Class: Bio::Velvet::Underground::BinarySequenceStore

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-velvet_underground/binary_sequence_store.rb

Instance Method Summary collapse

Constructor Details

#initialize(cny_unified_seq_file) ⇒ BinarySequenceStore

Parse a CnyUnifiedSeq file in so that sequences can be accessed



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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 4

def initialize(cny_unified_seq_file)
  Bio::Velvet::Underground.attach_shared_library
  readset_pointer = Bio::Velvet::Underground.importCnyReadSet cny_unified_seq_file
  @readset = Bio::Velvet::Underground::ReadSet.new(readset_pointer)
end

Instance Method Details

#[](sequence_id) ⇒ Object

Return a sequence from the store given its read ID.



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

def [](sequence_id)
  if sequence_id==0 or sequence_id > @readset[:readCount]
    raise "Invalid sequence_id #{sequence_id}"
  end

  pointer = Bio::Velvet::Underground.getTightStringInArray(
    @readset[:tSequences], sequence_id-1
    )
  Bio::Velvet::Underground.readTightString pointer
end

#is_second_in_pair?(sequence_id) ⇒ Boolean

Returns true if the sequence ID refers to the second in a pair of sequences.

Returns:

  • (Boolean) 


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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 41

def is_second_in_pair?(sequence_id)
  if sequence_id==0 or sequence_id > @readset[:readCount]
    raise "Invalid sequence_id #{sequence_id}"
  end
  Bio::Velvet::Underground.isSecondInPair @readset, sequence_id-1
end

#length ⇒ Object

Number of sequences in this store



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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 23

def length
  @readset[:readCount]
end

#num_paired_end_readsets ⇒ Object

Return the number of libraries used in this sequence store that were paired-end e.g.



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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 61

def num_paired_end_readsets
  Bio::Velvet::Underground.pairedCategories(@readset)
end

#pair_id(sequence_id) ⇒ Object

Returns the ID of the given sequence_id’s pair, or nil if it is not a paired sequence



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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 50

def pair_id(sequence_id)
  return nil unless paired?(sequence_id)
  if is_second_in_pair?(sequence_id)
    sequence_id-1
  else
    sequence_id+1
  end
end

#paired?(sequence_id) ⇒ Boolean

Return true if paired, else false

Returns:

  • (Boolean) 


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# File 'lib/bio-velvet_underground/binary_sequence_store.rb', line 28

def paired?(sequence_id)
  cat = FFI::Pointer.new(:int8, @readset[:categories])[sequence_id-1].read_int8
  if cat == 0
    return false
  elsif cat == 1
    return true
  else
    raise "Unexpected velvet sequence category found: #{cat}"
  end
end