""
  end

  if options[:format] == :sentence
    values[0].capitalize! unless values[0].match(/[a-zA-Z][A-Z]/)

    return values.join " "
  end

  if options[:format] == :nocaps
    return values.join " "
  end
end

.humanize_list(list) ⇒ `Object`

# File 'lib/rbbt/util/misc/format.rb', line 181

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`

Returns:

(Boolean)



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# File 'lib/rbbt/util/misc/math.rb', line 128

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…

# File 'lib/rbbt/util/misc/system.rb', line 81

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`

# File 'lib/rbbt/util/misc/omics.rb', line 488

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.chomp.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|
        next if line.empty?
        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`

# File 'lib/rbbt/util/misc/development.rb', line 137

def self.insist(times = 4, sleep = nil, msg = nil)
  sleep_array = nil

  try = 0
  begin
    begin
      yield
    rescue Exception
      if Array === times
        sleep_array = times
        times = sleep_array.length
        sleep = sleep_array.shift
      end

      if sleep.nil?
        sleep_array = ([0] + [0.001, 0.01, 0.1, 0.5] * (times / 3)).sort[0..times-1]
        sleep = sleep_array.shift
      end
      raise $!
    end
  rescue TryAgain
    sleep sleep
    retry
  rescue StopInsist
    raise $!.exception
  rescue Aborted, Interrupt
    if msg
      Log.warn("Not Insisting after Aborted: #{$!.message} -- #{msg}")
    else
      Log.warn("Not Insisting after Aborted: #{$!.message}")
    end
    raise $!
  rescue Exception
    Log.exception $! if ENV["RBBT_LOG_INSIST"] == 'true'
    if msg
      Log.warn("Insisting after exception: #{$!.class} #{$!.message} -- #{msg}")
    elsif FalseClass === msg
      nil
    else
      Log.warn("Insisting after exception:  #{$!.class} #{$!.message}")
    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`

# File 'lib/rbbt/util/misc/pipes.rb', line 664

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`

# 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`

# File 'lib/rbbt/util/misc/omics.rb', line 430

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 426

def self.intersect_streams_cmp_chr(chr1, chr2)
  chr1 <=> chr2
end

.intersect_streams_read(io, sep = ":") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 359

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, need_to_exists = true) ⇒ `Boolean` Also known as: filename?

Returns:

(Boolean)

# File 'lib/rbbt/util/misc/system.rb', line 94

def self.is_filename?(string, need_to_exists = true)
  return false if string.nil?
  return true if defined? Path and Path === string
  return true if string.respond_to? :exists
  return true if String === string and ! string.include?("\n") and string.split("/").select{|p| p.length > 265}.empty? and (! need_to_exists || File.exist?(string))
  return false
end

.IUPAC_to_base(iupac) ⇒ `Object`



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# File 'lib/rbbt/util/misc/omics.rb', line 294

def self.IUPAC_to_base(iupac)
  IUPAC2BASE[iupac]
end

.line_monitor_stream(stream, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 761

def self.line_monitor_stream(stream, &block)
  monitor, out = tee_stream stream
  monitor_thread = Thread.new do
    begin
      while line = monitor.gets
        block.call line
      end
    rescue
      Log.exception $!
      monitor.raise $!
      monitor.close unless monitor.closed?
      monitor.join if monitor.respond_to?(:join) && ! monitor.aborted?
      out.raise $! if out.respond_to?(:raise)
    ensure
      monitor.close unless monitor.closed?
      monitor.join if monitor.respond_to?(:join) && ! monitor.aborted?
    end
  end

  stream.annotate out if stream.respond_to? :annotate
  ConcurrentStream.setup out, :threads => monitor_thread
end

.load_yaml(yaml) ⇒ `Object`

# File 'lib/rbbt/util/misc/serialize.rb', line 2

def self.load_yaml(yaml)
  case yaml
  when IO, StringIO
    if YAML.respond_to?(:unsafe_load)
      YAML.unsafe_load(yaml)
    else
      YAML.load(yaml)
    end
  when (defined?(Path) && Path)
    yaml.open do |io|
      load_yaml(io)
    end
  when String
    if Misc.is_filename?(yaml)
      File.open(yaml) do |io|
        load_yaml(io)
      end
    else
      load_yaml(StringIO.new(yaml))
    end
  else
    raise "Unkown YAML object: #{Misc.fingerprint yaml}"
  end
end

