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
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
|
#!/usr/bin/env python
"""Unit tests for unigene-specific classes
"""
from cogent.parse.unigene import _read_sts, _read_expression, UniGeneSeqRecord,\
UniGeneProtSimRecord, _read_seq, LinesToUniGene
from cogent.parse.record_finder import GbFinder
from cogent.util.unit_test import TestCase, main
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
class unigeneTests(TestCase):
"""Tests toplevel functions."""
def test_read_sts(self):
"""_read_sts should perform correct conversions"""
self.assertEqual(_read_sts('ACC=RH128467 UNISTS=211775\n'), \
{'ACC':'RH128467', 'UNISTS':'211775'})
def test_read_expression(self):
"""_read_expression should perform correct conversions"""
self.assertEqual(_read_expression(\
'embryo ; whole body ; mammary gland ; brain\n'),
['embryo', 'whole body', 'mammary gland', 'brain'])
def test_read_seq(self):
"""_read_seq should perform correct conversions"""
#reset the found fields, since we can't guarantee order of test
#execution and it's persistent class data
UniGeneSeqRecord.found_fields = {}
self.assertEqual(_read_seq('ACC=BC025044.1\n'), \
UniGeneSeqRecord({'ACC':'BC025044.1'}))
self.assertEqual(_read_seq(\
"ACC=AI842963.1; NID=g5477176; CLONE=UI-M-AO1-aem-f-10-0-UI; END=3'; LID=1944; SEQTYPE=EST; TRACE=158501677\n"), \
UniGeneSeqRecord({ 'ACC':'AI842963.1','NID':'g5477176',
'CLONE':'UI-M-AO1-aem-f-10-0-UI', 'END':"3'",
'LID':'1944', 'SEQTYPE':'EST',
'TRACE':'158501677'}) )
def test_LinesToUniGene(self):
"""LinesToUniGene should give expected results on sample data"""
fake_file = \
"""ID Mm.1
TITLE S100 calcium binder
GENE S100a10
CYTOBAND 3 41.7 cM
LOCUSLINK 20194
EXPRESS embryo ; whole body ; mammary gland ; brain
CHROMOSOME 3
STS ACC=RH128467 UNISTS=211775
STS ACC=M16465 UNISTS= 178878
PROTSIM ORG=Homo sapiens; PROTGI=107251; PROTID=pir:JC1139; PCT=91; ALN=97
PROTSIM ORG=Mus musculus; PROTGI=116487; PROTID=sp:P08207; PCT=100; ALN=97
PROTSIM ORG=Rattus norvegicus; PROTGI=116489; PROTID=sp:P05943; PCT=94; ALN=94
SCOUNT 5
SEQUENCE ACC=BC025044.1; NID=g19263549; PID=g19263550; SEQTYPE=mRNA
SEQUENCE ACC=AA471893.1; NID=g2199884; CLONE=IMAGE:872193; END=5'; LID=539; SEQTYPE=EST
SEQUENCE ACC=AI842963.1; NID=g5477176; CLONE=UI-M-AO1-aem-f-10-0-UI; END=3'; LID=1944; SEQTYPE=EST; TRACE=158501677
SEQUENCE ACC=CB595147.1; NID=g29513003; CLONE=IMAGE:30300703; END=5'; LID=12885; MGC=6677832; SEQTYPE=EST
SEQUENCE ACC=BY144053.1; NID=g26280109; CLONE=L930184D22; END=5'; LID=12267; SEQTYPE=EST
//
ID Mm.5
TITLE homeo box A10
GENE Hoxa10
CYTOBAND 6 26.33 cM
LOCUSLINK 15395
EXPRESS kidney ; colon ; mammary gland
CHROMOSOME 6
