Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_compareOverlapping.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os, os.path
3 from SMART.Java.Python.misc import Utils
4
5 SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
6
7 class Test_F_compareOverlapping(unittest.TestCase):
8
9 def setUp(self):
10 self._inputFileQuery = "inputFileTest1.bed"
11 self._inputFileReference = "inputFileTest2.bed"
12 self._inputFileName3 = "inputFileTest3.bed"
13 self._expOutputFileName = "expOutput.gff3"
14 self._outputFileName = "output.gff3"
15 self._writeInputFileQuery()
16 self._writeInputFileRefence()
17 self._writeInputFile3()
18
19 def tearDown(self):
20 for fileName in (self._inputFileQuery, self._inputFileReference, self._inputFileName3, self._expOutputFileName, self._outputFileName):
21 if os.path.exists(fileName):
22 os.remove(fileName)
23
24 def test_runAsScript_withoutOption(self):
25 self._writeOutputFile_withoutOption(self._expOutputFileName)
26 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
27 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
28
29 def test_runAsScript_optionNFirstNucleotide(self):
30 self._writeOutputFile_NFirstNucleotide(self._expOutputFileName)
31 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -S 200 -s 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
32 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
33
34 def test_runAsScript_optionNLastNucleotide(self):
35 self._writeOutputFile_NLastNucleotide(self._expOutputFileName)
36 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -U 200 -u 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
37 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
38
39 def test_runAsScript_option_5PrimeExtension(self):
40 self._writeOutputFile_5PrimeExtension(self._expOutputFileName)
41 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -E 110 -e 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
42 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
43
44 def test_runAsScript_option_3PrimeExtension(self):
45 self._writeOutputFile_3PrimeExtension(self._expOutputFileName)
46 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -N 110 -n 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
47 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
48
49 def test_runAsScript_colinear(self):
50 self._writeOutputFile_colinear(self._expOutputFileName)
51 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -c -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
52 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
53
54 def test_runAsScript_antisense(self):
55 self._writeOutputFile_antisense(self._expOutputFileName)
56 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -a -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
57 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
58
59 def test_runAsScript_minOverlap(self):
60 self._writeOutputFile_minOverlap(self._expOutputFileName)
61 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -m 51 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
62 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
63
64 def test_runAsScript_pcOverlap(self):
65 self._writeOutputFile_pcOverlap(self._expOutputFileName)
66 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -p 60 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
67 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
68
69 def test_runAsScript_included(self):
70 self._writeOutputFile_included(self._expOutputFileName)
71 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -k -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
72 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
73
74 def test_runAsScript_including(self):
75 self._writeOutputFile_including(self._expOutputFileName)
76 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -K -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
77 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
78
79 def test_runAsScript_includeNotOverlap(self):
80 self._writeOutputFile_includeNotOverlap(self._expOutputFileName)
81 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -O -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
82 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
83
84 def test_runAsScript_exclude(self):
85 self._writeOutputFile_exclude(self._expOutputFileName)
86 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -x -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
87 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
88
89 def _writeInputFileQuery(self):
90 f = open(self._inputFileQuery, "w")
91 f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
92 f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
93 f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
94 f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t1\t3100,\t0,\n")
95 f.close()
96
97 def _writeInputFileRefence(self):
98 f = open(self._inputFileReference, "w")
99 f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
100 f.close()
101
102 def _writeInputFile3(self):
103 f = open(self._inputFileName3, "w")
104 f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
105 f.write("arm_X\t250\t350\ttest2.2\t1000\t+\t250\t350\t0\t1\t100,\t0,\n")
106 f.write("arm_X\t150\t250\ttest2.3\t1000\t+\t150\t250\t0\t1\t100,\t0,\n")
107 f.close()
108
109 def _writeOutputFile_withoutOption(self, outputFileName):
110 f = open(outputFileName, "w")
111 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
112 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
113 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
114 f.close()
115
116 def _writeOutputFile_NFirstNucleotide(self, outputFileName):
117 f = open(outputFileName, "w")
118 f.write("arm_X\tS-MART\ttranscript\t1000\t1199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
119 f.close()
120
121 def _writeOutputFile_NLastNucleotide(self, outputFileName):
122 f = open(outputFileName, "w")
123 f.write("arm_X\tS-MART\ttranscript\t1800\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
124 f.close()
125
126 def _writeOutputFile_5PrimeExtension(self, outputFileName):
127 f = open(outputFileName, "w")
128 f.write("arm_X\tS-MART\ttranscript\t0\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
129 f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
130 f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
131 f.close()
132
133 def _writeOutputFile_3PrimeExtension(self, outputFileName):
134 f = open(outputFileName, "w")
135 f.write("arm_X\tS-MART\ttranscript\t100\t3309\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
136 f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
137 f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
138 f.close()
139
140 def _writeOutputFile_colinear(self, outputFileName):
141 f = open(outputFileName, "w")
142 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
143 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
144 f.close()
145
146 def _writeOutputFile_antisense(self, outputFileName):
147 f = open(outputFileName, "w")
148 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
149 f.close()
150
151 def _writeOutputFile_minOverlap(self, outputFileName):
152 f = open(outputFileName, "w")
153 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.3,test2.2,test2.1;nbOverlaps=3.000000;ID=test1.4;Name=test1.4\n")
154 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
155 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
156 f.close()
157
158 def _writeOutputFile_pcOverlap(self, outputFileName):
159 f = open(outputFileName, "w")
160 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
161 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
162 f.close()
163
164 def _writeOutputFile_includeNotOverlap(self, outputFileName):
165 f = open(outputFileName, "w")
166 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
167 f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tnbOverlaps=0;ID=test1.3;Name=test1.3\n")
168 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
169 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
170 f.close()
171
172 def _writeOutputFile_exclude(self, outputFileName):
173 f = open(outputFileName, "w")
174 f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tID=test1.3;Name=test1.3\n")
175 f.close()
176
177 def _writeOutputFile_included(self, outputFileName):
178 f = open(outputFileName, "w")
179 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
180 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
181 f.close()
182
183 def _writeOutputFile_including(self, outputFileName):
184 f = open(outputFileName, "w")
185 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
186 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
187 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
188 f.close()
189
190 def _writeInputFileQuery_withExon(self):
191 f = open(self._inputFileQuery, "w")
192 f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
193 f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
194 f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
195 f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t2\t100,100,\t0,3000,\n")
196 f.close()
197
198 if __name__ == "__main__":
199 unittest.main()