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import gfapy
import unittest
class TestApiVersion(unittest.TestCase):
def test_header_conversion(self):
gfa1str = "H\tVN:Z:1.0"
gfa2str = "H\tVN:Z:2.0"
self.assertEqual(gfa1str, str(gfapy.Line(gfa2str).to_gfa1()))
self.assertEqual(gfa1str, str(gfapy.Line(gfa2str).to_gfa1()))
self.assertEqual(gfa2str, str(gfapy.Line(gfa1str).to_gfa2()))
self.assertEqual(gfa2str, str(gfapy.Line(gfa2str).to_gfa2()))
def test_comment_conversion(self):
self.assertEqual("# comment",
str(gfapy.Line("# comment",version="gfa1").to_gfa1()))
self.assertEqual("# comment",
str(gfapy.Line("# comment",version="gfa2").to_gfa1()))
self.assertEqual("# comment",
str(gfapy.Line("# comment",version="gfa1").to_gfa2()))
self.assertEqual("# comment",
str(gfapy.Line("# comment",version="gfa2").to_gfa2()))
def test_segment_conversion(self):
self.assertEqual("S\tA\tNNNN",
str(gfapy.Line("S\tA\tNNNN").to_gfa1()))
self.assertEqual("S\tA\t4\tNNNN",
str(gfapy.Line("S\tA\tNNNN").to_gfa2()))
self.assertEqual("S\tA\tNNNN\tLN:i:4",str(gfapy.Line("S\tA\t4\tNNNN").to_gfa1()))
self.assertEqual("S\tA\t*\tLN:i:4",str(gfapy.Line("S\tA\t4\t*").to_gfa1()))
self.assertEqual("S\tA\t4\tNNNN",str(gfapy.Line("S\tA\t4\tNNNN").to_gfa2()))
# wrong sequence alphabet for GFA2->GFA1
self.assertEqual("S\tA\t4\t[[]]",str(gfapy.Line("S\tA\t4\t[[]]").to_gfa2()))
self.assertRaises(gfapy.RuntimeError,gfapy.Line("S\tA\t4\t[[]]").to_gfa1)
# wrong identifier for GFA2->GFA1
self.assertEqual("S\tA+,\t3\tNNN", str(gfapy.Line("S\tA+,\t3\tNNN").to_gfa2()))
self.assertRaises(gfapy.RuntimeError,gfapy.Line("S\tA+,\t3\tNNN").to_gfa1)
# sequence not available but LN for GFA1->GFA2
self.assertEqual("S\tA\t4\t*",str(gfapy.Line("S\tA\t*\tLN:i:4").to_gfa2()))
# both sequence and LN not available for GFA1->GFA2
self.assertRaises(gfapy.RuntimeError,gfapy.Line("S\tA\t*").to_gfa2)
def test_link_conversion(self):
gfa1str = "L\tA\t+\tB\t-\t100M"
gfa1str_noov = "L\tA\t+\tB\t+\t*"
gfa2str = "E\t1\tA+\tB-\t100\t200$\t100\t200$\t100M"
# not connected
self.assertRaises(gfapy.RuntimeError,gfapy.Line(gfa1str).to_gfa2)
# connected
g = gfapy.Gfa()
g.add_line("S\tA\t*\tLN:i:200")
g.add_line("S\tB\t*\tLN:i:200")
gfa1line = gfapy.Line(gfa1str)
g.add_line(gfa1line)
gfa1line_noov = gfapy.Line(gfa1str_noov)
g.add_line(gfa1line_noov)
self.assertEqual(gfa2str,str(gfa1line.to_gfa2()))
self.assertEqual(gfa1str+"\tID:Z:1",str(gfa1line.to_gfa1()))
# placeholder overlap
self.assertRaises(gfapy.ValueError,gfa1line_noov.to_gfa2)
# TODO check if the alignment is compatible with the segment length
def test_containment_conversion(self):
