class Bio::Meme::Mast

Description¶ ↑

Bio::Meme::Mast is a wrapper for searching a database using sequence motifs. The code will read options from a Hash and run the program. Parsing of the output is provided by Bio::Meme::Mast::Report. Before running, options and options must be set in the constructor or Mast.config(options = {})

Usage¶ ↑

mast = Mast.new('/path/to/mast')
or with options
mast = Mast.new('/path/to/mast', {:mfile => 'meme.out', :d => '/shared/db/nr'})

report = Mast::Report.new(mast.run)
report.each do |motif|
  puts motif.length
end

Constants

DEFAULT_OPTIONS

Attributes

cmd[R]

The command line String to be executed

options[RW]

A Hash of options for Mast

Public Class Methods

new(mast_location, options = {}) click to toggle source

Create a mast instance

m = Mast.new('/usr/local/bin/mast')

Arguments:

(required) mast_location: String

Raises: ArgumentError if mast program is not found
Returns: a Bio::Meme::Mast object

    # File lib/bio/appl/meme/mast.rb
 96 def initialize(mast_location, options = {})
 97   unless File.exist?(mast_location)
 98     raise ArgumentError.new("mast: command not found : #{mast_location}")
 99   end
100   @binary = mast_location
101   options.empty? ? config(DEFAULT_OPTIONS) : config(options)
102 end

Public Instance Methods

check_options() click to toggle source

Checks if input/database files exist and options are valid

Raises: ArgumentError if the motifs file does not exist
Raises: ArgumentError if the database file does not exist
Raises: ArgumentError if there is an invalid option

    # File lib/bio/appl/meme/mast.rb
136 def check_options
137   @options.each_key do |k|
138     raise ArgumentError.new("Invalid option: #{k}") unless DEFAULT_OPTIONS.has_key?(k)
139   end
140   raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exist?(@options[:mfile])
141   raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exist?(@options[:d])
142 end

config(options) click to toggle source

Builds the command line string any options passed in will be merged with DEFAULT_OPTIONS Mast usage: mast <mfile> <opts> <flags>

mast.config({:mfile => "meme.out", :d => "/path/to/fasta/db"})

Arguments:

(required) options: Hash (see DEFAULT_OPTIONS)

Returns: the command line string

    # File lib/bio/appl/meme/mast.rb
114 def config(options)
115   @options = DEFAULT_OPTIONS.merge(options)
116   mfile, opts, flags = "", "", ""
117   @options.each_pair do |opt, val|
118     if val.nil? or val == false
119       next
120     elsif opt == :mfile
121       mfile = val
122     elsif val == true
123       flags << " -#{opt}"
124     else
125       opts << " -#{opt} #{val}"
126     end
127   end
128   @cmd = "#{@binary} #{mfile + opts + flags}"
129 end

run() click to toggle source

Run the mast program

Returns: Bio::Meme::Mast::Report object

    # File lib/bio/appl/meme/mast.rb
148 def run
149   check_options
150   call_command(@cmd) {|io| @output = io.read }
151   Report.new(@output)
152 end