Class: Bio::FlatFileIndex::Flat_1::FlatMappingFile

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/io/flatfile/index.rb

Overview

FlatMappingFile class.

Internal use only.

Constant Summary collapse

@@recsize_width =
4
@@recsize_regex =
/\A\d{4}\z/

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename, mode = 'rb') ⇒ FlatMappingFile


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# File 'lib/bio/io/flatfile/index.rb', line 734

def initialize(filename, mode = 'rb')
  @filename = filename
  @mode = mode
  @file = nil
  #@file = File.open(filename, mode)
  @record_size = nil
  @records = nil
end

Instance Attribute Details

#filenameObject (readonly)

Returns the value of attribute filename


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# File 'lib/bio/io/flatfile/index.rb', line 743

def filename
  @filename
end

#modeObject

Returns the value of attribute mode


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# File 'lib/bio/io/flatfile/index.rb', line 742

def mode
  @mode
end

Class Method Details

.external_merge_proc(sort_program = [ '/usr/bin/env', 'LC_ALL=C', '/usr/bin/sort' ]) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 923

def self.external_merge_proc(sort_program =  [ '/usr/bin/env', 
                                               'LC_ALL=C',
                                               '/usr/bin/sort' ])
  Proc.new do |out, in1, *files|
    # files (and in1) must be sorted
    cmd = sort_program + [ '-m', '-o', out, in1, *files ]
    system(*cmd)
  end
end

.external_merge_sort_proc(sort_program = [ '/usr/bin/env', 'LC_ALL=C', '/usr/bin/sort' ]) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 900

def self.external_merge_sort_proc(sort_program = [ '/usr/bin/env', 
                                                   'LC_ALL=C',
                                                   '/usr/bin/sort' ])
  Proc.new do |out, in1, *files|
    # (in1 may be sorted)
    tf_all = []
    tfn_all = []
    files.each do |fn|
      tf = Tempfile.open('sort')
      tf.close(false)
      cmd = sort_program + [ '-o', tf.path, fn ]
      system(*cmd)
      tf_all << tf
      tfn_all << tf.path
    end
    cmd_fin = sort_program + [ '-m', '-o', out, in1, *tfn_all ]
    system(*cmd_fin)
    tf_all.each do |tf|
      tf.close(true)
    end
  end
end

.external_sort_proc(sort_program = [ '/usr/bin/env', 'LC_ALL=C', '/usr/bin/sort' ]) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 891

def self.external_sort_proc(sort_program = [ '/usr/bin/env', 
                                             'LC_ALL=C',
                                             '/usr/bin/sort' ])
  Proc.new do |out, in1, *files|
    cmd = sort_program + [ '-o', out, in1, *files ]
    system(*cmd)
  end
end

.internal_sort_procObject


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# File 'lib/bio/io/flatfile/index.rb', line 933

def self.internal_sort_proc
  Proc.new do |out, in1, *files|
    a = IO.readlines(in1)
    files.each do |fn|
      IO.foreach(fn) do |x|
        a << x
      end
    end
    a.sort!
    of = File.open(out, 'w')
    a.each { |x| of << x }
    of.close
  end
end

.open(*arg) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 730

def self.open(*arg)
  self.new(*arg)
end

Instance Method Details

#add_record(str) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 806

def add_record(str)
  n = records
  rs = record_size
  @file.seek(0, IO::SEEK_END)
  write_record(str)
  @records += 1
end

#closeObject


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# File 'lib/bio/io/flatfile/index.rb', line 755

def close
  if @file then
    DEBUG.print "FlatMappingFile: close #{@filename}\n"
    @file.close
    @file = nil
  end
  nil
end

#eachObject

export/import/edit data


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# File 'lib/bio/io/flatfile/index.rb', line 841

def each
  n = records
  seek(0)
  (0...n).each do |i|
    yield Record.new(get_record(i))
  end
  self
end

#export_tsv(stream) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 850

def export_tsv(stream)
  self.each do |x|
    stream << "#{x.to_s}\n"
  end
  stream
end

#get_record(i) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 776

def get_record(i)
  rs = record_size
  seek(i)
  str = @file.read(rs)
  #DEBUG.print "get_record(#{i})=#{str.inspect}\n"
  str
end

