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
79
80
81
|
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit test for Cla"""
import unittest
from Bio.SCOP import Cla
class ClaTests(unittest.TestCase):
def setUp(self):
self.filename = './SCOP/dir.cla.scop.txt_test'
def testParse(self):
"""Test if all records in a CLA file are being read"""
f=open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count +=1
self.assertEqual(count, 14)
finally:
f.close()
def testStr(self):
"""Test if we can convert each record to a string correctly"""
f = open(self.filename)
try:
for line in f:
record = Cla.Record(line)
#End of line is platform dependent. Strip it off
self.assertEqual(str(record).rstrip(), line.rstrip())
finally:
f.close()
def testError(self):
"""Test if a corrupt record raises the appropriate exception"""
corruptRec = "49268\tsp\tb.1.2.1\t-\n"
self.assertRaises(ValueError, Cla.Record, corruptRec)
def testRecord(self):
"""Test one record in detail"""
recLine = 'd1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953'
record = Cla.Record(recLine)
self.assertEqual(record.sid, 'd1dan.1')
self.assertEqual(record.residues.pdbid, '1dan')
self.assertEqual(record.residues.fragments, (('T','',''),('U','91','106')))
self.assertEqual(record.sccs, 'b.1.2.1')
self.assertEqual(record.sunid, 21953)
self.assertEqual(record.hierarchy, [['cl',48724],
['cf',48725],
['sf',49265],
['fa',49266],
['dm',49267],
['sp',49268],
['px',21953]])
def testIndex(self):
"""Test CLA file indexing"""
index = Cla.Index(self.filename)
self.assertEqual(len(index), 14)
self.assertTrue(index.has_key('d4hbia_'))
rec = index['d1hbia_']
self.assertEqual(rec.sunid, 14996)
if __name__=='__main__':
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
|
