comparison SMART/Java/Python/mySql/test/Test_MySqlTranscriptTable.py @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
2 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
3 from SMART.Java.Python.structure.Transcript import Transcript
4 from SMART.Java.Python.structure.Interval import Interval
5 from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection
6 from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable
7 import unittest
8
9
10 class Test_MySqlTranscriptTable(unittest.TestCase):
11
12 def test_getRange(self):
13 transcript = Transcript()
14 transcript.setName("test1.1")
15 transcript.setChromosome("arm_X")
16 transcript.setStart(1000)
17 transcript.setEnd(4000)
18 transcript.setSize(2000)
19 transcript.setDirection("+")
20
21 exon1 = Interval()
22 exon1.setName("test1.1")
23 exon1.setChromosome("arm_X")
24 exon1.setStart(1000)
25 exon1.setEnd(2000)
26 exon1.setSize(1000)
27
28 exon2 = Interval()
29 exon2.setName("test1.1")
30 exon2.setChromosome("arm_X")
31 exon2.setStart(3000)
32 exon2.setEnd(4000)
33 exon2.setSize(1000)
34
35 transcript.addExon(exon1)
36 transcript.addExon(exon2)
37
38 connection = MySqlConnection()
39 writer = MySqlTranscriptWriter(connection, "testMySqlTranscriptTableGetRange")
40 writer.addTranscript(transcript)
41 writer.write()
42
43 transcriptContainer = TranscriptContainer("testMySqlTranscriptTableGetRange", "sql")
44 transcriptContainer.mySqlConnection = connection
45 self.assertEqual(transcriptContainer.getNbTranscripts(), 1)
46 for transcript in transcriptContainer.getIterator():
47 self.assertEqual(transcript.getName(), "test1.1")
48 self.assertEqual(transcript.getChromosome(), "arm_X")
49 self.assertEqual(transcript.getStart(), 1000)
50 self.assertEqual(transcript.getEnd(), 4000)
51 self.assertEqual(transcript.getSize(), 2002)
52 self.assertEqual(transcript.getNbExons(), 2)
53 exons = transcript.getExons()
54 self.assertEqual(exons[0].getStart(), 1000)
55 self.assertEqual(exons[0].getEnd(), 2000)
56 self.assertEqual(exons[1].getStart(), 3000)
57 self.assertEqual(exons[1].getEnd(), 4000)
58
59
60 def test_setDefaultTagValue(self):
61 transcript1 = Transcript()
62 transcript1.setName("test1.1")
63 transcript1.setChromosome("arm_X")
64 transcript1.setStart(1000)
65 transcript1.setEnd(2000)
66 transcript1.setDirection("+")
67
68 exon1 = Interval()
69 exon1.setName("test1.1")
70 exon1.setChromosome("arm_X")
71 exon1.setStart(1000)
72 exon1.setEnd(2000)
73
74 transcript1.addExon(exon1)
75
76 transcript2 = Transcript()
77 transcript2.setName("test2.1")
78 transcript2.setChromosome("arm_X")
79 transcript2.setStart(1000)
80 transcript2.setEnd(2000)
81 transcript2.setDirection("+")
82 transcript2.setTagValue("nbOccurrences", "2")
83
84 exon2 = Interval()
85 exon2.setName("test2.1")
86 exon2.setChromosome("arm_X")
87 exon2.setStart(1000)
88 exon2.setEnd(2000)
89
90 transcript2.addExon(exon2)
91
92 transcript3 = Transcript()
93 transcript3.setName("test3.1")
94 transcript3.setChromosome("arm_X")
95 transcript3.setStart(1000)
96 transcript3.setEnd(2000)
97 transcript3.setDirection("+")
98 transcript3.setTagValue("occurrences", "2")
99
100 exon3 = Interval()
101 exon3.setName("test3.1")
102 exon3.setChromosome("arm_X")
103 exon3.setStart(1000)
104 exon3.setEnd(2000)
105
106 transcript3.addExon(exon3)
107
108 connection = MySqlConnection()
109 table = MySqlTranscriptTable(connection, "testMySqlTranscriptTableSetDefaultTagValue")
110 table.createTranscriptTable()
111 table.addTranscript(transcript1)
112 table.addTranscript(transcript2)
113 table.addTranscript(transcript3)
114 table.setDefaultTagValue("occurrence", "1")
115
116 cpt = 0
117 for transcript in table.getIterator():
118 cpt += 1
119 self.assert_(cpt != 4)
120 if cpt == 1:
121 self.assertEqual(transcript.name, "test1.1")
122 self.assertEqual(transcript.getChromosome(), "arm_X")
123 self.assertEqual(transcript.getStart(), 1000)
124 self.assertEqual(transcript.getEnd(), 2000)
125 self.assertEqual(transcript.getSize(), 1001)
126 self.assertEqual(transcript.getNbExons(), 1)
127 exons = transcript.getExons()
128 self.assertEqual(exons[0].getStart(), 1000)
129 self.assertEqual(exons[0].getEnd(), 2000)
130 self.assertEqual(transcript.getTagValue("occurrence"), 1)
131 elif cpt == 2:
132 self.assertEqual(transcript.name, "test2.1")
133 self.assertEqual(transcript.getChromosome(), "arm_X")
134 self.assertEqual(transcript.getStart(), 1000)
135 self.assertEqual(transcript.getEnd(), 2000)
136 self.assertEqual(transcript.getSize(), 1001)
137 self.assertEqual(transcript.getNbExons(), 1)
138 exons = transcript.getExons()
139 self.assertEqual(exons[0].getStart(), 1000)
140 self.assertEqual(exons[0].getEnd(), 2000)
141 self.assertEqual(transcript.getTagValue("nbOccurrences"), 2)
142 self.assertEqual(transcript.getTagValue("occurrence"), 1)
143 elif cpt == 2:
144 self.assertEqual(transcript.name, "test3.1")
145 self.assertEqual(transcript.getChromosome(), "arm_X")
146 self.assertEqual(transcript.getStart(), 1000)
147 self.assertEqual(transcript.getEnd(), 2000)
148 self.assertEqual(transcript.getSize(), 1001)
149 self.assertEqual(transcript.getNbExons(), 1)
150 exons = transcript.getExons()
151 self.assertEqual(exons[0].getStart(), 1000)
152 self.assertEqual(exons[0].getEnd(), 2000)
153 self.assertEqual(transcript.getTagValue("occurrence"), 2)
154
155 table.remove()
156
157 if __name__ == '__main__':
158 unittest.main()