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import gfapy
import unittest
class TestAPILinesCreators(unittest.TestCase):
def test_add_headers(self):
gfa = gfapy.Gfa()
h = "H\tVN:Z:1.0"
gfa.append(h) # nothing raised
self.assertEqual([h], [str(x) for x in gfa.headers])
def test_add_segments(self):
gfa = gfapy.Gfa()
s1 = gfapy.Line("S\t1\t*")
s2 = gfapy.Line("S\t2\t*")
s2c = gfapy.Line("S\t2\t*")
gfa.append(s1) # nothing raised
gfa.append(s2) # nothing raised
self.assertSetEqual(set([str(s) for s in [s1, s2]]), set([str(s) for s in gfa.segments]))
self.assertSetEqual(set(["1", "2"]), set(gfa.segment_names))
self.assertEqual(s1, gfa.segment("1"))
self.assertEqual(None, gfa.segment("0"))
gfa.try_get_segment("1") # nothing raised
with self.assertRaises(gfapy.NotFoundError): gfa.try_get_segment("0")
with self.assertRaises(gfapy.NotUniqueError): gfa.append(s2c)
def test_add_links(self):
s1 = "S\t1\t*"
s2 = "S\t2\t*"
l1 = gfapy.Line("L\t1\t+\t2\t+\t12M")
l2 = "L\t1\t+\t3\t+\t12M"
gfa = gfapy.Gfa()
gfa.append(s1)
gfa.append(s2)
gfa.append(l1) # nothing raised
self.assertEqual([l1], gfa.dovetails)
self.assertEqual([l1], gfa.segment("1").end_relations("R", ["2", "L"]))
self.assertEqual([l1], gfa.segment("2").end_relations("L", ["1", "R"]))
self.assertEqual([], gfa.segment("2").end_relations("R", gfapy.SegmentEnd("1", "L")))
gfa.append(l2) # nothing raised
def test_add_containments(self):
s1 = "S\t1\t*"
s2 = "S\t2\t*"
c1 = gfapy.Line("C\t1\t+\t2\t+\t12\t12M")
c2 = "C\t1\t+\t3\t+\t12\t12M"
gfa = gfapy.Gfa()
gfa.append(s1)
gfa.append(s2)
gfa.append(c1) # nothing raised
self.assertEqual([c1], gfa.containments)
self.assertEqual([c1],
gfa.segment("1").relations_to("2", "edges_to_contained"))
self.assertEqual([],
gfa.segment("2").relations_to("1", "edges_to_contained"))
gfa.append(c2) # nothing raised
def test_add_paths(self):
s1 = "S\t1\t*"
s2 = "S\t2\t*"
p1 = gfapy.Line("P\t4\t1+,2+\t122M")
p2 = "P\t1\t1+,2+\t122M"
p3 = "P\t5\t1+,2+,3+\t122M,120M"
gfa = gfapy.Gfa()
gfa.append(s1)
gfa.append(s2)
gfa.append(p1) # nothing raised
self.assertEqual([p1], gfa.paths)
self.assertEqual(["4"], gfa.path_names)
self.assertEqual(p1, gfa.line("4"))
self.assertEqual(None, gfa.line("5"))
with self.assertRaises(gfapy.NotUniqueError): gfa.append(p2)
gfa.append(p3) # nothing raised
## def test_segments_first_order(self):
## 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 = gfapy.Gfa()
## gfa.append(s1)
## gfa.append(s2)
## gfa.append(l1) # nothing raised
## with self.assertRaises(gfapy.NotFoundError): gfa.append(l2)
## gfa.append(c1) # nothing raised
## with self.assertRaises(gfapy.NotFoundError): gfa.append(c2)
## gfa.append(p1) # nothing raised
## with self.assertRaises(gfapy.NotUniqueError): gfa.append(p2)
## with self.assertRaises(gfapy.NotFoundError): gfa.append(p3)
def test_header_add(self):
gfa = gfapy.Gfa()
gfa.append("H\tVN:Z:1.0")
gfa.append("H\taa:i:12\tab:Z:test1")
gfa.append("H\tac:Z:test2")
gfa.header.add("aa", 15)
self.assertSetEqual(
set([
"H\tVN:Z:1.0",
"H\taa:i:12",
"H\taa:i:15",
"H\tab:Z:test1",
"H\tac:Z:test2",
]),
set([str(x) for x in gfa.headers]))
gfa.header.add("aa", 16)
self.assertSetEqual(
set([
"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",
]),
set([str(x) for x in gfa.headers]))
gfa.header.delete("aa")
gfa.header.aa = 26
self.assertEqual(
set([
"H\tVN:Z:1.0",
"H\taa:i:26",
"H\tab:Z:test1",
"H\tac:Z:test2",
]),
set([str(x) for x in gfa.headers]))
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