.lock(file, unlock = true, options = {}) ⇒ `Object`

# File 'lib/rbbt/util/misc/lock.rb', line 21

def self.lock(file, unlock = true, options = {})
  unlock, options = true, unlock if Hash === unlock
  return yield if file.nil? and not Lockfile === options[:lock]

  file = file.find if Path === file
  FileUtils.mkdir_p File.dirname(File.expand_path(file)) unless File.exist? File.dirname(File.expand_path(file))


  begin
    case options[:lock]
    when Lockfile
      lockfile = options[:lock]
      lockfile.lock unless lockfile.locked?
    when FalseClass
      lockfile = nil
      unlock = false
    when Path, String
      lock_path = options[:lock].find
      lockfile = Lockfile.new(lock_path, options)
      lockfile.lock
    else
      lock_path = File.expand_path(file + '.lock')
      lockfile = Lockfile.new(lock_path, options)
      lockfile.lock
    end
  rescue Aborted, Interrupt
    raise LockInterrupted
  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`

# File 'lib/rbbt/util/misc/lock.rb', line 76

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}: #{$!.message}. 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 9

def self.log10(x)
  Math.log(x) * Log10Multiplier
end

.log2(x) ⇒ `Object`



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# File 'lib/rbbt/util/misc/math.rb', line 5

def self.log2(x)
  Math.log(x) * Log2Multiplier
end

.match_fields(field1, field2) ⇒ `Object`

# 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`

# File 'lib/rbbt/util/misc.rb', line 43

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`

# File 'lib/rbbt/util/misc/math.rb', line 13

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 44

def self.mean(list)
  sum(list.compact.collect{|v| v.to_f } ) / list.compact.length
end

.median(array) ⇒ `Object`

# File 'lib/rbbt/util/misc/math.rb', line 48

def self.median(array)
  sorted = array.sort
  len = sorted.length
  (sorted[(len - 1) / 2] + sorted[len / 2]).to_f / 2
end

.memory_use(pid = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 399

def self.memory_use(pid=nil)
  pid ||= $$
  begin
    Open.read("/proc/#{pid}/status").match(/VmRSS:\s+(\d+)/)[1].to_i
  rescue ProcessFailed
    raise "Process with #{pid} not found"
  end
  #`ps -o rss -p #{pid || $$}`.strip.split.last.to_i
end

.memprof ⇒ `Object`

# 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`

# 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`

# File 'lib/rbbt/util/misc/math.rb', line 22

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`

# File 'lib/rbbt/util/misc/inspect.rb', line 267

def self.mtime_str(path)
  path = path.find if Path === path
  if File.exist? 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 24

def self.name2basename(file)
  sanitize_filename(file.gsub("/",'>').gsub("~", '-'))
end

.notify(description, event = 'notification', key = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/communication.rb', line 15

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`

# File 'lib/rbbt/util/misc/inspect.rb', line 418

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 428

def self.obj2md5(obj)
  obj2digest(obj)
end

.obj2str(obj) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 307

def self.obj2str(obj)
  _obj = obj
  obj = Annotated.purge(obj) if Annotated === obj

  str = case obj
        when nil
          'nil'
        when Numeric
          Float === obj && obj % 1 == 0 ? obj.to_i.to_s : obj.to_s
        when Symbol 
          obj.to_s
        when TrueClass
          'true'
        when FalseClass
          'false'
        when Hash
          "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}"
        when (defined?(Path) && Path)
          if defined?(Step) && Open.exists?(Step.info_file(obj))
            obj2str(Workflow.load_step(obj))
          elsif step_file_path = step_file?(obj)
            "Step file: " + step_file_path
          else
            if obj.exists?
              obj = (obj.resource || Rbbt).identify obj if RBBT_IDENTIFY_PATH
              if obj.directory?
                files = obj.glob("**/*")
                "directory: #{Misc.fingerprint(files.collect{|f| Misc.path_relative_to(obj.find, f)}.sort)}"
              elsif obj.located?
                "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
              else
                "path: " << obj 
              end
            else
              obj + " (file missing)"
            end
          end
        when String
          good_filename = Misc.is_filename?(obj, false) && ! %w(. ..).include?(obj) && %w(. /).include?(obj[0])
          if good_filename 
            obj = obj.dup
            obj.extend Path
            obj2str obj
          else
            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
          end
        when Array
          if obj.length > HASH2MD5_MAX_ARRAY_LENGTH
            "[" << sample_large_obj(obj, HASH2MD5_MAX_ARRAY_LENGTH).collect{|v| obj2str(v.nil? ? "" : v) } * "," << "]"
          else
            "[" << obj.collect{|v| obj2str(v.nil? ? "" : v) } * "," << "]"
          end
        when TSV::Parser
          remove_long_items(obj)
        when File 
          if obj.respond_to? :filename and obj.filename
            if defined?(Step) && Open.exists?(Step.info_file(obj.filename))
              obj2str(Workflow.load_step(obj.filename))
            else
              "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
            end
          else
            "<IO:" << obj.path << "--" << mtime_str(obj.path) << ">"
          end
        when (defined? Step and Step)
          "<IO:" << obj.short_path_real << ">"
        when IO
          if obj.respond_to? :filename and obj.filename
            if defined?(Step) && Open.exists?(Step.info_file(obj.filename))
              obj2str(Workflow.load_step(obj.filename))
            else
              "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
            end
          else

