1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
require "rgfatools.rb"
require "test/unit"
class TestRGFAToolsLinearPaths < 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
(s + l).each {|line| gfa << line }
gfa.merge_linear_path([["0", :E],["1", :E],["2", :B],["3", :E]],
enable_tracking: true)
assert_nothing_raised {gfa.segment!("0_1_2^_3")}
assert_equal("ACGACGACGTCGA", gfa.segment("0_1_2^_3").sequence)
gfa = RGFA.new
gfa.enable_extensions
(s + l).each {|line| gfa << line }
gfa.merge_linear_path([["0", :E],["1", :E],["2", :B],["3", :E]])
assert_nothing_raised {gfa.segment!("0_1_2^_3")}
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.enable_extensions
(s + l).each {|line| gfa << line }
gfa.merge_linear_paths
assert_equal([:"0_1_2^_3"], gfa.segment_names)
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.enable_extensions
(s + l).each {|line| gfa << line }
gfa.merge_linear_paths
assert_equal([:"0",:"3",:"1_2^"], gfa.segments.map(&:name))
end
end
|
