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require "rgfa.rb"
require "test/unit"
class TestRGFATraverse < Test::Unit::TestCase
def test_linear_path_merging
s = ["S\t0\tACGA",
"S\t1\tACGA",
"S\t2\tACGA",
"S\t3\tACGA"]
l = ["L\t0\t+\t1\t+\t1M",
"L\t1\t+\t2\t-\t1M",
"L\t2\t+\t3\t+\t1M"]
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
(s + l).each {|line| gfa << line }
assert_raises(ArgumentError) do
gfa.merge_linear_path([["0", :E],["1", :E],["2", :B],["3", :E]])
end
s = ["S\t0\tACGA",
"S\t1\tACGA",
"S\t2\tACGT",
"S\t3\tTCGA"]
l = ["L\t0\t+\t1\t+\t1M",
"L\t1\t+\t2\t-\t1M",
"L\t2\t-\t3\t+\t1M"]
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
(s + l).each {|line| gfa << line }
assert_nothing_raised do
gfa.merge_linear_path([["0", :E],["1", :E],["2", :B],["3", :E]])
end
assert_raises(RGFA::LineMissingError) {gfa.segment!("0")}
assert_raises(RGFA::LineMissingError) {gfa.segment!("1")}
assert_raises(RGFA::LineMissingError) {gfa.segment!("2")}
assert_raises(RGFA::LineMissingError) {gfa.segment!("3")}
assert_nothing_raised {gfa.segment!("0_1_2_3")}
assert_equal([], gfa.links)
assert_equal("ACGACGACGTCGA", gfa.segment("0_1_2_3").sequence)
end
def test_linear_path_merge_all
s = ["S\t0\t*",
"S\t1\t*",
"S\t2\t*",
"S\t3\t*"]
l = ["L\t0\t+\t1\t+\t1M",
"L\t1\t+\t2\t-\t1M",
"L\t2\t-\t3\t+\t1M"]
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
(s + l).each {|line| gfa << line }
gfa.merge_linear_paths
assert_nothing_raised { gfa.merge_linear_paths }
assert_equal([:"0_1_2_3"], gfa.segment_names)
assert_equal(1, gfa.segments.size)
assert_equal([], gfa.links)
s = ["S\t0\t*",
"S\t1\t*",
"S\t2\t*",
"S\t3\t*"]
l = ["L\t0\t+\t1\t+\t1M",
"L\t0\t+\t2\t+\t1M",
"L\t1\t+\t2\t-\t1M",
"L\t2\t-\t3\t+\t1M"].map(&:to_rgfa_line)
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
(s + l).each {|line| gfa << line }
assert_nothing_raised { gfa.merge_linear_paths }
assert_equal(3, gfa.segments.size)
assert_equal([:"0",:"3",:"1_2"], gfa.segments.map(&:name))
s = ["S\t0\t*",
"S\t1\t*",
"S\t2\t*",
"S\t3\t*"]
l = ["L\t0\t+\t1\t+\t1M",
"L\t0\t+\t2\t+\t1M",
"L\t1\t+\t2\t+\t1M",
"L\t2\t+\t3\t+\t1M"].map(&:to_rgfa_line)
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
(s + l).each {|line| gfa << line }
assert_nothing_raised { gfa.merge_linear_paths }
assert_equal(3, gfa.segments.size)
assert_equal([:"0", :"1", :"2_3"], gfa.segments.map(&:name))
end
def test_linear_path_merge_example1
gfa = RGFA.from_file("test/testdata/example1.gfa")
assert_equal([%w[18 19 1],
%w[11 9 12],
%w[22 16 20 21 23]],
gfa.linear_paths.map{|sp|sp.map{|sn,et|sn.to_sym.to_s}})
end
end
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