Class: FbinFile

Inherits:
Object
  • Object
show all
Extended by:
FFI::Library
Defined in:
lib/scbi_fqbin/fbin_file.rb

Constant Summary collapse

CREATE_NEW_FILE = 
1
APPEND_TO_FILE = 
2

Instance Method Summary collapse

Constructor Details

#initialize(file_path, mode = 'r', qual_to_phred = true, qual_to_array = true, discretize_qual = 0, flatten_qual = 0, create_index = 1) ⇒ FbinFile

Initializes the file



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# File 'lib/scbi_fqbin/fbin_file.rb', line 58

def initialize(file_path, mode = 'r', qual_to_phred=true, qual_to_array=true, discretize_qual=0, flatten_qual=0, create_index=1)
  @file_path = file_path
  @open_mode=mode
  
  @qual_to_phred = qual_to_phred
  @qual_to_array = qual_to_array
  
  @to_phred = lambda{|q| q - 33}
  
  if @open_mode.index('r')
    @gzf_bin = FFI::MemoryPointer.new :pointer
    initialize_sequential_reads(@gzf_bin,@file_path)
    # inspect_file_data_struct(@gzf_bin)
    @gzf_bin = @gzf_bin.get_pointer(0)
    
  elsif @open_mode.index('w')
    @write_struct = FFI::MemoryPointer.new :pointer
    initialize_writes(@write_struct,@file_path, CREATE_NEW_FILE,discretize_qual, flatten_qual, create_index)
    @write_struct = @write_struct.get_pointer(0)
    # inspect_file_data_struct(@write_struct)
    
  elsif @open_mode.index('a')
     
     @write_struct = FFI::MemoryPointer.new :pointer
     initialize_writes(@write_struct,@file_path, APPEND_TO_FILE,discretize_qual, flatten_qual, create_index)
     @write_struct = @write_struct.get_pointer(0)
     # inspect_file_data_struct(@write_struct)
     
  else
    raise "Invalid aperture mode #{mode}. Use r/w"
  end
end

Instance Method Details

#close ⇒ Object

Closes file



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# File 'lib/scbi_fqbin/fbin_file.rb', line 202

def close

  if @open_mode.index('r')
    close_sequential_reads(@gzf_bin)
  else # CREATE_NEW_FILE or APPEND_TO_FILE
    # inspect_write_struct(@write_struct)
    close_writes(@write_struct)
  end
  
end

#count ⇒ Object

Returns the number of sequences in file. Iterating over it



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# File 'lib/scbi_fqbin/fbin_file.rb', line 214

def count
  res=0
  each do #|n,f,q,e|
    # puts n
    res+=1
  end
  return res
end

#each ⇒ Object

Iterates over all sequences in file



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# File 'lib/scbi_fqbin/fbin_file.rb', line 177

def each
                                                 
  gzf_bin = FFI::MemoryPointer.new :pointer
  initialize_sequential_reads(gzf_bin,@file_path)
  gzf_bin = gzf_bin.get_pointer(0)
  
   while seq=get_next_seq(gzf_bin)
     yield seq
   end
   
  close_sequential_reads(gzf_bin)
end

#get_next_seq(gzf_bin) ⇒ Object 



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# File 'lib/scbi_fqbin/fbin_file.rb', line 134

def get_next_seq(gzf_bin)
  seq_namePtr = FFIString.new
  fastaPtr = FFIString.new
  qualPtr = FFIString.new
  extrasPtr = FFIString.new
  
  if ((r=read_data_sequential(gzf_bin, seq_namePtr, fastaPtr, qualPtr, extrasPtr))==0)
    
    qual=qualPtr.to_s
    if @qual_to_phred
      qual=qual.each_char.map{|e| (@to_phred.call(e.ord))}
      
      if !@qual_to_array
        qual=qual.join(' ')
      end
    end
    
    seq_name=seq_namePtr.to_s
    fasta=fastaPtr.to_s
    extras=extrasPtr.to_s
    
    # seq_namePtr.free
    # fastaPtr.free
    # qualPtr.free
    # extrasPtr.free
    
    free_string(seq_namePtr)
    free_string(fastaPtr)
    free_string(qualPtr)
    free_string(extrasPtr)
    
    return seq_name, fasta, qual, extras
    
  else
    free_string(seq_namePtr)
    free_string(fastaPtr)
    free_string(qualPtr)
    free_string(extrasPtr)
    return nil
  end
end

#next_sequence ⇒ Object

Returns the next sequence in file, or nil if no more ara available



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# File 'lib/scbi_fqbin/fbin_file.rb', line 130

def next_sequence
  return get_next_seq(@gzf_bin)
end

#read_sequence(seq_name) ⇒ Object

Access a sequence by its name using the indexed read



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# File 'lib/scbi_fqbin/fbin_file.rb', line 92

def read_sequence(seq_name)
  
  fastaPtr = FFIString.new
  qualPtr = FFIString.new
  extrasPtr = FFIString.new
      
  if read_seq(@file_path,seq_name,fastaPtr,qualPtr,extrasPtr)==0
    
    qual=qualPtr.to_s
    
    if @qual_to_phred
      qual=qual.each_char.map{|e| (@to_phred.call(e.ord))}
      if !@qual_to_array
        qual=qual.join(' ')
      end
    end
    
    fasta=fastaPtr.to_s
    extras = extrasPtr.to_s
    
    free_string(qualPtr)
    free_string(fastaPtr)
    free_string(extrasPtr)

    return seq_name, fasta, qual, extras
    
  else
    
    free_string(qualPtr)
    free_string(fastaPtr)
    free_string(extrasPtr)
    
    return nil
    # raise "Invalid sequence"
  end
end

#write_sequence(seq_name, fasta, qual, extras) ⇒ Object

Writes a sequence to file



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# File 'lib/scbi_fqbin/fbin_file.rb', line 191

def write_sequence(seq_name,fasta,qual,extras)

  if qual.is_a?(Array)
      qual=qual.join(' ')
  end
    
  write_seq(@write_struct,seq_name,fasta,qual,extras)
end