gfa1str = "C\tA\t+\tB\t-\t20\t100M"
gfa1str_noov = "C\tA\t+\tB\t+\t20\t*"
gfa2str = "E\t1\tA+\tB-\t20\t120\t0\t100$\t100M"
# not connected
self.assertRaises(gfapy.RuntimeError,gfapy.Line(gfa1str).to_gfa2)
# connected
g = gfapy.Gfa()
g.add_line("S\tA\t*\tLN:i:200")
g.add_line("S\tB\t*\tLN:i:100")
gfa1line = gfapy.Line(gfa1str)
g.add_line(gfa1line)
gfa1line_noov = gfapy.Line(gfa1str_noov)
g.add_line(gfa1line_noov)
self.assertEqual(gfa2str,str(gfa1line.to_gfa2()))
self.assertEqual(gfa1str+"\tID:Z:1",str(gfa1line.to_gfa1()))
# placeholder overlap
self.assertRaises(gfapy.ValueError,gfa1line_noov.to_gfa2)
# TODO check if the alignment is compatible with the segment length
def test_edge_conversion(self):
dovetail = "E\t*\tA+\tB-\t100\t200$\t100\t200$\t100M"
dovetail_gfa1 = "L\tA\t+\tB\t-\t100M"
containment = "E\t*\tA+\tB-\t20\t120\t0\t100$\t100M"
containment_gfa1 = "C\tA\t+\tB\t-\t20\t100M"
internal = "E\t*\tA+\tB-\t20\t110\t10\t100$\t90M"
self.assertEqual(dovetail_gfa1,str( gfapy.Line(dovetail).to_gfa1()))
self.assertEqual(containment_gfa1,str( gfapy.Line(containment).to_gfa1()))
self.assertRaises(gfapy.RuntimeError,gfapy.Line(internal).to_gfa1)
def test_L_to_E(self):
g = gfapy.Gfa(version="gfa1")
g.add_line("S\t1\t*\tLN:i:100")
g.add_line("S\t2\t*\tLN:i:100")
g.add_line("S\t3\t*\tLN:i:100")
g.add_line("S\t4\t*\tLN:i:100")
g.add_line("L\t1\t+\t2\t+\t10M")
g.add_line("L\t1\t-\t2\t-\t20M")
g.add_line("L\t3\t-\t4\t+\t30M")
g.add_line("L\t3\t+\t4\t-\t40M")
dovetails_gfa1 = g.dovetails
dovetails_gfa2 = {dovetails_gfa1[0].to_gfa2_s(),
dovetails_gfa1[1].to_gfa2_s(),
dovetails_gfa1[2].to_gfa2_s(),
dovetails_gfa1[3].to_gfa2_s()}
expected_dovetails_gfa2 = {
"E 5 1+ 2+ 90 100$ 0 10 10M",
"E 6 1- 2- 0 20 80 100$ 20M",
"E 7 3- 4+ 0 30 0 30 30M",
"E 8 3+ 4- 60 100$ 60 100$ 40M"}
try:
self.assertEqual(expected_dovetails_gfa2, dovetails_gfa2)
except:
# sometimes 7 and 8 are assigned with a different order
# despite using a fixed hash seed in the tests
expected_dovetails_gfa2 = {
"E 5 1+ 2+ 90 100$ 0 10 10M",
"E 6 1- 2- 0 20 80 100$ 20M",
"E 8 3- 4+ 0 30 0 30 30M",
"E 7 3+ 4- 60 100$ 60 100$ 40M"}
self.assertEqual(expected_dovetails_gfa2, dovetails_gfa2)
assert(isinstance(g.dovetails[0].to_gfa1(),gfapy.line.edge.Link))
assert(isinstance(g.dovetails[0].to_gfa2(),gfapy.line.edge.GFA2))
def test_E_to_L(self):
e1 = gfapy.Line("E\t*\t1+\t2+\t90\t100$\t0\t10\t10M")
l1 = "L\t1\t+\t2\t+\t10M"
self.assertEqual(l1, e1.to_gfa1_s())
e2 = gfapy.Line("E\t*\t1+\t2+\t0\t20\t80\t100$\t20M")
l2 = "L\t2\t+\t1\t+\t20M"
self.assertEqual(l2, e2.to_gfa1_s())
