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require "rgfa.rb"
require "test/unit"
class TestRGFALineCreators < Test::Unit::TestCase
def test_add_headers
gfa = RGFA.new
h = "H\tVN:Z:1.0"
assert_nothing_raised { gfa << h }
assert_equal([h], gfa.headers.map(&:to_s))
end
def test_add_comments
gfa = RGFA.new
c1 = "#this is a comment"
c2 = "# this is also a comment"
c3 = "#and \tthis too!"
assert_nothing_raised { gfa << c1 }
assert_nothing_raised { gfa << c2 }
assert_nothing_raised { gfa << c3 }
end
def test_add_segments
gfa = RGFA.new
s1 = "S\t1\t*".to_rgfa_line
s2 = "S\t2\t*".to_rgfa_line
assert_nothing_raised { gfa << s1 }
assert_nothing_raised { gfa << s2 }
assert_equal([s1, s2], gfa.segments)
assert_equal([:"1", :"2"], gfa.segment_names)
assert_equal(s1, gfa.segment("1"))
assert_equal(nil, gfa.segment("0"))
assert_nothing_raised { gfa.segment!("1") }
assert_raises(RGFA::LineMissingError) { gfa.segment!("0") }
assert_raises(RGFA::DuplicatedLabelError) { gfa << s2 }
end
def test_add_links
s1 = "S\t1\t*"
s2 = "S\t2\t*"
l1 = "L\t1\t+\t2\t+\t12M".to_rgfa_line
l2 = "L\t1\t+\t3\t+\t12M"
gfa = RGFA.new
gfa << s1
gfa << s2
assert_nothing_raised { gfa << l1 }
assert_equal([l1], gfa.links)
assert_equal(l1, gfa.link(["1", :E], ["2", :B]))
assert_equal(l1, gfa.link(["2", :B], ["1", :E]))
assert_equal(nil, gfa.link(["2", :E], ["1", :B]))
assert_nothing_raised {gfa.link!(["1", :E], ["2", :B])}
assert_raises(RGFA::LineMissingError) {gfa.link!(["2", :E], ["1", :B])}
assert_nothing_raised { gfa << l2 }
end
def test_add_containments
s1 = "S\t1\t*"
s2 = "S\t2\t*"
c1 = "C\t1\t+\t2\t+\t12\t12M".to_rgfa_line
c2 = "C\t1\t+\t3\t+\t12\t12M"
gfa = RGFA.new
gfa << s1
gfa << s2
assert_nothing_raised { gfa << c1 }
assert_equal([c1], gfa.containments)
assert_equal(c1, gfa.containment("1", "2"))
assert_nothing_raised {gfa.containment!("1", "2")}
assert_raises(RGFA::LineMissingError) {gfa.containment!("2", "1")}
assert_nothing_raised { gfa << c2 }
end
def test_add_paths
s1 = "S\t1\t*"
s2 = "S\t2\t*"
p1 = "P\t4\t1+,2+\t122M".to_rgfa_line
p2 = "P\t1\t1+,2+\t122M"
p3 = "P\t5\t1+,2+,3+\t122M,120M"
gfa = RGFA.new
gfa << s1
gfa << s2
assert_nothing_raised { gfa << p1 }
assert_equal([p1], gfa.paths)
assert_equal([:"4"], gfa.path_names)
assert_equal(p1, gfa.path("4"))
assert_equal(nil, gfa.path("5"))
assert_nothing_raised {gfa.path!("4")}
assert_raises(RGFA::LineMissingError) {gfa.path!("5")}
assert_raises(RGFA::DuplicatedLabelError) { gfa << p2 }
assert_nothing_raised { gfa << p3 }
end
def test_segments_first_order
s1 = "S\t1\t*"
s2 = "S\t2\t*"
l1 = "L\t1\t+\t2\t+\t122M"
l2 = "L\t1\t+\t3\t+\t122M"
c1 = "C\t1\t+\t2\t+\t12\t12M"
c2 = "C\t1\t+\t3\t+\t12\t12M"
p1 = "P\t4\t1+,2+\t122M"
p2 = "P\t1\t1+,2+\t122M"
p3 = "P\t5\t1+,3+\t122M"
gfa = RGFA.new
gfa.require_segments_first_order
gfa << s1
gfa << s2
assert_nothing_raised { gfa << l1 }
assert_raises(RGFA::LineMissingError) { gfa << l2 }
assert_nothing_raised { gfa << c1 }
assert_raises(RGFA::LineMissingError) { gfa << c2 }
assert_nothing_raised { gfa << p1 }
assert_raises(RGFA::DuplicatedLabelError) { gfa << p2 }
assert_raises(RGFA::LineMissingError) { gfa << p3 }
end
def test_header_add
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
gfa << "H\taa:i:12\tab:Z:test1"
gfa << "H\tac:Z:test2"
gfa.header.add(:aa, 15)
assert_equal(
[
"H\tVN:Z:1.0",
"H\taa:i:12",
"H\taa:i:15",
"H\tab:Z:test1",
"H\tac:Z:test2",
],
gfa.headers.map(&:to_s).sort)
gfa.header.add(:aa, 16)
assert_equal(
[
"H\tVN:Z:1.0",
"H\taa:i:12",
"H\taa:i:15",
"H\taa:i:16",
"H\tab:Z:test1",
"H\tac:Z:test2",
],
gfa.headers.map(&:to_s).sort)
gfa.header.delete(:aa)
gfa.header.aa = 26
assert_equal(
[
"H\tVN:Z:1.0",
"H\taa:i:26",
"H\tab:Z:test1",
"H\tac:Z:test2",
],
gfa.headers.map(&:to_s).sort)
end
end
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