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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 1.9 2008/01/10 03:51:06 ngoto 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 String object
# # by using Bio::EMBOSS.run method.
# xlrhodop = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
# puts xlrhodop
#
# # Or all in one go:
# puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
#
# # Similarly:
# puts Bio::EMBOSS.run('transeq', '-sbegin', '110','-send', '1171',
# 'embl:xlrhodop')
# puts Bio::EMBOSS.run('showfeat', 'embl:xlrhodop')
# puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop', '-osformat', 'acedb')
#
# # A shortcut exists for this two-step process for +seqret+ and +entret+.
# puts Bio::EMBOSS.seqret('embl:xlrhodop')
# puts Bio::EMBOSS.entret('embl:xlrhodop')
#
# # You can use %w() syntax.
# puts Bio::EMBOSS.run(*%w( transeq -sbegin 110 -send 1171 embl:xlrhodop ))
#
# # You can also use Shellwords.shellwords.
# require 'shellwords'
# str = 'transeq -sbegin 110 -send 1171 embl:xlrhodop'
# cmd = Shellwords.shellwords(str)
# puts Bio::EMBOSS.run(*cmd)
#
#
# == 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) _arg_: argument given to the emboss seqret command
# *Returns*:: String
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) _arg_: argument given to the emboss entret command
# *Returns*:: String
def self.entret(arg)
str = self.retrieve('entret', arg)
end
# WARNING: Bio::EMBOSS.new will be changed in the future because
# Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole.
# Using Bio::EMBOSS.run(program, options...) is strongly recommended.
#
# 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)
warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
@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
# Runs an emboss program and get the result as string.
# Note that "-auto -stdout" are automatically added to the options.
#
# Example 1:
#
# result = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
#
# Example 2:
#
# result = Bio::EMBOSS.run('water',
# '-asequence', 'swissprot:slpi_human',
# '-bsequence', 'swissprot:slpi_mouse')
#
# Example 3:
# options = %w( -asequence swissprot:slpi_human
# -bsequence swissprot:slpi_mouse )
# result = Bio::EMBOSS.run('needle', *options)
#
# For an overview of commands that can be used with this method, see the
# emboss website.
# ---
# *Arguments*:
# * (required) _program_: command name, or filename of an emboss program
# * _options_: options given to the emboss program
# *Returns*:: String
def self.run(program, *options)
cmd = [ program, *options ]
cmd.push '-auto'
cmd.push '-stdout'
return Bio::Command.query_command(cmd)
end
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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