Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_F_GameXmlMaker.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
3 import glob
4 from commons.core.utils.FileUtils import FileUtils
5 from commons.core.sql.DbFactory import DbFactory
6 from commons.tools.GameXmlMaker import GameXmlMaker
7
8
9 class Test_F_GameXmlMaker(unittest.TestCase):
10
11 def setUp(self):
12 pass
13
14
15 def tearDown(self):
16 FileUtils.removeFilesByPattern("*gamexml")
17
18
19 def test_run_as_script_step1(self):
20 fastaFileName = "input.fa"
21 self._writeFastaFile(fastaFileName)
22
23 cmd = "GameXmlMaker.py -f %s " % fastaFileName
24 os.system(cmd)
25
26 lObsGameXmlNew = glob.glob("*.gamexml")
27 self._writeStep1ExpectedXmls()
28 self.assertTrue(len(lObsGameXmlNew) > 0)
29 for obsGameXmlNew in lObsGameXmlNew:
30 expGameXmlNew = "exp_%s" % obsGameXmlNew
31 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
32
33 os.remove(fastaFileName)
34
35 def test_run_as_script_step2(self):
36 self._tableFileName = "annotation_tables.txt"
37
38 self._writeStep2InputTableFile()
39 self._writeStep2InputXmls()
40 self._writeStep2InputPathFile()
41 self._writeStep2InputSetFile()
42 self._writeStep2InputMapFile()
43 self._createStep2Tables()
44
45 lObsGameXmlNew = glob.glob("*.gamexml")
46
47 cmd = "GameXmlMaker.py -t %s " % self._tableFileName
48 os.system(cmd)
49
50 self._writeStep2ExpXmls()
51
52 self.assertTrue(len(lObsGameXmlNew) > 0)
53 for obsGameXmlNew in lObsGameXmlNew:
54 expGameXmlNew = "exp_%s" % obsGameXmlNew
55 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
56
57 os.remove("Test_F_GameXmlMaker_path.path")
58 os.remove("Test_F_GameXmlMaker_set.set")
59 os.remove("Test_F_GameXmlMaker_chk_map.map")
60
61 os.remove(self._tableFileName)
62 os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
63
64 def test_run_step2(self):
65 self._tableFileName = "annotation_tables.txt"
66
67 self._writeStep2InputTableFile()
68 self._writeStep2InputXmls()
69 self._writeStep2InputPathFile()
70 self._writeStep2InputSetFile()
71 self._writeStep2InputMapFile()
72 self._createStep2Tables()
73
74 lObsGameXmlNew = glob.glob("*.gamexml")
75
76 iGameXmlMaker = GameXmlMaker(tablesFileName = self._tableFileName)
77 iGameXmlMaker.run()
78 self._writeStep2ExpXmls()
79 self.assertTrue(len(lObsGameXmlNew) > 0)
80 for obsGameXmlNew in lObsGameXmlNew:
81 expGameXmlNew = "exp_%s" % obsGameXmlNew
82 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
83
84 os.remove("Test_F_GameXmlMaker_path.path")
85 os.remove("Test_F_GameXmlMaker_set.set")
86 os.remove("Test_F_GameXmlMaker_chk_map.map")
87
88 os.remove(self._tableFileName)
89 os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
90
91 def _writeFastaFile(self, inFileName):
92 f = open(inFileName,'w')
93 f.write('>seq1\n')
94 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
95 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
96 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA\n')
97 f.write('>seq2\n')
98 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
99 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
100 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
101 f.write('>seq3\n')
102 f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n')
103 f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n')
104 f.write('>seq4\n')
105 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
106 f.write('CAGGAATCATGAAGGGTACGACTGTTCG\n')
107 f.close()
108
109 def _writeStep1ExpectedXmls(self):
110 f = open("exp_seq1.gamexml", 'w')
111 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
112 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
113 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
114 f.close()
115 f = open("exp_seq2.gamexml", 'w')
116 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
117 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
118 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
119 f.close()
120 f = open("exp_seq3.gamexml", 'w')
121 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
122 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
123 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
124 f.close()
125 f = open("exp_seq4.gamexml", 'w')
126 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
127 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
128 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
129 f.close()
130
131 def _createStep2Tables(self):
132 iDb = DbFactory.createInstance()
133 iDb.createTable("Test_F_GameXmlMaker_set", "set", "Test_F_GameXmlMaker_set.set", True)