            if obj.respond_to? :obj2str
              obj.obj2str
            else
              class << obj
                attr_accessor :obj2str
              end
              obj.obj2str = obj.inspect + rand(1000000).to_s
            end
          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`

# File 'lib/rbbt/util/misc/development.rb', line 276

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_gz_pipe ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 784

def self.open_gz_pipe
  sout = Misc.open_pipe do |sin|
    yield sin
    sin.close
  end

  Open.gzip(sout)
end

.open_pipe(do_fork = false, close = true) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 67

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
    ConcurrentStream.setup sout, :pair => sin

    thread = Thread.new do 
      begin
        
        yield sin

        sin.close if close and not sin.closed? and not sin.aborted?

      rescue Aborted
        Log.medium "Aborted open_pipe: #{$!.message}"
        raise $!
      rescue Exception
        Log.medium "Exception in open_pipe: #{$!.message}"
        Log.exception $!
        begin
          sin.raise($!) if sin.respond_to? :raise
          sin.join if sin.respond_to? :join
        ensure
          raise $!
        end
      end
    end

    sin.threads = [thread]
    sout.threads = [thread]
  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.

# File 'lib/rbbt/util/misc/development.rb', line 221

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`

# 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`

# File 'lib/rbbt/util/misc/format.rb', line 190

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, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 636

def self.paste_streams(streams, lines = nil, sep = "\t", header = nil, &block)
  sep ||= "\t"
  num_streams = streams.length
  Misc.open_pipe do |sin|
    self._paste_streams(streams, sin, lines, sep, header, &block)
  end
end

.path_relative_to(basedir, path) ⇒ `Object`

# File 'lib/rbbt/util/misc/system.rb', line 39

def self.path_relative_to(basedir, path)
  path = File.expand_path(path) unless path[0] == "/"
  basedir = File.expand_path(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`

Returns:

(Boolean)

# File 'lib/rbbt/util/misc/system.rb', line 7

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 26

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`

# 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`

# 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`

# File 'lib/rbbt/util/misc/objects.rb', line 16

def self.prepare_entity(entity, field, options = {})
  return entity unless defined? Entity
  return entity unless String === entity or Array === entity
  options ||= {}

  dup_array = options.delete :dup_array

  if Entity === field or (Entity.respond_to?(:formats) and (_format = Entity.formats.find(field)))
    params = options.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 = entity.dup
    entity = (entity.frozen? and not entity.nil?) ? entity.dup : ((Array === entity and dup_array) ? entity.collect{|e| e.nil? ? e : e.dup} : entity) 

    entity = mod.setup(entity, params)
  end

  entity
end

.process_options(hash, *keys) ⇒ `Object`

# File 'lib/rbbt/util/misc/options.rb', line 142

def self.process_options(hash, *keys)
  defaults = keys.pop if Hash === keys.last
  hahs = Misc.add_defaults hash, defaults if defaults

  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`

# File 'lib/rbbt/util/misc/pipes.rb', line 449

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`

# 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`

# File 'lib/rbbt/util/misc/development.rb', line 93

def self.profile(options = {})
  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, options)
  end

  res
end

.profile_graph(options = {}) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 75

def self.profile_graph(options = {})
  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, options)
  end

  res
end

.profile_html(options = {}) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 54

def self.profile_html(options = {})
  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`

