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require "rgfa.rb"
require "test/unit"
require "tempfile"
class TestRGFA < Test::Unit::TestCase
def test_initialize
assert_nothing_raised { RGFA.new }
gfa = RGFA.new
assert_equal(RGFA, gfa.class)
end
def test_segment_names
gfa = RGFA.new
assert_equal([], gfa.segment_names)
gfa << "S\t1\t*"
gfa << "S\t2\t*"
assert_equal([:"1", :"2"], gfa.segment_names)
gfa.delete_segment("1")
assert_equal([:"2"], gfa.segment_names)
end
def test_path_names
gfa = RGFA.new
assert_equal([], gfa.path_names)
gfa << "P\t3\t1+,4-\t*"
assert_equal([:"3"], gfa.path_names)
gfa.delete_path("3")
assert_equal([], gfa.path_names)
end
def test_validate!
gfa = RGFA.new
gfa << "S\t1\t*"
assert_nothing_raised { gfa.validate! }
gfa << "L\t1\t+\t2\t-\t*"
assert_raise(RGFA::LineMissingError) { gfa.validate! }
gfa << "S\t2\t*"
assert_nothing_raised { gfa.validate! }
gfa << "P\t3\t1+,4-\t*"
assert_raise(RGFA::LineMissingError) { gfa.validate! }
gfa << "S\t4\t*"
assert_raise(RGFA::LineMissingError) { gfa.validate! }
gfa << "L\t4\t+\t1\t-\t*"
assert_nothing_raised { gfa.validate! }
end
def test_to_s
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa = RGFA.new
lines.each {|l| gfa << l}
assert_equal(lines.join("\n")+"\n", gfa.to_s)
end
def test_to_rgfa
gfa = RGFA.new
gfa2 = gfa.to_rgfa
assert(gfa2)
assert_equal(RGFA, gfa2.class)
end
def test_from_file
filename = "test/testdata/example1.gfa"
gfa = RGFA.from_file(filename)
assert(gfa)
assert_equal(IO.read(filename), gfa.to_s)
end
def test_to_file
filename = "test/testdata/example1.gfa"
gfa = RGFA.from_file(filename)
tmp = Tempfile.new("example1")
gfa.to_file(tmp.path)
tmp.rewind
assert_equal(IO.read(filename), IO.read(tmp))
end
def test_string_to_rgfa
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa1 = RGFA.new
lines.each {|l| gfa1 << l}
gfa2 = lines.join("\n").to_rgfa
assert(gfa2)
assert_equal(RGFA, gfa2.class)
assert_equal(gfa1.to_s, gfa2.to_s)
end
def test_array_to_rgfa
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa1 = RGFA.new
lines.each {|l| gfa1 << l}
gfa2 = lines.to_rgfa
assert(gfa2)
assert_equal(RGFA, gfa2.class)
assert_equal(gfa1.to_s, gfa2.to_s)
end
end
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