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require "rgfa.rb"
require "test/unit"
class TestRGFAEdit < Test::Unit::TestCase
def test_rename
gfa = ["S\t0\t*", "S\t1\t*", "S\t2\t*", "L\t0\t+\t2\t-\t12M",
"C\t1\t+\t0\t+\t12\t12M", "P\t4\t2+,0-\t12M"].to_rgfa
gfa.rename("0", "X")
assert_equal([:"X", :"1", :"2"].sort, gfa.segment_names.sort)
assert_equal("L\tX\t+\t2\t-\t12M", gfa.links[0].to_s)
assert_equal("C\t1\t+\tX\t+\t12\t12M", gfa.containments[0].to_s)
assert_equal("P\t4\t2+,X-\t12M", gfa.paths[0].to_s)
assert_raises(RGFA::LineMissingError){gfa.links_of(["0", :E])}
assert_equal("L\tX\t+\t2\t-\t12M", gfa.links_of(["X", :E])[0].to_s)
assert_equal("C\t1\t+\tX\t+\t12\t12M", gfa.contained_in("1")[0].to_s)
assert_raises(RGFA::LineMissingError){gfa.containing("0")}
assert_equal("C\t1\t+\tX\t+\t12\t12M", gfa.containing("X")[0].to_s)
assert_raises(RGFA::LineMissingError){gfa.paths_with("0")}
assert_equal("P\t4\t2+,X-\t12M", gfa.paths_with("X")[0].to_s)
end
def test_multiply_segment
gfa = RGFA.new
gfa << "H\tVN:Z:1.0"
s = ["S\t0\t*\tRC:i:600",
"S\t1\t*\tRC:i:6000",
"S\t2\t*\tRC:i:60000"]
l = "L\t1\t+\t2\t+\t12M"
c = "C\t1\t+\t0\t+\t12\t12M"
p = "P\t3\t2+,0-\t12M"
(s + [l,c,p]).each {|line| gfa << line }
assert_equal(s, gfa.segments.map(&:to_s))
assert_equal([l], gfa.links.select{|n|!n.virtual?}.map(&:to_s))
assert_equal([c], gfa.containments.map(&:to_s))
assert_equal(l, gfa.link(["1", :E], ["2", :B]).to_s)
assert_equal(c, gfa.containment("1", "0").to_s)
assert_raises(RGFA::LineMissingError){gfa.link(["1a", :E], ["2", :B])}
assert_raises(RGFA::LineMissingError){gfa.containment("5", "0")}
assert_equal(6000, gfa.segment("1").RC)
gfa.multiply("1", 2)
assert_equal(l, gfa.link(["1", :E], ["2", :B]).to_s)
assert_equal(c, gfa.containment("1", "0").to_s)
assert_not_equal(nil, gfa.link(["1b", :E], ["2", :B]))
assert_not_equal(nil, gfa.containment("1b", "0"))
assert_equal(3000, gfa.segment("1").RC)
assert_equal(3000, gfa.segment("1b").RC)
gfa.multiply("1b", 3 , copy_names:["6","7"])
assert_equal(l, gfa.link(["1", :E], ["2", :B]).to_s)
assert_not_equal(nil, gfa.link(["1b", :E], ["2", :B]))
assert_not_equal(nil, gfa.link(["6", :E], ["2", :B]))
assert_not_equal(nil, gfa.link(["7", :E], ["2", :B]))
assert_not_equal(nil, gfa.containment("1b", "0"))
assert_not_equal(nil, gfa.containment("6", "0"))
assert_not_equal(nil, gfa.containment("7", "0"))
assert_equal(3000, gfa.segment("1").RC)
assert_equal(1000, gfa.segment("1b").RC)
assert_equal(1000, gfa.segment("6").RC)
assert_equal(1000, gfa.segment("7").RC)
end
def test_multiply_segment_copy_names
gfa = ["H\tVN:Z:1.0",
"S\t1\t*\tRC:i:600",
"S\t1b\t*\tRC:i:6000",
"S\t2\t*\tRC:i:60000",
"S\t3\t*\tRC:i:60000"].to_rgfa
gfa.multiply("2", 2, copy_names: :upcase)
assert_nothing_raised {gfa.segment!("2B")}
gfa.multiply("2", 2, copy_names: :upcase)
assert_nothing_raised {gfa.segment!("2C")}
gfa.multiply("2", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("2_copy")}
gfa.multiply("2", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("2_copy2")}
gfa.multiply("2", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("2_copy3")}
gfa.multiply("2_copy", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("2_copy4")}
gfa.multiply("2_copy4", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("2_copy5")}
gfa.multiply("2", 2, copy_names: :number)
assert_nothing_raised {gfa.segment!("4")}
gfa.multiply("1b", 2)
assert_nothing_raised {gfa.segment!("1c")}
gfa.multiply("1b", 2, copy_names: :number)
assert_nothing_raised {gfa.segment!("1b2")}
gfa.multiply("1b", 2, copy_names: :copy)
assert_nothing_raised {gfa.segment!("1b_copy")}
gfa.multiply("1b_copy", 2, copy_names: :lowcase)
assert_nothing_raised {gfa.segment!("1b_copz")}
gfa.multiply("1b_copy", 2, copy_names: :upcase)
assert_nothing_raised {gfa.segment!("1b_copyB")}
end
end
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