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 = {})

Source

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

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

Public Instance Methods

check_options ()

Source

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

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

config (options)

Source

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

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

run ()

Source

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

Run the mast program

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