Graphical Fragment Assembly (GFA) for Ruby

This implementation follows the specifications of GFA-spec.

To load the library:

require 'gfa'

Parsing GFA

To parse a file in GFA format:

my_gfa = GFA.load('assembly.gfa')

For large GFA files, you can also parse them in parallel:

my_gfa = GFA.load_parallel('large-graph.gfa', 4)

To load GFA strings line-by-line:

my_gfa = GFA.new
File.open('assembly.gfa', 'r') do |fh|
  fh.each do |ln|
    my_gfa << ln
  end
end

Saving GFA

After altering a GFA object, you can simply save it in a file as:

my_gfa.save('alt-assembly.gfa')

Or line-by-line as:

fh = File.open('alt-assembly.gfa', 'w')
my_gfa.each_line do |ln|
  fh.puts ln
end
fh.close

Visualizing GFA

Any GFA object can be exported as an RGL graph using the methods adjacency_graph and implicit_graph. For example, you can render tiny.gfa:

require 'rgl/dot'

my_gfa = GFA.load('data/tiny.gfa')
dg = my_gfa.implicit_graph
dg.write_to_graphic_file('jpg')

If you don't care about orientation, you can also build an undirected graph without orientation:

ug = my_gfa.implicit_graph(orient: false)
ug.write_to_graphic_file('jpg')

Installation

gem install gfa

Or add the following line to your Gemfile:

gem 'gfa'

Author

Luis M. Rodriguez-R.

License

Artistic License 2.0.