# File 'lib/rbbt/util/misc/math.rb', line 87

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`

# File 'lib/rbbt/util/misc/options.rb', line 153

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 58

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`

# File 'lib/rbbt/util/misc/development.rb', line 233

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 277

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 353

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

.relative_link(source, target_dir) ⇒ `Object`

# File 'lib/rbbt/util/misc/system.rb', line 68

def self.relative_link(source, target_dir)
  path = "."
  current = target_dir
  while ! Misc.common_path current, source
    current = File.dirname(current)
    path = File.join(path, '..')
    return nil if current == "/"
  end

  File.join(path, Misc.path_relative_to(current, source))
end

.release_pipes(*pipes) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 50

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 709

def self.remove_lines(stream1, stream2, sort)
  self.compare_lines(stream1, stream2, '-2 -3', sort)
end

.remove_long_items(obj) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 117

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.options))
  when TSV === obj
    tsv = obj
    fields = tsv.fields

    if obj.size > TSV_MAX_ROWS
      tsv = obj.head(TSV_MAX_ROWS)
      tsv["Truncated rows at #{TSV_MAX_ROWS} (#{obj.size})"] = nil
    end

    if fields && fields.length > TSV_MAX_FIELDS
      tsv = obj.slice(fields[0..TSV_MAX_ROWS-1])
      tsv.add_field "Truncated at #{TSV_MAX_ROWS} (#{fields.length})" do
        nil
      end
    elsif fields.nil?
      new = tsv.annotate({})
      tsv.each do |k,v|
        new[k] = Misc.remove_long_items(v)
      end
      tsv = new
    end

    tsv
  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 757

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`

# File 'lib/rbbt/util/misc/development.rb', line 264

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`

# File 'lib/rbbt/util/misc/inspect.rb', line 173

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`

# File 'lib/rbbt/util/misc/inspect.rb', line 28

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`

# File 'lib/rbbt/util/misc/pipes.rb', line 644

def self.save_stream(file, stream)
  save, out = 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: #{$!.message}"
      raise $!
    end
  end

  out
end

.scan_version_text(text, cmd = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/inspect.rb', line 457

def self.scan_version_text(text, cmd = nil)
  text = Misc.fixutf8 text
  cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
  text.split("\n").each do |line|
    next unless line =~ /\W#{cmd}\W/i
    m = line.match(/(v(?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
    return m[1] if m
    m = line.match(/((?:\d+\.)*\d+(?:-[a-z_]+)?v)/i)
    return m[1] if m
    next unless line =~ /\Wversion\W/i
    m = line.match(/((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
    return m[1] if m
  end
  m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.to_s.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
  return m[1] if m
  m = text.match(/(?:#{cmd}.*(v.*|.*v))/i)
  return m[1] if m
  nil
end

.sd(list) ⇒ `Object`

# File 'lib/rbbt/util/misc/math.rb', line 71

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 713

def self.select_lines(stream1, stream2, sort)
  self.compare_lines(stream1, stream2, '-1 -2', sort)
end

.select_ranges(stream1, stream2, sep = "\t") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 482

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`

# File 'lib/rbbt/util/misc/communication.rb', line 48

def self.send_email(from, to, subject, message, options = {})
  require 'mail'

  IndiferentHash.setup(options)
  options = Misc.add_defaults options, :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login, :files => []

  server, port, user, pass, from_alias, to_alias, auth, files = Misc.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth, :files

  files = [] if files.nil?
  files = [files] unless Array === files

  Mail.defaults do
    delivery_method :smtp, address: server, port: port, user_name: user, password: pass
  end

  mail = Mail.deliver do 
    from  "#{from_alias} <#{from}>"
    to "#{to_alias} <#{to}>"
    subject subject

    text_part do 
      body message
    end

    files.each do |file|
      file = file.find if Path === file
      file = file.path if Step === file
    end
  end
end

.send_email_old(from, to, subject, message, options = {}) ⇒ `Object`

# File 'lib/rbbt/util/misc/communication.rb', line 29

def self.send_email_old(from, to, subject, message, options = {})
  IndiferentHash.setup(options)
  options = Misc.add_defaults options, :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.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth

  msg = <<-END_OF_MESSAGE
From: #{from_alias} <#{from}>
To: #{to_alias} <#{to}>
Subject: #{subject}

#{message}
END_OF_MESSAGE

  Net::SMTP.start(server, port, server, user, pass, auth) do |smtp|
    smtp.send_message msg, from, to
  end
end