134 iDb.createTable("Test_F_GameXmlMaker_chk_map", "map", "Test_F_GameXmlMaker_chk_map.map", True)
135 iDb.createTable("Test_F_GameXmlMaker_path", "path", "Test_F_GameXmlMaker_path.path", True)
136 iDb.close()
137
138 def _writeStep2InputXmls(self):
139 f = open("seq1.gamexml", 'w')
140 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
141 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
142 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
143 f.close()
144 f = open("seq2.gamexml", 'w')
145 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
146 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
147 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
148 f.close()
149 f = open("seq3.gamexml", 'w')
150 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
151 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
152 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
153 f.close()
154 f = open("seq4.gamexml", 'w')
155 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
156 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
157 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
158 f.close()
159
160 def _writeStep2InputPathFile(self):
161 f = open("Test_F_GameXmlMaker_path.path", 'w')
162 f.write("1\tseq1\t1\t10\tTE1\t1\t10\t0\t550\t80.7\n")
163 f.write("2\tseq1\t15\t50\tTE1\t12\t47\t0\t770\t90.8\n")
164 f.write("2\tseq1\t55\t70\tTE1\t50\t65\t0\t5410\t97.7\n")
165 f.write("3\tseq1\t75\t80\tTE2\t10\t15\t0\t8710\t60.0\n")
166 f.write("4\tseq2\t1\t10\tTE2\t20\t30\t0\t5410\t75.7\n")
167 f.write("5\tseq3\t1\t120\tTE2\t450\t550\t0\t5410\t75.7\n")
168 f.close()
169
170 def _writeStep2InputSetFile(self):
171 f = open("Test_F_GameXmlMaker_set.set", 'w')
172 f.write("1\tseq1\tseq1\t1\t10\n")
173 f.write("2\tseq1\tseq1\t15\t50\n")
174 f.write("3\tseq1\tseq1\t75\t80\n")
175 f.write("4\tseq2\tseq2\t1\t10\n")
176 f.write("5\tseq3\tseq3\t1\t120\n")
177 f.close()
178
179 def _writeStep2InputMapFile(self):
180 f = open("Test_F_GameXmlMaker_chk_map.map", 'w')
181 f.write("chunk1\tseq1\t1\t200000\n")
182 f.write("chunk2\tseq1\t190001\t390000\n")
183 f.write("chunk3\tseq3\t380001\t580000\n")
184 f.write("chunk4\tseq4\t570001\t770000\n")
185 f.write("chunk5\tseq5\t760001\t960000\n")
186 f.write("chunk6\tseq6\t950001\t1150000\n")
187 f.write("chunk7\tseq7\t1140001\t1281640\n")
188 f.close()
189
190 def _writeStep2ExpXmls(self):
191 f = open("exp_seq1.gamexml", 'w')
192 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
193 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
194 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position>')
195 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="1"><name>TE1::1</name>')
196 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship><seq_relationship seq="TE1::1" type="subject"><span>')
197 f.write('<start>1</start><end>10</end></span></seq_relationship><score>80.7</score></result_span></result_set><result_set id="2"><name>TE1::2</name><result_span>')
198 f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship><seq_relationship seq="TE1::2" type="subject"><span><start>12</start>')
199 f.write('<end>47</end></span></seq_relationship><score>90.8</score></result_span><result_span><seq_relationship seq="seq1" type="query"><span><start>55</start><end>70</end></span></seq_relationship>')
200 f.write('<seq_relationship seq="TE1::2" type="subject"><span><start>50</start><end>65</end></span></seq_relationship><score>97.7</score></result_span></result_set><result_set id="3"><name>TE2::3</name>')
201 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship><seq_relationship seq="TE2::3" type="subject"><span><start>10</start><end>15</end></span></seq_relationship>')
202 f.write('<score>60.0</score></result_span></result_set></computational_analysis>')
203 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database>')
204 f.write('<result_set id="1"><name>seq1::1</name><result_span>')
205 f.write('<seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
206 f.write('<seq_relationship seq="seq1::1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
207 f.write('<score>0</score></result_span></result_set>')
208 f.write('<result_set id="2"><name>seq1::2</name><result_span>')
209 f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship>')
210 f.write('<seq_relationship seq="seq1::2" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
211 f.write('<score>0</score></result_span></result_set>')
212 f.write('<result_set id="3"><name>seq1::3</name><result_span>')