e3 = gfapy.Line("E\t*\t3-\t4+\t0\t30\t0\t30\t30M")
l3 = "L\t3\t-\t4\t+\t30M"
self.assertEqual(l3, e3.to_gfa1_s())
e4 = gfapy.Line("E\t*\t3+\t4-\t60\t100$\t60\t100$\t40M")
l4 = "L\t3\t+\t4\t-\t40M"
self.assertEqual(l4, e4.to_gfa1_s())
def test_path_conversion(self):
path_gfa1 = "P\t1\ta+,b-\t100M"
path_gfa2 = "O\t1\ta+ a_to_b+ b-"
# gfa1 => gfa2
l1 = "L\ta\t+\tb\t-\t100M\tID:Z:a_to_b"
g1 = gfapy.Gfa()
path_gfa1_line = gfapy.Line(path_gfa1)
g1.add_line(path_gfa1_line)
g1.add_line(l1)
g1.process_line_queue()
# not connected
self.assertRaises(gfapy.RuntimeError,
gfapy.Line(path_gfa1).to_gfa2)
# connected
self.assertEqual(path_gfa1,str(path_gfa1_line.to_gfa1()))
self.assertEqual(path_gfa2,str(path_gfa1_line.to_gfa2()))
# gfa2 => gfa1
e = "E\ta_to_b\ta+\tb-\t100\t200$\t100\t200$\t100M"
sA = "S\ta\t200\t*"
sB = "S\tb\t200\t*"
g2 = gfapy.Gfa()
path_gfa2_line = gfapy.Line(path_gfa2)
g2.add_line(path_gfa2_line)
g2.add_line(e)
g2.add_line(sA)
g2.add_line(sB)
# not connected
self.assertRaises(gfapy.RuntimeError,
gfapy.Line(path_gfa2).to_gfa1)
# connected
self.assertEqual(path_gfa1,str( path_gfa2_line.to_gfa1()))
self.assertEqual(path_gfa2,str( path_gfa2_line.to_gfa2()))
def test_gap_conversion(self):
s = "G\t*\tA-\tB+\t100\t*"
self.assertEqual(s, str(gfapy.Line(s).to_gfa2()))
self.assertRaises(gfapy.VersionError,gfapy.Line(s).to_gfa1)
def test_fragment_conversion(self):
s = "F\tA\tread1-\t0\t100\t0\t100\t*"
self.assertEqual(s,str( gfapy.Line(s).to_gfa2()))
self.assertRaises(gfapy.VersionError,gfapy.Line(s).to_gfa1)
def test_set_conversion(self):
s = "U\t1\tA B C"
self.assertEqual(s,str( gfapy.Line(s).to_gfa2()))
self.assertRaises(gfapy.VersionError,gfapy.Line(s).to_gfa1)
def test_custom_record_conversion(self):
s = "X\tx1\tA\tC"
self.assertEqual(s,str( gfapy.Line(s).to_gfa2()))
self.assertRaises(gfapy.VersionError,gfapy.Line(s).to_gfa1)
def test_unknown_record_conversion(self):
record = gfapy.line.Unknown([None, "A"])
self.assertEqual(record, record.to_gfa2())
self.assertRaises(gfapy.VersionError,record.to_gfa1)
def test_gfa_conversion(self):
gfa1_str ='''# comment
H\tVN:Z:1.0
S\tB\t*\tLN:i:200
S\tC\t*\tLN:i:100
S\tA\t*\tLN:i:200
L\tA\t+\tB\t-\t100M\tID:Z:a_to_b
C\tA\t+\tC\t-\t20\t100M\tID:Z:2
P\t1\tA+,B-\t100M'''
gfa2_str ='''# comment
H\tVN:Z:2.0
S\tB\t200\t*
S\tC\t100\t*
S\tA\t200\t*
E\ta_to_b\tA+\tB-\t100\t200$\t100\t200$\t100M
E\t2\tA+\tC-\t20\t120\t0\t100$\t100M
O\t1\tA+ a_to_b+ B-'''
self.assertEqual(gfa2_str, str(gfapy.Gfa(gfa1_str).to_gfa2()))
self.assertEqual(gfa1_str, str(gfapy.Gfa(gfa2_str).to_gfa1()))
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