.sensiblewrite(path, content = nil, options = {}, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 372

def self.sensiblewrite(path, content = nil, options = {}, &block)
  force = Misc.process_options options, :force

  if Open.exists? path and not force
    Misc.consume_stream content 
    return
  end

  lock_options = Misc.pull_keys options.dup, :lock
  lock_options = lock_options[:lock] if Hash === lock_options[: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 === options[:lock]

  Misc.lock tmp_path_lock, lock_options 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, lock_options
          end
        rescue Exception
          raise $! unless Open.exists? path
        end

        Open.touch path if Open.exists? path
        content.join if content.respond_to?(:join) and not Path === content and not (content.respond_to?(:joined?) && content.joined?)

        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.message} -- #{ 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
        if Lockfile === lock_options[:lock] and lock_options[:lock].locked?
          lock_options[:lock].unlock
        end
      end
    end
  end
end

.snake_case(string) ⇒ `Object`

# File 'lib/rbbt/util/misc/format.rb', line 101

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, sep = ":") ⇒ `Object`



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# File 'lib/rbbt/util/misc/omics.rb', line 355

def self.sort_genomic_locations(stream, sep = ":")
  sort_stream(stream, '#', "-k1,1 -k2,2n -t#{sep}")
end

.sort_genomic_locations_by_contig(stream, contigs, sep = ":") ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 339

def self.sort_genomic_locations_by_contig(stream, contigs, sep = ":")
  ext_stream = TSV.traverse stream, :type => :array, :into => :stream do |line|
    chr = line.partition(sep).first
    num = contigs.index chr
    num.to_s + sep + line
  end

  TSV.traverse sort_stream(ext_stream, '#', "-k1,1n -k3,3n -t#{sep}"), :type => :array, :into => :stream do |line|
    line.partition(sep).last
  end
end

.sort_genomic_locations_strict(stream, sep = ":") ⇒ `Object`



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# File 'lib/rbbt/util/misc/omics.rb', line 351

def self.sort_genomic_locations_strict(stream, sep = ":")
  sort_stream(stream, '#', "-k1,1V -k2,2n -t#{sep}")
end

.sort_mutation_stream(stream, sep = ":") ⇒ `Object`



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# File 'lib/rbbt/util/misc/pipes.rb', line 731

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_mutation_stream_strict(stream, sep = ":") ⇒ `Object`



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# File 'lib/rbbt/util/misc/pipes.rb', line 727

def self.sort_mutation_stream_strict(stream, sep=":")
  CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -V -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
end

.sort_mutations_strict(mutations) ⇒ `Object` Also known as: sort_mutations

# File 'lib/rbbt/util/misc/omics.rb', line 299

def self.sort_mutations_strict(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`

# File 'lib/rbbt/util/misc/pipes.rb', line 459

def self.sort_stream(stream, header_hash = "#", cmd_args = "-u")
  Misc.open_pipe do |sin|
    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
      begin
        Misc.consume_stream(stream, false, line_stream_in)
      rescue
        raise $!
      end
    end

    sorted = CMD.cmd("env LC_ALL=C sort #{cmd_args || ""}", :in => line_stream, :pipe => true)

    begin
      Misc.consume_stream(sorted, false, sin)
    rescue
      Log.exception $!
      begin
        sorted.raise($!) if sorted.respond_to? :raise
        stream.raise($!) if stream.respond_to? :raise
      ensure
        raise $!
      end
    end
  end
end

.sorted_array_hits(a1, a2) ⇒ `Object`

# 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

.ssh_connection(server, reset = false) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 438

def self.ssh_connection(server, reset = false)
  @@ssh_connections ||= {}
  @@ssh_connections.delete server if reset
  @@ssh_connections[server] ||= begin
                                  require 'pty'
                                  master, slave = PTY.open
                                  read, write = Misc.pipe
                                  pid = spawn("ssh '#{server}' 'shopt -s expand_aliases; bash -l' ", :in => read, :out => slave, :err => STDERR.fileno)
                                  read.close
                                  slave.close
                                  [write, master, pid]
                                end
end

.ssh_run(server, script = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 433

def self.ssh_run(server, script = nil)
  require 'rbbt/util/ssh'
  SSHLine.ruby(server, script)
end

