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
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
# Copyright 2009 by James Casbon. All rights reserved.
# Revisions copyright 2009-2010 by Michiel de Hoon. 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.
"""Tests for parsing Compass output.
"""
import os
import unittest
from Bio import Compass
class CompassTest(unittest.TestCase):
def setUp(self):
file_dir = os.path.join("Compass")
self.test_files = [
os.path.join(file_dir, "comtest1"),
os.path.join(file_dir, "comtest2"),
os.path.join(file_dir, "comtest3"),
]
def testCompassScanAndConsume(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertEqual("60456.blo.gz.aln", com_record.hit)
self.assertEqual(0.5, com_record.gap_threshold)
self.assertEqual(388, com_record.query_length)
self.assertEqual(386, com_record.query_filtered_length)
self.assertEqual(388, com_record.hit_length)
self.assertEqual(386, com_record.hit_filtered_length)
self.assertEqual(399, com_record.query_nseqs)
self.assertEqual(12.972, com_record.query_neffseqs)
self.assertEqual(399, com_record.hit_nseqs)
self.assertEqual(12.972, com_record.hit_neffseqs)
self.assertEqual(2759, com_record.sw_score)
self.assertEqual(float("0.00e+00"), com_record.evalue)
def testCompassParser(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassIteratorEasy(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertRaises(StopIteration, next, records)
handle.close()
def testCompassIteratorHard(self):
handle = open(self.test_files[1])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEqual(float('5.75e+02'), com_record.evalue)
handle.close()
def testAlignmentParsingOne(self):
handle = open(self.test_files[1])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual(178, com_record.query_start)
self.assertEqual("KKDLEEIAD", com_record.query_aln)
self.assertEqual(9, com_record.hit_start)
self.assertEqual("QAAVQAVTA", com_record.hit_aln)
self.assertEqual("++ ++++++", com_record.positives)
com_record = next(records)
com_record = next(records)
self.assertEqual(371, com_record.query_start)
self.assertEqual("LEEAMDRMER~~~V", com_record.query_aln)
self.assertEqual(76, com_record.hit_start)
self.assertEqual("LQNFIDQLDNpddL", com_record.hit_aln)
self.assertEqual("+ ++++ + + +", com_record.positives)
handle.close()
def testAlignmentParsingTwo(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual(2, com_record.query_start)
self.assertEqual(2, com_record.hit_start)
self.assertEqual("LKERKL", com_record.hit_aln[-6:])
handle.close()
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