#import_tsv_files(flag_primary, mode, sort_proc, *files) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 948

def import_tsv_files(flag_primary, mode, sort_proc, *files)
  require 'tempfile'

  tmpfile1 = Tempfile.open('flat')
  self.export_tsv(tmpfile1) unless mode == :new
  tmpfile1.close(false)

  tmpfile0 = Tempfile.open('sorted')
  tmpfile0.close(false)

  sort_proc.call(tmpfile0.path, tmpfile1.path, *files)

  tmpmap = self.class.new(self.filename + ".#{$$}.tmp~", 'wb+')
  tmpmap.init_with_sorted_tsv_file(tmpfile0.path, flag_primary)
  tmpmap.close
  self.close

  begin
    File.rename(self.filename, self.filename + ".#{$$}.bak~")
  rescue Errno::ENOENT
  end
  File.rename(tmpmap.filename, self.filename)
  begin
    File.delete(self.filename + ".#{$$}.bak~")
  rescue Errno::ENOENT
  end

  tmpfile0.close(true)
  tmpfile1.close(true)
  self
end

#init(rs) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 827

def init(rs)
  unless 0 < rs and rs < 10 ** @@recsize_width then
    raise 'record size out of range'
  end
  open
  @record_size = rs
  str = sprintf("%0*d", @@recsize_width, rs)
  @file.truncate(0)
  @file.seek(0, IO::SEEK_SET)
  @file.write(str)
  @records = 0
end

#init_with_sorted_tsv_file(filename, flag_primary = false) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 857

def init_with_sorted_tsv_file(filename, flag_primary = false)
  rec_size = 1
  f = File.open(filename)
  f.each do |y|
    rec_size = y.chomp.length if rec_size < y.chomp.length
  end
  self.init(rec_size)

  prev = nil
  f.rewind
  if flag_primary then
    f.each do |y|
      x = Record.new(y.chomp, rec_size)
      if prev then
        if x.key == prev.key
          DEBUG.print "Warining: overwrote unique id #{x.key.inspect}\n"
        else
          self.add_record(prev.to_s)
        end
      end
      prev = x
    end
    self.add_record(prev.to_s) if prev
  else
    f.each do |y|
      x = Record.new(y.chomp, rec_size)
      self.add_record(x.to_s) if x != prev
      prev = x
    end
  end
  f.close
  self
end

#openObject


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# File 'lib/bio/io/flatfile/index.rb', line 745

def open
  unless @file then
    DEBUG.print "FlatMappingFile: open #{@filename}\n"
    @file = File.open(@filename, @mode)
    true
  else
    nil
  end
end

#put_record(i, str) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 814

def put_record(i, str)
  n = records
  rs = record_size
  if i >= n then
    @file.seek(0, IO::SEEK_END)
    @file.write(sprintf("%-*s", rs, '') * (i - n))
    @records = i + 1
  else
    seek(i)
  end
  write_record(str)
end

#record_sizeObject


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# File 'lib/bio/io/flatfile/index.rb', line 764

def record_size
  unless @record_size then
    open
    @file.seek(0, IO::SEEK_SET)
    s = @file.read(@@recsize_width)
    raise 'strange record size' unless s =~ @@recsize_regex
    @record_size = s.to_i
    DEBUG.print "FlatMappingFile: record_size: #{@record_size}\n"
  end
  @record_size
end

#recordsObject Also known as: size


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# File 'lib/bio/io/flatfile/index.rb', line 789

def records
  unless @records then
    rs = record_size
    @records = (@file.stat.size - @@recsize_width) / rs
    DEBUG.print "FlatMappingFile: records: #{@records}\n"
  end
  @records
end

#search(key) ⇒ Object

methods for searching


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# File 'lib/bio/io/flatfile/index.rb', line 982

def search(key)
  n = records
  return [] if n <= 0
  i = n / 2
  i_prev = nil
  DEBUG.print "binary search starts...\n"
  begin
    rec = Record.new(get_record(i))
    i_prev = i
    if key < rec.key then
      n = i
      i = i / 2
    elsif key > rec.key then
      i = (i + n) / 2
    else # key == rec.key
      result = [ rec.val ]
      j = i - 1
      while j >= 0 and
          (rec = Record.new(get_record(j))).key == key
        result << rec.val
        j = j - 1
      end
      result.reverse!
      j = i + 1
      while j < n and
          (rec = Record.new(get_record(j))).key == key
        result << rec.val
        j = j + 1
      end
      DEBUG.print "#{result.size} hits found!!\n"
      return result
    end
  end until i_prev == i
  DEBUG.print "no hits found\n"
  #nil
  []
end

#seek(i) ⇒ Object


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# File 'lib/bio/io/flatfile/index.rb', line 784

def seek(i)
  rs = record_size
  @file.seek(@@recsize_width + rs * i)
end

#write_record(str) ⇒ Object

methods for writing file


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# File 'lib/bio/io/flatfile/index.rb', line 800

def write_record(str)
  rs = record_size
  rec = sprintf("%-*s", rs, str)[0..rs]
  @file.write(rec)
end