Class: BioDSL::Usearch

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/BioDSL/usearch.rb

Overview

Class with methods to execute Usearch and parse the results.

Defined Under Namespace

Classes: IO

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(options) ⇒ Usearch

Constructor for Usearch class.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 136

def initialize(options)
  @options = options
  @stderr  = nil

  return self unless File.size(@options[:input]) == 0

  fail UsearchError, %(Empty input file -> "#{@options[:input]}")
end

Class Method Details

.cluster_otus(options) ⇒ Object

Execute cluster_otus.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 62

def self.cluster_otus(options)
  usearch = new(options)
  usearch.cluster_otus
end

.cluster_smallmem(options) ⇒ Object

Execute cluster_smallmem.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 48

def self.cluster_smallmem(options)
  usearch = new(options)
  usearch.cluster_smallmem
end

.open(*args) {|IO| ... } ⇒ IO

Open a Usearch file.

Parameters:

  • List (Array) —

    of open arguments.

Yields:

  • (IO) —

    stream.

Returns:

  • (IO) —

    stream.



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# File 'lib/BioDSL/usearch.rb', line 115

def self.open(*args)
  ios = IO.open(*args)

  if block_given?
    yield ios
  else
    return ios
  end
end

.uchime_ref(options) ⇒ Object

Execute uchime_ref.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 76

def self.uchime_ref(options)
  usearch = new(options)
  usearch.uchime_ref
end

.usearch_global(options) ⇒ Object

Execute usearch_local.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 90

def self.usearch_global(options)
  usearch = new(options)
  usearch.usearch_global
end

.usearch_local(options) ⇒ Object

Execute usearch_local.

Parameters:

  • options (Hash) —

    Options Hash

Options Hash (options):



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# File 'lib/BioDSL/usearch.rb', line 104

def self.usearch_local(options)
  usearch = new(options)
  usearch.usearch_local
end

Instance Method Details

#cluster_otus ⇒ self

Combose a command list and execute cluster_otus with this.

Returns:

  • (self) 


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# File 'lib/BioDSL/usearch.rb', line 170

def cluster_otus
  command = []
  command << 'usearch'
  command << "-cluster_otus #{@options[:input]}"
  command << "-otus #{@options[:output]}"
  command << "-id #{@options[:identity]}"
  command << "-threads #{@options[:cpus]}" if @options[:cpus]

  execute(command)

  self
end

#cluster_smallmem ⇒ self

Combose a command list and execute cluster_smallmem with this.

Returns:

  • (self) 


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# File 'lib/BioDSL/usearch.rb', line 148

def cluster_smallmem
  command = []
  command << 'usearch'
  command << "-cluster_smallmem #{@options[:input]}"
  command << "-id #{@options[:identity]}"
  command << "-threads #{@options[:cpus]}" if @options[:cpus]
  command << "-strand #{@options[:strand]}"

  if @options[:align]
    command << "-msaout #{@options[:output]}"
  else
    command << "-uc #{@options[:output]}"
  end

  execute(command)

  self
end

#uchime_ref ⇒ self

Combose a command list and execute uchime_ref with this.

Returns:

  • (self) 


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# File 'lib/BioDSL/usearch.rb', line 186

def uchime_ref
  command = []
  command << 'usearch'
  command << "-uchime_ref #{@options[:input]}"
  command << "-db #{@options[:database]}"
  command << "-strand #{@options[:strand]}"
  command << "-threads #{@options[:cpus]}" if @options[:cpus]
  command << "-nonchimeras #{@options[:output]}"

  execute(command)

  self
end

#usearch_global ⇒ self

Combose a command list and execute usearch_global with this.

Returns:

  • (self) 


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# File 'lib/BioDSL/usearch.rb', line 203

def usearch_global
  command = []
  command << 'usearch'
  command << '-notrunclabels'
  command << "-usearch_global #{@options[:input]}"
  command << "-db #{@options[:database]}"
  command << "-strand #{@options[:strand]}" if @options[:strand]
  command << "-threads #{@options[:cpus]}"  if @options[:cpus]
  command << "-id #{@options[:identity]}"
  command << "-uc #{@options[:output]}"

  execute(command)

  self
end

#usearch_local ⇒ self

Combose a command list and execute usearch_local with this.

Returns:

  • (self) 


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# File 'lib/BioDSL/usearch.rb', line 222

def usearch_local
  command = []
  command << 'usearch'
  command << '-notrunclabels'
  command << "-usearch_local #{@options[:input]}"
  command << "-db #{@options[:database]}"
  command << "-strand #{@options[:strand]}" if @options[:strand]
  command << "-threads #{@options[:cpus]}"  if @options[:cpus]
  command << "-id #{@options[:identity]}"
  command << "-uc #{@options[:output]}"

  execute(command)

  self
end