Class: BioMummer::DeltaFile

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

Constant Summary collapse

NUCMER = 
1
PROMER = 
2

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(io) ⇒ DeltaFile

Returns a new instance of DeltaFile.

Raises:

  • (EncodingError) 


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

def initialize(io)
  raise EncodingError, "Not delta format" unless format_ok?(io)
  @alignments = parse(io.read)
end

Instance Attribute Details

#alignments ⇒ Object (readonly)

Returns the value of attribute alignments.



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# File 'lib/bio-mummer/mummer.rb', line 53

def alignments
  @alignments
end

#alternate_filename ⇒ Object

Returns the value of attribute alternate_filename.



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# File 'lib/bio-mummer/mummer.rb', line 52

def alternate_filename
  @alternate_filename
end

#reference_filename ⇒ Object

Returns the value of attribute reference_filename.



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# File 'lib/bio-mummer/mummer.rb', line 52

def reference_filename
  @reference_filename
end

Class Method Details

.open(filename) ⇒ Object 



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# File 'lib/bio-mummer/mummer.rb', line 60

def self.open(filename)
  io = File.open(filename)
  self.new(super(io))
end

Instance Method Details

#format_ok?(io) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-mummer/mummer.rb', line 87

def format_ok?(io)
  line = io.gets.chomp
  unless line.match(/^(\/.*) (\/.*)$/)
    return false
  else
    reference_filename = $1
    alternate_filename = $2
  end

  case io.gets.chomp
  when /NUCMER/
    @format = NUCMER
    return true
  when /PROMER/
    @format = PROMER
    return true
  else
    return false
  end
end

#parse(string) ⇒ Object 



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# File 'lib/bio-mummer/mummer.rb', line 65

def parse(string)
  string.split("\n").slice_before(/^>/).flat_map do |block|
    refname, qryname = block.shift.match(/>(.*) (.*) \d+ \d+/).captures
    block.slice_before(/\d+ \d+ \d+ \d+/).map do |alignment|
      refstart, refstop, qrystart, qrystop = alignment
        .shift
        .match(/(\d+) (\d+) (\d+) (\d+) /)
        .captures
        .map{ |c| c.to_i }
      alignment.pop
      Alignment.new(refname,
                    qryname,
                    refstart,
                    refstop,
                    [qrystart, qrystop].min,
                    [qrystart, qrystop].max,
                    qrystart < qrystop,
                    alignment.map{ |i| i.to_i })
    end
  end
end

#transpose_region(refname, startpos, endpos) ⇒ Object 



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# File 'lib/bio-mummer/mummer.rb', line 108

def transpose_region(refname, startpos, endpos)
  a = alignments.find do |a|
    a.refname == refname && a.refstart <= startpos && a.refstop >= endpos
  end
  if a
    qryname = a.qryname
    qrystart = a.ref_to_query(startpos)
    qrystop = a.ref_to_query(endpos)
    if qrystart.nil? || qrystop.nil?
      return nil
    else
      return [qryname, qrystart, qrystop, a.strand]
    end
  else
    return nil
  end
end