Class: BioDSL::Filesys

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/BioDSL/filesys.rb

Overview

Class for handling filesystem manipulations.

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ios) ⇒ Filesys

Returns a new instance of Filesys.



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# File 'lib/BioDSL/filesys.rb', line 111

def initialize(ios)
  @io = ios
end

Instance Attribute Details

#io ⇒ Object (readonly)

Returns the value of attribute io.



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# File 'lib/BioDSL/filesys.rb', line 109

def io
  @io
end

Class Method Details

.open(*args) ⇒ Object

Open a file which may be compressed with gzip og bzip2.



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# File 'lib/BioDSL/filesys.rb', line 67

def self.open(*args)
  file    = args.shift
  mode    = args.shift
  options = args.shift || {}

  if mode == 'w'
    case options[:compress]
    when :gzip
      ios, = Open3.pipeline_w('gzip -f', out: file)
    when :bzip, :bzip2
      ios, = Open3.pipeline_w('bzip2 -c', out: file)
    else
      ios = File.open(file, mode, options)
    end
  else
    type = if file.respond_to? :path
             `file -Lk #{file.path}`
           else
             `file -Lk #{file}`
           end

    ios = case type
          when /gzip/
            IO.popen("gzip -cd #{file}")
          when /bzip/
            IO.popen("bzcat #{file}")
          else
            File.open(file, mode, options)
          end
  end

  if block_given?
    begin
      yield new(ios)
    ensure
      ios.close
    end
  else
    return new(ios)
  end
end

.tmpfile(tmp_dir = ) ⇒ Object

Class method that returns a path to a unique temporary file. If no directory is specified reverts to the systems tmp directory.



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# File 'lib/BioDSL/filesys.rb', line 58

def self.tmpfile(tmp_dir = ENV['TMPDIR'])
  time = Time.now.to_i
  user = ENV['USER']
  pid  = $PID
  path = tmp_dir + [user, time + pid, pid].join('_') + '.tmp'
  path
end

.which(cmd) ⇒ Object

Cross-platform way of finding an executable in the $PATH.

which('ruby') #=> /usr/bin/ruby



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# File 'lib/BioDSL/filesys.rb', line 43

def self.which(cmd)
  exts = ENV['PATHEXT'] ? ENV['PATHEXT'].split(';') : ['']

  ENV['PATH'].split(File::PATH_SEPARATOR).each do |path|
    exts.each do |ext|
      exe = File.join(path, "#{cmd}#{ext}")
      return exe if File.executable?(exe) && !File.directory?(exe)
    end
  end

  nil
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/BioDSL/filesys.rb', line 131

def close
  @io.close
end

#each ⇒ Object

Iterator method for parsing entries.



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# File 'lib/BioDSL/filesys.rb', line 140

def each
  return to_enum :each unless block_given?

  @io.each { |line| yield line }
end

#eof? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/BioDSL/filesys.rb', line 135

def eof?
  @io.eof?
end

#gets ⇒ Object 



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# File 'lib/BioDSL/filesys.rb', line 115

def gets
  @io.gets
end

#puts(*args) ⇒ Object 



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# File 'lib/BioDSL/filesys.rb', line 119

def puts(*args)
  @io.puts(*args)
end

#read ⇒ Object 



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# File 'lib/BioDSL/filesys.rb', line 123

def read
  @io.read
end

#write(arg) ⇒ Object 



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# File 'lib/BioDSL/filesys.rb', line 127

def write(arg)
  @io.write arg
end