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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
"""Tests for SeqIO GFA module."""
import unittest
from Bio import BiopythonWarning
from Bio import SeqIO
class TestRead(unittest.TestCase):
def test_read_GFA1(self):
"""Test parsing valid GFA 1.x files."""
records = list(SeqIO.parse("GFA/seq.gfa", "gfa1"))
self.assertEqual(len(records), 8)
self.assertEqual(records[6].id, "MTh13014")
self.assertEqual(
records[6].seq,
"TTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACC",
)
self.assertEqual(records[0].annotations["SN"], ("Z", "MT_human"))
self.assertEqual(records[0].annotations["SO"], ("i", "0"))
records = list(SeqIO.parse("GFA/seq_with_len.gfa", "gfa1"))
self.assertEqual(len(records), 9)
self.assertEqual(
records[8].seq,
"GAAAAATTGCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGTTAATACTT",
)
records = list(SeqIO.parse("GFA/fake_with_checksum.gfa", "gfa1"))
self.assertEqual(len(records), 1)
self.assertEqual(records[0].seq, "AAA")
records = list(SeqIO.parse("GFA/no_seq.gfa", "gfa1"))
self.assertEqual(len(records), 9)
self.assertEqual(len(records[0]), 528)
def test_read_GFA2(self):
"""Test parsing valid GFA 2.0 files."""
records = list(SeqIO.parse("GFA/fake_gfa2.gfa", "gfa2"))
self.assertEqual(len(records), 1)
self.assertEqual(records[0].seq, "AAA")
class TestCorrupt(unittest.TestCase):
def test_corrupt_gfa2(self):
"""Check a GFA 1.x file does not parse in GFA 2."""
with self.assertRaises(ValueError):
list(SeqIO.parse("GFA/seq.gfa", "gfa2"))
def test_corrupt_segment_fields(self):
"""Check a GFA file with invalid fields on a segment line."""
with self.assertRaises(ValueError):
list(SeqIO.parse("GFA/corrupt_segment_fields.gfa", "gfa1"))
def test_corrupt_len(self):
"""Check a GFA file with an incorrect length."""
with self.assertWarns(BiopythonWarning):
list(SeqIO.parse("GFA/corrupt_len.gfa", "gfa1"))
def test_corrupt_checksum(self):
"""Check a GFA file with an incorrect checksum."""
with self.assertWarns(BiopythonWarning):
list(SeqIO.parse("GFA/corrupt_checksum.gfa", "gfa1"))
def test_corrupt_tag_name(self):
"""Check a GFA file with an invalid tag name."""
with self.assertWarns(BiopythonWarning):
list(SeqIO.parse("GFA/corrupt_tag_name.gfa", "gfa1"))
def test_corrupt_tag_type(self):
"""Check a GFA file with an incorrect tag type."""
with self.assertWarns(BiopythonWarning):
list(SeqIO.parse("GFA/corrupt_tag_type.gfa", "gfa1"))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