213 f.write('<seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship>')
214 f.write('<seq_relationship seq="seq1::3" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
215 f.write('<score>0</score></result_span></result_set></computational_analysis>')
216 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
217 f.write('<result_set id="-1"><name>chunk1::-1</name>')
218 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>200000</end></span></seq_relationship>')
219 f.write('<seq_relationship seq="chunk1::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
220 f.write('<score>0</score></result_span></result_set>')
221 f.write('<result_set id="-1"><name>chunk2::-1</name>')
222 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>190001</start><end>390000</end></span></seq_relationship>')
223 f.write('<seq_relationship seq="chunk2::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship><score>0</score></result_span></result_set></computational_analysis></game>')
224 f.close()
225
226 f = open("exp_seq2.gamexml", 'w')
227 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
228 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
229 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position>')
230 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="4"><name>TE2::4</name>')
231 f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span>')
232 f.write('</seq_relationship><seq_relationship seq="TE2::4" type="subject"><span><start>20</start><end>30</end></span></seq_relationship>')
233 f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
234 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="4"><name>seq2::4</name>')
235 f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
236 f.write('<seq_relationship seq="seq2::4" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
237 f.write('<score>0</score></result_span></result_set></computational_analysis>')
238 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database></computational_analysis></game>')
239 f.close()
240
241 f = open("exp_seq3.gamexml", 'w')
242 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
243 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
244 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position>')
245 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="5"><name>TE2::5</name>')
246 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span>')
247 f.write('</seq_relationship><seq_relationship seq="TE2::5" type="subject"><span><start>450</start><end>550</end></span></seq_relationship>')
248 f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
249 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="5"><name>seq3::5</name>')
250 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span></seq_relationship>')
251 f.write('<seq_relationship seq="seq3::5" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
252 f.write('<score>0</score></result_span></result_set></computational_analysis>')
253 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
254 f.write('<result_set id="-1"><name>chunk3::-1</name>')
255 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>380001</start><end>580000</end></span></seq_relationship>')
256 f.write('<seq_relationship seq="chunk3::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
257 f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
258 f.close()
259
260 f = open("exp_seq4.gamexml", 'w')
261 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
262 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
263 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position>')
264 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database></computational_analysis>')
265 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database></computational_analysis>')
266 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
267 f.write('<result_set id="-1"><name>chunk4::-1</name>')
268 f.write('<result_span><seq_relationship seq="seq4" type="query"><span><start>570001</start><end>770000</end></span></seq_relationship>')
269 f.write('<seq_relationship seq="chunk4::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
270 f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
271 f.close()
272
273 def _writeStep2InputTableFile(self):
274 f = open(self._tableFileName,'w')
275 f.write("Test_F_GameXmlMaker_path\tpath\tTest_F_GameXmlMaker_path\n")
276 f.write("Test_F_GameXmlMaker_set\tset\tTest_F_GameXmlMaker_set\n")
277 f.write("Test_F_GameXmlMaker_chk_map\tmap\tTest_F_GameXmlMaker_chk_map")
278 f.close()
279
280 if __name__ == "__main__":
281 unittest.main()