PROTSIM ORG=Caenorhabditis elegans; PROTGI=7510074; PROTID=pir:T31611; PCT=30; ALN=326
SCOUNT 1
SEQUENCE ACC=AW990320.1; NID=g8185938; CLONE=IMAGE:1513482; END=5'; LID=1043; SEQTYPE=EST; TRACE=94472873
//
"""
records = list(GbFinder(fake_file.split('\n')))
self.assertEqual(len(records), 2)
first, second = map(LinesToUniGene, records)
self.assertEqual(first.ID, 'Mm.1')
self.assertEqual(first.TITLE, 'S100 calcium binder')
self.assertEqual(first.GENE, 'S100a10')
self.assertEqual(first.CYTOBAND, '3 41.7 cM')
self.assertEqual(first.CHROMOSOME, '3')
self.assertEqual(first.LOCUSLINK, 20194)
self.assertEqual(first.EXPRESS, ['embryo', 'whole body', \
'mammary gland', 'brain'])
self.assertEqual(first.STS, [{'ACC':'RH128467','UNISTS':'211775'},
{'ACC':'M16465', 'UNISTS':'178878'}])
exp_prot_sim = map(UniGeneProtSimRecord, [
{'ORG':'Homo sapiens','PROTGI':'107251',
'PROTID':'pir:JC1139','PCT':'91','ALN':'97'},
{'ORG':'Mus musculus','PROTGI':'116487',
'PROTID':'sp:P08207','PCT':'100','ALN':'97'},
{'ORG':'Rattus norvegicus','PROTGI':'116489',
'PROTID':'sp:P05943','PCT':'94','ALN':'94'},])
for obs, exp in zip(first.PROTSIM, exp_prot_sim):
self.assertEqual(obs, exp)
self.assertEqual(first.SCOUNT, 5)
exp_seqs = map(UniGeneSeqRecord, [
{'ACC':'BC025044.1', 'NID':'g19263549','PID':'g19263550',
'SEQTYPE':'mRNA'},
{'ACC':'AA471893.1','NID':'g2199884','END':"5'",
'CLONE':'IMAGE:872193','LID':'539', 'SEQTYPE':'EST'},
{'ACC':'AI842963.1','NID':'g5477176',
'CLONE':'UI-M-AO1-aem-f-10-0-UI','END':"3'",'LID':'1944',
'SEQTYPE':'EST','TRACE':'158501677'},
{'ACC':'CB595147.1','NID':'g29513003',
'CLONE':'IMAGE:30300703','END':"5'",'LID':'12885',
'MGC':'6677832', 'SEQTYPE':'EST'},
{'ACC':'BY144053.1','NID':'g26280109',
'CLONE':'L930184D22','END':"5'",'LID':'12267',
'SEQTYPE':'EST'}])
for obs, exp in zip(first.SEQUENCE, exp_seqs):
self.assertEqual(obs, exp)
self.assertEqual(second.ID, 'Mm.5')
self.assertEqual(second.TITLE, 'homeo box A10')
self.assertEqual(second.GENE, 'Hoxa10')
self.assertEqual(second.CYTOBAND, '6 26.33 cM')
self.assertEqual(second.LOCUSLINK, 15395)
self.assertEqual(second.EXPRESS,['kidney','colon','mammary gland'])
self.assertEqual(second.CHROMOSOME, '6')
self.assertEqual(second.PROTSIM, map(UniGeneProtSimRecord, [
{'ORG':'Caenorhabditis elegans', 'PROTGI':'7510074',
'PROTID':'pir:T31611','PCT':'30',
'ALN':'326'}]))
self.assertEqual(second.SCOUNT, 1)
self.assertEqual(second.STS, [])
self.assertEqual(second.SEQUENCE, map(UniGeneSeqRecord, [
{'ACC':'AW990320.1','NID':'g8185938',
'CLONE':'IMAGE:1513482','END':"5'",'LID':'1043',
'SEQTYPE':'EST','TRACE':'94472873'}]))
#test that the synonym mapping works OK
self.assertEqual(second.SequenceIds[0].NucleotideId, 'g8185938')
if __name__ == '__main__':
main()
|
