Class: Bio::MAF::FASTARangeReader

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/maf/tiler.rb

Constant Summary collapse

GT = 
'>'.getbyte(0)

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fspec) ⇒ FASTARangeReader

Returns a new instance of FASTARangeReader.



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# File 'lib/bio/maf/tiler.rb', line 217

def initialize(fspec)
  if fspec.respond_to? :seek
    @f = fspec
  else
    reader_class = if fspec =~ /.gz$/
                     Zlib::GzipReader
                   else
                     File
                   end
    @f = reader_class.open(fspec)
  end
  position_at_start
end

Instance Attribute Details

#f ⇒ Object (readonly)

Returns the value of attribute f.



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# File 'lib/bio/maf/tiler.rb', line 215

def f
  @f
end

#pos ⇒ Object (readonly)

Returns the value of attribute pos.



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# File 'lib/bio/maf/tiler.rb', line 215

def pos
  @pos
end

Instance Method Details

#position_at_start ⇒ Object 



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# File 'lib/bio/maf/tiler.rb', line 233

def position_at_start
  first = f.readline
  raise "expected FASTA comment" unless first =~ /^>/
  @pos = 0
end

#read_interval(z_start, z_end) ⇒ Object 



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# File 'lib/bio/maf/tiler.rb', line 239

def read_interval(z_start, z_end)
  if z_start < pos
    position_at_start
  end
  data = ''
  region_size = z_end - z_start
  in_region = false
  f.each_line do |line_raw|
    if line_raw.getbyte(0) == GT
      raise "unexpected description line: #{line_raw.inspect}"
    end
    line = line_raw.strip
    end_pos = pos + line.size
    if (! in_region) && pos <= z_start && z_start < end_pos
      offset = z_start - pos
      end_offset = [(offset + region_size), line.size].min
      data << line.slice(offset...end_offset)
      in_region = true
    elsif in_region
      need = region_size - data.size
      raise "should not happen: region #{region_size}, data #{data.size}, need #{need}" if need < 0
      if need > line.size
        data << line
      else
        # last line
        data << line.slice(0, need)
        break
      end
    end
    @pos = end_pos
  end
  return data
end