Class: Bio::Velvet::Underground

Inherits:
Object
  • Object
show all
Extended by:
FFI::Library
Includes:
UndergroundLogging
Defined in:
lib/bio-velvet_underground.rb,
lib/bio-velvet_underground/graph.rb,
lib/bio-velvet_underground/runner.rb,
lib/bio-velvet_underground/constants.rb,
lib/bio-velvet_underground/binary_sequence_store.rb

Defined Under Namespace

Classes: ArcStruct, BinarySequenceStore, Graph, GraphStruct, NodeStruct, ReadSet, Runner, ShortReadMarker

Constant Summary collapse

DEFAULT_MAXKMERLENGTH = 
31

Class Method Summary collapse

Methods included from UndergroundLogging

#log

Class Method Details

.attach_runner_functions ⇒ Object 



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# File 'lib/bio-velvet_underground/runner.rb', line 55

def self.attach_runner_functions
  attach_function :velveth, [:int32, :pointer], :int32
  attach_function :velvetg, [:int32, :pointer], :int32
end

.attach_shared_library(velvet_compilation_options = {}) ⇒ Object

Attach the correct shared velvet library with ffi. Options: :kmer: attach library with at least this much kmer length



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# File 'lib/bio-velvet_underground.rb', line 30

def self.attach_shared_library(velvet_compilation_options={})
  max_kmer_length = nil
  given_kmer = velvet_compilation_options[:kmer]
  if !given_kmer.nil?
    max_kmer_length = compilation_max_kmer(given_kmer)
    raise "No installed velvet library available for max kmer #{given_kmer}" if max_kmer_length.nil?
  end
  log.debug "Found max kmer length #{max_kmer_length} to load with the velvet library"

  # Set the ffi library path to the correct velvet one
  lib_location = self.library_location_of(max_kmer_length)
  log.debug "Loading velvet underground FFI library #{lib_location}.."
  ffi_lib lib_location
  log.debug "Velvet library loaded."

  attach_graph_functions
  attach_binary_sequence_functions
  attach_runner_functions
end

.compilation_max_kmer(graph_hash_length) ⇒ Object

Return the minimum kmer length greater than or equal to the given graph hash length e.g. 29 => 31, 31 => 31, 33 => 63.



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# File 'lib/bio-velvet_underground.rb', line 24

def self.compilation_max_kmer(graph_hash_length)
  max_kmers.select{|k| graph_hash_length<=k}.min
end

.library_location_of(max_kmer_length = nil) ⇒ Object

Where is the library given the max_kmer_length



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# File 'lib/bio-velvet_underground/constants.rb', line 16

def self.library_location_of(max_kmer_length=nil)
  if !Bio::Velvet::Underground.max_kmers.include?(max_kmer_length) and
    !max_kmer_length.nil?
    raise "bad max kmer length #{max_kmer_length}"
  end

  extras = []
  if !max_kmer_length.nil? and max_kmer_length != DEFAULT_MAXKMERLENGTH
    extras.push "-maxkmer#{max_kmer_length}"
  end
  return File.join(
    File.dirname(__FILE__),
    'external',
    "libvelvet#{extras.join('') }.so.1.0")
end

.log ⇒ Object 



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# File 'lib/bio-velvet_underground.rb', line 18

def self.log
  Bio::Log::LoggerPlus['bio-velvet_underground']
end

.max_kmers ⇒ Object

Different versions of velvet are compiled on installation of bio-velvet_underground. These are the different MAXKMERLENGTH parameters that are given to the velvet Makefile. See the velvet manual for more information on this.



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# File 'lib/bio-velvet_underground/constants.rb', line 11

def self.max_kmers
  [31,63,127,255]
end