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#
# = bio/appl/emboss.rb - EMBOSS wrapper
#
# Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org>
# Copyright:: Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
# License:: The Ruby License
#
# $Id: emboss.rb,v 1.8 2007/04/05 23:35:39 trevor Exp $
#
module Bio
# == Description
#
# This file holds classes pertaining to the EMBOSS software suite.
#
# This class provides a wrapper for the applications of the EMBOSS suite, which
# is a mature and stable collection of open-source applications that can handle
# a huge range of sequence formats.
# Applications include:
# * Sequence alignment
# * Rapid database searching with sequence patterns
# * Protein motif identification, including domain analysis
# * Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats
# * Codon usage analysis for small genomes
# * Rapid identification of sequence patterns in large scale sequence sets
# * Presentation tools for publication
#
# See the emboss website for more information: http://emboss.sourceforge.net.
#
#
# == Usage
#
# require 'bio'
#
# # Suppose that you could get the sequence for XLRHODOP by running
# # the EMBOSS command +seqret embl:xlrhodop+ on the command line.
# # Then you can get the output of that command in a Bio::EMBOSS object
# # by creating a new Bio::EMBOSS object and subsequently executing it.
# xlrhodop = Bio::EMBOSS.new('seqret embl:xlrhodop')
# puts xlrhodop.exec
#
# # Or all in one go:
# puts Bio::EMBOSS.new('seqret embl:xlrhodop').exec
#
# # Similarly:
# puts Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
# puts Bio::EMBOSS.new('showfeat embl:xlrhodop').exec
# puts Bio::EMBOSS.new('seqret embl:xlrhodop -osformat acedb').exec
#
# # A shortcut exists for this two-step process for +seqret+ and +entret+.
# puts Bio::EMBOSS.seqret('embl:xlrhodop')
# puts Bio::EMBOSS.entret('embl:xlrhodop')
#
# == Pre-requisites
#
# You must have the EMBOSS suite installed locally. You can download from the
# project website (see References below).
#
# = Rereferences
#
# * http://emboss.sourceforge.net
# * Rice P, Longden I and Bleasby A. \
# EMBOSS: the European Molecular Biology Open Software Suite. \
# Trends Genet. 2000 Jun ; 16(6): 276-7
#
class EMBOSS
# Combines the initialization and execution for the emboss +seqret+ command.
#
# puts Bio::EMBOSS.seqret('embl:xlrhodop')
#
# is equivalent to:
#
# object = Bio::EMBOSS.new('seqret embl:xlrhodop')
# puts object.exec
# ---
# *Arguments*:
# * (required) _command_: emboss command
# *Returns*:: Bio::EMBOSS object
def self.seqret(arg)
str = self.retrieve('seqret', arg)
end
# Combines the initialization and execution for the emboss +entret+ command.
#
# puts Bio::EMBOSS.entret('embl:xlrhodop')
#
# is equivalent to:
#
# object = Bio::EMBOSS.new('entret embl:xlrhodop')
# puts object.exec
# ---
# *Arguments*:
# * (required) _command_: emboss command
# *Returns*:: Bio::EMBOSS object
def self.entret(arg)
str = self.retrieve('entret', arg)
end
# Initializes a new Bio::EMBOSS object. This provides a holder that can
# subsequently be executed (see Bio::EMBOSS.exec). The object does _not_
# hold any actual data when initialized.
#
# e = Bio::EMBOSS.new('seqret embl:xlrhodop')
#
# For e to actually hold data, it has to be executed:
# puts e.exec
#
# For an overview of commands that can be used with this method, see the
# emboss website.
# ---
# *Arguments*:
# * (required) _command_: emboss command
# *Returns*:: Bio::EMBOSS object
def initialize(cmd_line)
@cmd_line = cmd_line + ' -stdout -auto'
end
# A Bio::EMBOSS object has to be executed before it can return any result.
# obj_A = Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
# puts obj_A.result #=> nil
# obj_A.exec
# puts obj_A.result #=> a FASTA-formatted sequence
#
# obj_B = Bio::EMBOSS.new('showfeat embl:xlrhodop')
# obj_B.exec
# puts obj_B.result
def exec
begin
@io = IO.popen(@cmd_line, "w+")
@result = @io.read
return @result
ensure
@io.close
end
end
# Pipe for the command
attr_reader :io
# Result of the executed command
attr_reader :result
private
def self.retrieve(cmd, arg)
cmd = [ cmd, arg, '-auto', '-stdout' ]
return Bio::Command.query_command(cmd)
end
end # EMBOSS
end # Bio
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