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import gfapy
import unittest
class TestAPIMultiplication(unittest.TestCase):
def test_multiply_segment(self):
gfa = gfapy.Gfa()
gfa.append("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"
for line in (list(s) + [l,c,p]): gfa.append(line)
self.assertEqual(s, {str(x) for x in gfa.segments})
self.assertEqual([l], [str(x) for x in gfa.dovetails if not x.virtual])
self.assertEqual([c], [str(x) for x in gfa.containments])
self.assertEqual([l], [str(x) for x in gfa.segment("1").end_relations("R", ["2", "L"])])
self.assertEqual([c], [str(x) for x in gfa.segment("1").relations_to("0")])
self.assertEqual(6000, gfa.segment("1").RC)
gfa.multiply("1", 2)
self.assertEqual([l], [str(x) for x in gfa.segment("1").end_relations("R", ["2", "L"])])
self.assertEqual([c], [str(x) for x in gfa.segment("1").relations_to("0")])
self.assertNotEqual([], [str(x) for x in gfa.segment("1*2").end_relations("R", ["2", "L"])])
self.assertNotEqual([], [str(x) for x in gfa.segment("1*2").relations_to("0")])
self.assertEqual(3000, gfa.segment("1").RC)
self.assertEqual(3000, gfa.segment("1*2").RC)
gfa.multiply("1*2", 3, copy_names=["6","7"])
self.assertEqual([l], [str(x) for x in gfa.segment("1").end_relations("R", ["2", "L"])])
self.assertNotEqual([], [str(x) for x in gfa.segment("1*2").end_relations("R", ["2", "L"])])
self.assertNotEqual([], [str(x) for x in gfa.segment("6").end_relations("R", ["2", "L"])])
self.assertNotEqual([], [str(x) for x in gfa.segment("7").end_relations("R", ["2", "L"])])
self.assertNotEqual([], gfa.segment("1*2").relations_to("0"))
self.assertNotEqual([], gfa.segment("6").relations_to("0"))
self.assertNotEqual([], gfa.segment("7").relations_to("0"))
self.assertEqual(3000, gfa.segment("1").RC)
self.assertEqual(1000, gfa.segment("1*2").RC)
self.assertEqual(1000, gfa.segment("6").RC)
self.assertEqual(1000, gfa.segment("7").RC)
def test_multiply_segment_copy_names(self):
gfa = gfapy.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"])
gfa.multiply("2", 2)
gfa.try_get_segment("2*2") # nothing raised
gfa.multiply("2*2", 2)
gfa.try_get_segment("2*3") # nothing raised
gfa.multiply("2*2", 2, copy_names = ["x"])
gfa.try_get_segment("x") # nothing raised
def test_links_distribution_l1_m2(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l1.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l1.m2.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True)
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_links_distribution_l2_m2(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m2.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True)
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_no_links_distribution_l2_m2(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m2.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="off")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_links_distribution_l2_m3(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m3.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 3, extended=True)
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_no_links_distribution_l2_m3(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m3.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 3, extended=True, distribute="off")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_links_distribution_l3_m2(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.m2.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True)
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_no_links_distribution_l3_m2(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.m2.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="off")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_muliply_without_rgfatools(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.m2.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2)
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_distribution_policy_equal_with_equal(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m2.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="equal")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_distribution_policy_equal_with_not_equal(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l3.m2.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="equal")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_distribution_policy_L(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m2.no_ld.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="L")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
def test_distribution_policy_R(self):
for sfx in ["gfa", "gfa2"]:
g1 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.{}".format(sfx))
g2 = gfapy.Gfa.from_file("tests/testdata/links_distri.l2.m2.{}".format(sfx))
self.assertNotEqual(set(g2.segment_names),set(g1.segment_names))
self.assertNotEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
g1.multiply("1", 2, extended=True, distribute="R")
self.assertEqual(set(g2.segment_names),set(g1.segment_names))
self.assertEqual(set([str(x) for x in g2.dovetails]),
set([str(x) for x in g1.dovetails]))
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