.ssh_run_alt(server, script = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 452

def self.ssh_run_alt(server, script = nil)
  Log.debug "Run ssh script in #{server}:\n#{script}"

  write, master, pid = ssh_connection(server)
  write, master = ssh_connection(server, true) if PTY.check pid
  write.puts "echo '#{script.gsub("'", '"') + "\n" + 'puts "\nCMD_OUT_END"'}' | ruby "
  lines = []
  while true
    line = master.gets
    break if line.strip == "CMD_OUT_END"
    lines << line.strip unless line.strip.empty?
  end
  lines * "\n"

end

.ssh_run_old(server, script = nil) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 426

def self.ssh_run_old(server, script = nil)
  Log.debug "Run ssh script in #{server}:\n#{script}"

  #CMD.cmd("ssh '#{server}' 'shopt -s expand_aliases; bash -l -c \"ruby\"' ", :in => script, :log => true).read
  CMD.cmd("ssh '#{server}' ruby", :in => script, :log => true).read
end

.std_num_vector(v, min, max) ⇒ `Object`

# File 'lib/rbbt/util/misc/math.rb', line 31

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| (e.nil? || e.nan?) ? e : min + range * (e.to_f - v_min) / v_range } 
end

.step_file?(path) ⇒ `Boolean`

Returns:

(Boolean)

# File 'lib/rbbt/util/misc/inspect.rb', line 277

def self.step_file?(path)
  return false unless path =~ /\.files(?:\/|$)/
  parts = path.split("/")
  job = parts.select{|p| p =~ /\.files$/}.first
  if job
    i = parts.index job
    begin
      workflow, task = parts.values_at i - 2, i - 1
      _loaded = false
      begin
        Kernel.const_get(workflow)
      rescue 
        if ! _loaded
          Workflow.require_workflow workflow 
          _loaded = true
          retry
        end
        raise $!
      end
      #return Kernel.const_get(workflow).tasks.include? task.to_sym
      return parts[i-2..-1] * "/"
    rescue
      Log.exception $!
    end
  end
  false
end

.string2const(string) ⇒ `Object`

# 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

# File 'lib/rbbt/util/misc/options.rb', line 219

def self.string2hash(string)
  options = {}

  string.split('#').each do |str|
    key, sep, value = str.partition "="

    key = key[1..-1].to_sym if key[0] == ":"

    options[key] = true and next if value.empty?
    options[key] = value[1..-1].to_sym and next if value[0] == ":"
    options[key] = Regexp.new(/#{value[1..-2]}/) and next if value[0] == "/" and value[-1] == "/"
    options[key] = value[1..-2] and next if value =~ /^['"].*['"]$/
    options[key] = value.to_i and next if value =~ /^\d+$/
    options[key] = value.to_f and next if value =~ /^\d*\.\d+$/
    options[key] = true and next if value == "true"
    options[key] = false and next if value == "false"
    options[key] = value and next 

    options[key] = begin
                     saved_safe = $SAFE
                     $SAFE = 0
                     eval(value)
                   rescue Exception
                     value
                   ensure
                     $SAFE = saved_safe
                   end
  end

  return options

end

.sum(list) ⇒ `Object`



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# File 'lib/rbbt/util/misc/math.rb', line 40

def self.sum(list)
  list.compact.inject(0.0){|acc,e| acc += e }
end

.swap_quoted_character(stream, charout = "\n", charin = " ", quote = '"') ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 735

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.

# 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`

# 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 248

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

# File 'lib/rbbt/util/misc/pipes.rb', line 177

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: #{$!.message} (#{Misc.fingerprint sin})");
              skip[i] = true
            rescue
              Log.error("Tee stream #{i} #{Misc.fingerprint stream} Exception: #{$!.message} (#{Misc.fingerprint sin})");
              raise $!
            end unless skip[i] 
          end
        end
      rescue IOError
      end

      stream.close unless stream.closed?
      #stream.join if stream.respond_to? :join
      in_pipes.first.close unless in_pipes.first.closed?
      #Log.medium "Tee done #{Misc.fingerprint stream}"
    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

  main_pipe = out_pipes.first
  main_pipe.autojoin = true

  main_pipe.callback = Proc.new do 
    stream.join if stream.respond_to? :join
    in_pipes[1..-1].each do |sin|
      sin.close unless sin.closed?
    end
  end

  out_pipes
end

.time_tick ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 299

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

.timeout_insist(time, msg = nil, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 468

def self.timeout_insist(time, msg = nil, &block)
  Misc.insist do
    begin
      Timeout.timeout(time, TryAgain, msg, &block)
    rescue TryAgain
      Log.low "Timeout detected after #{time} seconds"
      raise $!
    end
  end
end

