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import gfapy
import unittest
class TestgfapyGfaToolsLinearPaths(unittest.TestCase):
def test_linear_path_merging(self):
for sfx in ["gfa", "gfa2"]:
gfa = gfapy.Gfa.from_file("tests/testdata/linear_merging.2."+"{}".format(sfx))
gfa.merge_linear_path([["0", "R"],["1", "R"],["2", "L"],["3", "R"]],
enable_tracking=True)
gfa.try_get_segment("0_1_2^_3") # nothing raised
self.assertEqual("ACGACGACGTCGA", gfa.segment("0_1_2^_3").sequence)
gfa = gfapy.Gfa.from_file("tests/testdata/linear_merging.2."+"{}".format(sfx))
gfa.merge_linear_path([["0", "R"],["1", "R"],["2", "L"],["3", "R"]],
enable_tracking=True)
gfa.try_get_segment("0_1_2^_3") # nothing raised
self.assertEqual("ACGACGACGTCGA", gfa.segment("0_1_2^_3").sequence)
def test_linear_path_merge_all(self):
for sfx in ["gfa", "gfa2"]:
gfa = gfapy.Gfa.from_file("tests/testdata/linear_merging.3.{}".format(sfx))
gfa.merge_linear_paths(enable_tracking=True)
self.assertIn(gfa.segment_names[0], ["0_1_2^_3","3^_2_1^_0^"])
gfa = gfapy.Gfa.from_file("tests/testdata/linear_merging.4.{}".format(sfx))
gfa.merge_linear_paths(enable_tracking=True)
try:
self.assertEqual({"0","3","1_2^"}, {x.name for x in gfa.segments})
except:
self.assertEqual({"0","3","2_1^"}, {x.name for x in gfa.segments})
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