Module: Genfrag

Defined in:
lib/genfrag.rb,
lib/genfrag/app.rb,
lib/genfrag/app/command.rb,
lib/genfrag/app/index_command.rb,
lib/genfrag/app/search_command.rb,
lib/genfrag/app/index_command/db.rb,
lib/genfrag/app/search_command/trim.rb,
lib/genfrag/app/search_command/match.rb,
lib/genfrag/app/search_command/process_file.rb

Defined Under Namespace

Classes: App

Constant Summary collapse

VERSION =

:stopdoc:

'0.0.0.4'
LIBPATH = 
::File.expand_path(::File.dirname(__FILE__)) + ::File::SEPARATOR
PATH = 
::File.dirname(LIBPATH) + ::File::SEPARATOR

Class Method Summary collapse

Class Method Details

.libpath(*args) ⇒ Object

Returns the library path for the module. If any arguments are given, they will be joined to the end of the libray path using File.join.



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# File 'lib/genfrag.rb', line 20

def self.libpath( *args )
  args.empty? ? LIBPATH : ::File.join(LIBPATH, args.flatten)
end

.name_adapters(fileadapters = nil) ⇒ Object

Return the name of the adapters file without its extension



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# File 'lib/genfrag.rb', line 120

def self.name_adapters(fileadapters=nil)
  return nil if !fileadapters
  return fileadapters.gsub(/\.(db|tdf)$/, '')
end

.name_freq_lookup(input_filenames = [], filefasta = nil, filelookup = nil, re5 = nil, re3 = nil) ⇒ Object

Create a unique filename for the frequency file out of a combination of filenames



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# File 'lib/genfrag.rb', line 82

def self.name_freq_lookup(input_filenames=[],filefasta=nil,filelookup=nil,re5=nil,re3=nil)
  input_filenames = [] if input_filenames.nil?
  if filelookup
    # FIXME used to be gsub! - make sure it still works in code
    return filelookup.gsub(/\.(db|tdf)$/, '')
  elsif !input_filenames.empty?
    if re5 and re3
      [input_filenames.sort,re5.downcase,re3.downcase,'index'].join('_').gsub(/\//,'x')
    else
      raise "re5 or re3 is undefined"
    end
  elsif filefasta
  # construct default name
    if re5 and re3
      [name_normalized_fasta(nil,filefasta),re5.downcase,re3.downcase,'index'].join('_').gsub(/\//,'x')
    else
      raise "re5 or re3 is undefined"
    end
  else
    raise "--lookup undefined and no default filenames passed"
  end
end

.name_normalized_fasta(input_filenames = [], filefasta = nil) ⇒ Object

Create a unique filename out of a combination of filenames



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# File 'lib/genfrag.rb', line 107

def self.name_normalized_fasta(input_filenames=[],filefasta=nil)
  if filefasta
    # FIXME used to be gsub! - make sure it still works in code
    return filefasta.gsub(/\.(db|tdf)$/, '')
  elsif !input_filenames.empty?
    return [input_filenames.sort, 'normalized'].join('_').gsub(/\//,'x')
  else
    raise "--fasta undefined and no default filenames passed"
  end
end

.path(*args) ⇒ Object

Returns the lpath for the module. If any arguments are given, they will be joined to the end of the path using File.join.



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# File 'lib/genfrag.rb', line 28

def self.path( *args )
  args.empty? ? PATH : ::File.join(PATH, args.flatten)
end

.require_all_libs_relative_to(fname, dir = nil) ⇒ Object

Utility method used to require all files ending in .rb that lie in the directory below this file that has the same name as the filename passed in. Optionally, a specific directory name can be passed in such that the filename does not have to be equivalent to the directory.



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# File 'lib/genfrag.rb', line 37

def self.require_all_libs_relative_to( fname, dir = nil )
  dir ||= ::File.basename(fname, '.*')
  search_me = ::File.expand_path(
      ::File.join(::File.dirname(fname), dir, '**', '*.rb'))

  Dir.glob(search_me).sort.each {|rb| require rb}
end

.tracktime(verbose = true, f = nil) ⇒ Object 



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# File 'lib/genfrag.rb', line 45

def self.tracktime verbose=true, f=nil
# Info:: Pjotr's shared Ruby modules
# Author:: Pjotr Prins
# mail:: [email protected]
# Copyright:: July 2007
# License:: Ruby License
  begin
    t1 = Time.now
    yield

  ensure
    t2 = Time.now
    dt = t2 - t1
    if verbose
      if f == nil
        f = $stdout
      end
      f.print "\nElapsed time "
      hours = dt.to_i/3600
      dt -= hours*3600
      mins  = dt.to_i/60
      dt -= mins*60
      secs  = dt
      secs = secs.to_i if secs > 25
      if hours > 0
        f.print hours.to_i," hours "
      end
      if mins > 0
        f.print mins.to_i," minutes "
      end
      f.print secs," seconds\n" 
    end
  end
end

.version ⇒ Object

Returns the version string for the library.



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# File 'lib/genfrag.rb', line 12

def self.version
  VERSION
end