Graphical Fragment Assembly (GFA) for Ruby

This implementation follows the specifications of GFA-spec.

Parsing GFA

To parse a file in GFA format:

require "gfa"

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

To load GFA strings line-by-line:

require "gfa"

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

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

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 "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")

gem install gfa

Or add the following line to your Gemfile:

gem "gfa"

and run bundle install from your shell.

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data	gfa/graph docs	Mar 24, 2016
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test	v0.1.2: Full test coverage	Mar 25, 2016
.codeclimate.yml	code-climate fix	Mar 25, 2016
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LICENSE	Initial commit	Mar 22, 2016
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