.timespan(str, default = "s") ⇒ `Object`

# File 'lib/rbbt/util/misc.rb', line 75

def self.timespan(str, default = "s")

  return - timespan(str[1..-1], default) if str[0] == "-"
  
  if str.include?(":")
    seconds, minutes, hours = str.split(":").reverse
    return seconds.to_i + minutes.to_i * 60 + hours.to_i * 60 * 60
  end

  tokens = {
    "s" => (1),
    "sec" => (1),
    "m" => (60),
    "min" => (60),
    "''" => (1),
    "'" => (60),
    "h" => (60 * 60),
    "d" => (60 * 60 * 24),
    "w" => (60 * 60 * 24 * 7),
    "mo" => (60 * 60 * 24 * 31),
    "y" => (60 * 60 * 24 * 365),
  }

  tokens[nil] = tokens[default]
  tokens[""] = tokens[default]
  time = 0
  str.scan(/(\d+)(\w*)/).each do |amount, measure|
    time += amount.to_i * tokens[measure]
  end
  time
end

.to_utf8(string) ⇒ `Object`



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# File 'lib/rbbt/util/misc/format.rb', line 163

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 71

def self.tokenize(str)
  str.scan(/"([^"]*)"|'([^']*)'|([^"'\s]+)/).flatten.compact
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`

# File 'lib/rbbt/util/misc/omics.rb', line 205

def self.translate_dna_mutation_hgvs2rbbt(cds)
  change = begin
             case
             when cds =~ />/
               cds.split(">").last
             when cds =~ /delins/
               del, ins = cds.split("delins")
               start, eend = del.split("_")
               del_size = eend.to_i - start.to_i + 1
               if ins =~ /^[ACTG]+$/i
                 ("-" * del_size) + ins
               else
                 Log.debug "Unknown delins: #{ cds }"
                 "?(" << cds << ")"
               end
             when cds =~ /del/
               deletion = cds.split("del").last.chomp
               case
               when deletion =~ /^\d+$/
                 "-" * deletion.to_i
               when deletion =~ /^[ACTG]+$/i
                 "-" * deletion.length
               else
                 Log.debug "Unknown deletion: #{ cds }"
                 "?(" << cds << ")"
               end
             when cds =~ /ins/
               insertion = cds.split("ins").last
               case
               when insertion =~ /^\d+$/
                 "+" + "N" * insertion.to_i
               when insertion =~ /^[NACTG]+$/i
                 "+" + insertion
               else
                 Log.debug "Unknown insertion: #{cds }"
                 "?(" << cds << ")"
               end
             else
               Log.debug "Unknown change: #{cds}"
               "?(" << cds << ")"
             end
           rescue
             Log.debug "Error processing change: #{cds}"
             "?(" << cds << ")"
           end
  change
end

.translate_prot_mutation_hgvs2rbbt(mutation) ⇒ `Object`

# File 'lib/rbbt/util/misc/omics.rb', line 253

def self.translate_prot_mutation_hgvs2rbbt(mutation)
  mutation.sub!('p.', '')
  if m = mutation.match(/([a-z]{3})(\d+)([a-z]{3})/i)
    ref = m[1]
    num = m[2]
    alt = m[3]
    alt = "*" if alt == "Ter"
    ref = THREE_TO_ONE_AA_CODE[ref.downcase]
    alt = THREE_TO_ONE_AA_CODE[alt.downcase] unless alt == "*"
    mutation = [ref, num, alt] * ""
  end
  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 = 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 192

def self.try3times(&block)
  insist(3, &block)
end

.txt_digest_str(txt) ⇒ `Object`



263
264
265

# File 'lib/rbbt/util/misc/inspect.rb', line 263

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

# 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

# File 'lib/rbbt/util/tar.rb', line 94

def self.untar(io, destination)
  io = io.find if Path === io
  if String === io and File.exist?(io)
    Open.open(io) do |f|
      untar(f, destination)
    end
  else
    return _untar_cmd(io, destination)
  end
end

.unzip_in_dir(file, dir) ⇒ `Object`

# File 'lib/rbbt/util/misc/development.rb', line 410

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`

# 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`

# File 'lib/rbbt/util/misc/math.rb', line 54

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_env(var, value, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/system.rb', line 27

def self.with_env(var, value, &block)
  var = var.to_s
  value = value.to_s
  current = ENV[var]
  begin
    ENV[var] = value
    yield
  ensure
    ENV[var] = current
  end
end

