Class: Bio::EMBOSS

Inherits:
Object show all
Defined in:
lib/bio/appl/emboss.rb

Overview

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: 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

  • 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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(cmd_line) ⇒ EMBOSS

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



116
117
118
 
# File 'lib/bio/appl/emboss.rb', line 116

def initialize(cmd_line)
  @cmd_line = cmd_line + ' -stdout -auto'
end

Instance Attribute Details

#io ⇒ Object (readonly)

Pipe for the command



140
141
142
 
# File 'lib/bio/appl/emboss.rb', line 140

def io
  @io
end

#result ⇒ Object (readonly)

Result of the executed command



143
144
145
 
# File 'lib/bio/appl/emboss.rb', line 143

def result
  @result
end

Class Method Details

.entret(arg) ⇒ Object

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



97
98
99
 
# File 'lib/bio/appl/emboss.rb', line 97

def self.entret(arg)
  str = self.retrieve('entret', arg)
end

.seqret(arg) ⇒ Object

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



81
82
83
 
# File 'lib/bio/appl/emboss.rb', line 81

def self.seqret(arg)
  str = self.retrieve('seqret', arg)
end

Instance Method Details

#exec ⇒ Object

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



129
130
131
132
133
134
135
136
137
 
# File 'lib/bio/appl/emboss.rb', line 129

def exec
  begin
    @io = IO.popen(@cmd_line, "w+")
    @result = @io.read
    return @result
  ensure
    @io.close
  end
end