.with_fifo(path = nil, clean = true, &block) ⇒ `Object`

# File 'lib/rbbt/util/misc/pipes.rb', line 38

def self.with_fifo(path = nil, clean = true, &block)
  begin
    erase = path.nil?
    path = TmpFile.tmp_file if path.nil?
    File.rm path if clean && File.exist?(path)
    File.mkfifo path
    yield path
  ensure
    FileUtils.rm path if erase && File.exist?(path)
  end
end

.zip2hash(list1, list2) ⇒ `Object`

# 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`

# File 'lib/rbbt/util/misc/objects.rb', line 78

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

.zscore(e, list) ⇒ `Object`

# File 'lib/rbbt/util/misc/math.rb', line 132

def self.zscore(e, list)
  m = Misc.mean(list)
  sd = Misc.sd(list)
  (e.to_f - m) / sd
end

Module: Misc

Overview

Constant Summary collapse

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.sensiblewrite_dir ⇒ Object

.sensiblewrite_lock_dir ⇒ Object

Class Method Details

._convert_match_condition(condition) ⇒ Object

._paste_streams(streams, output, lines = nil, sep = "\t", header = nil, &block) ⇒ 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 = nil, options = {}, &block) ⇒ Object

.bootstrap_in_threads(elems, num = :current, options = {}, &block) ⇒ Object

.break_lines(text, char_size = 80) ⇒ Object

.buffer_stream(stream) ⇒ Object

.camel_case(string) ⇒ Object

.camel_case_lower(string) ⇒ Object

.choose(array, select) ⇒ Object

.chr_cmp_contigs(chr1, chr2, contigs) ⇒ Object

.chr_cmp_strict(chr1, chr2) ⇒ Object

.chunk(array, num) ⇒ 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

.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

.file2md5(file) ⇒ Object

.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

.genomic_location_cmp(gpos1, gpos2, sep = ":") ⇒ Object

.genomic_location_cmp_contigs(gpos1, gpos2, contigs, sep = ":") ⇒ Object

.genomic_location_cmp_strict(gpos1, gpos2, sep = ":") ⇒ Object

.genomic_mutations_to_BED(mutations, chr_prefix = false, sort_order = :normal) ⇒ 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

.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

.humanize_list(list) ⇒ Object

.in_delta?(a, b, delta = 0.0001) ⇒ Boolean

.in_dir(dir) ⇒ Object

.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

.sensiblewrite_dir ⇒ `Object`

.sensiblewrite_lock_dir ⇒ `Object`

._convert_match_condition(condition) ⇒ `Object`

._paste_streams(streams, output, lines = nil, sep = "\t", header = nil, &block) ⇒ `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 = nil, options = {}, &block) ⇒ `Object`

.bootstrap_in_threads(elems, num = :current, options = {}, &block) ⇒ `Object`

.break_lines(text, char_size = 80) ⇒ `Object`

.buffer_stream(stream) ⇒ `Object`

.camel_case(string) ⇒ `Object`

.camel_case_lower(string) ⇒ `Object`

.choose(array, select) ⇒ `Object`

.chr_cmp_contigs(chr1, chr2, contigs) ⇒ `Object`

.chr_cmp_strict(chr1, chr2) ⇒ `Object`

.chunk(array, num) ⇒ `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`

.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`

.file2md5(file) ⇒ `Object`

.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`

.genomic_location_cmp(gpos1, gpos2, sep = ":") ⇒ `Object`

.genomic_location_cmp_contigs(gpos1, gpos2, contigs, sep = ":") ⇒ `Object`

.genomic_location_cmp_strict(gpos1, gpos2, sep = ":") ⇒ `Object`

.genomic_mutations_to_BED(mutations, chr_prefix = false, sort_order = :normal) ⇒ `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`

.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`

.humanize_list(list) ⇒ `Object`

.in_delta?(a, b, delta = 0.0001) ⇒ `Boolean`

.in_dir(dir) ⇒ `Object`

.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, need_to_exists = true) ⇒ `Boolean` Also known as: filename?

.IUPAC_to_base(iupac) ⇒ `Object`

.line_monitor_stream(stream, &block) ⇒ `Object`

.load_yaml(yaml) ⇒ `Object`