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comparison commons/tools/tests/Test_F_PostAnalyzeTELib.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 from commons.core.utils.FileUtils import FileUtils
2 from commons.core.sql.DbFactory import DbFactory
3 from commons.tools.PostAnalyzeTELib import PostAnalyzeTELib
4 import subprocess
5 import unittest
6 import os
7
8
9 class Test_F_PostAnalyzeTELib(unittest.TestCase):
10
11 def setUp(self):
12 self._expStatFileName = "expStats.tab"
13 self._obsStatFileName = ""
14 self._genomeSize = 1281640
15 self._pathTableName = "dummyDmelChr4_chr_allTEs_nr_noSSR_join_path"
16 self._seqTableName = "dummyDmelChr4_denovoLibTEs_seq"
17
18 def tearDown(self):
19 try:
20 os.remove(self._expStatFileName)
21 except: pass
22 try:
23 os.remove(self._obsStatFileName)
24 except: pass
25
26 def test_run_analysis1(self):
27 libFileName = "TElib.fa"
28 self._writeInputFasta_analysis1(libFileName)
29 expClusterFileName = "expClusters.tab"
30 self._writeExpClusterFile_analysis1(expClusterFileName)
31 expGlobalStatFileName = "expGlobalStats.txt"
32 self._writeExpGlobalStats_analysis1(expGlobalStatFileName)
33 self._writeExpStatsFile_analysis1(self._expStatFileName)
34 obsClusterFileName = "TElib.tab"
35 obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt"
36 self._obsStatFileName = "TElib.statsPerCluster.tab"
37
38 iPATEL = PostAnalyzeTELib(analysis=1, fastaFileName=libFileName, doClean=True)
39 iPATEL.run()
40
41 self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName))
42 self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
43 self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
44
45 os.remove(libFileName)
46 os.remove(expClusterFileName)
47 os.remove(expGlobalStatFileName)
48 os.remove(obsClusterFileName)
49 os.remove(obsGlobalStatFileName)
50
51 def test_run_as_script_analysis1(self):
52 libFileName = "TElib.fa"
53 with open(libFileName, "w") as f:
54 f.write(">transib2\n")
55 f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
56 f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
57 f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTC\n")
58 f.write(">transib3\n")
59 f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
60 f.write("TGAAACTCGTCAGCGTCGTTTCCAAGTCCT\n")
61 f.write(">transib4\n")
62 f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
63 f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
64 f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCAT\n")
65 f.write("AAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
66 expClusterFileName = "expClusters.tab"
67 with open(expClusterFileName, "w") as f:
68 f.write("transib4 \n")
69 f.write("transib2 \n")
70 f.write("transib3 \n")
71 with open(self._expStatFileName, "w") as f:
72 f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n")
73 f.write("1\t1\t238\t238\t238\t238\n")
74 f.write("2\t1\t178\t178\t178\t178\n")
75 f.write("3\t1\t90\t90\t90\t90\n")
76 expGlobalStatFileName = "expGlobalStats.txt"
77 with open(expGlobalStatFileName, "w") as f:
78 f.write("nb of clusters: 3\n")
79 f.write("nb of clusters with 1 sequence: 3\n")
80 f.write("nb of clusters with 2 sequences: 0\n")
81 f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n")
82 f.write("nb of sequences: 3\n")
83 f.write("nb of sequences in the largest cluster: 1\n")
84 f.write("nb of sequences in the smallest cluster: 1\n")
85 f.write("size of the smallest sequence: 90\n")
86 f.write("size of the largest sequence: 238\n")
87 f.write("average sequences size: 168\n")
88 f.write("median sequences size: 178\n")
89 obsClusterFileName = "TElib.tab"
90 obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt"
91 self._obsStatFileName = "TElib.statsPerCluster.tab"
92
93 cmd = "PostAnalyzeTELib.py -i %s -L 98 -S 95 -b -c -v 3" % libFileName
94 process = subprocess.Popen(cmd, shell = True)
95 process.communicate()
96
97 self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName))
98 self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
99 self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
100
101 os.remove(libFileName)
102 os.remove(expClusterFileName)
103 os.remove(expGlobalStatFileName)
104 os.remove(obsClusterFileName)
105 os.remove(obsGlobalStatFileName)
106
107 def test_run_analysis2(self):
108 clusterFileName = "ConsensusClusters.tab"
109 self._writeClusterFile_analysis2(clusterFileName)
110 self._writeExpStatsFile_analysis2(self._expStatFileName)
111 self._obsStatFileName = "ConsensusClusters.classifStatsPerCluster.tab"
112
113 iPATEL = PostAnalyzeTELib(analysis=2, clusterFileName=clusterFileName, verbosity=3)
114 iPATEL.run()
115 print "exp: %s, obs: %s" % (self._expStatFileName, self._obsStatFileName)
116 self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
117
118 os.remove(clusterFileName)
119
120 def test_run_analysis3(self):
121 iDb = DbFactory.createInstance()
122 iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True)
123 iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True)
124
125 expGlobalStatFileName = "expGlobalStats.txt"
126 self._writeExpGlobalStats_analysis3(expGlobalStatFileName)
127 self._writeExpStatsFile_analysis3(self._expStatFileName)
128 obsGlobalStatFileName = "%s.globalAnnotStatsPerTE.txt" % self._pathTableName
129 self._obsStatFileName = "%s.annotStatsPerTE.tab" % self._pathTableName
130
131 iPATEL = PostAnalyzeTELib(analysis=3, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize)
132 iPATEL.run()
133
134 self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName))
135 self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
136
137 iDb.dropTable(self._pathTableName)
138 iDb.dropTable(self._seqTableName)
139 iDb.close()
140 os.remove(expGlobalStatFileName)
141 os.remove(obsGlobalStatFileName)
142
143 def test_run_analysis4(self):
144 iDb = DbFactory.createInstance()
145 iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True)
146 iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True)
147
148 clusterFileName = "clusters.tab"
149 self._writeClusterFile_analysis4(clusterFileName)
150 self._writeExpStatsFile_analysis4(self._expStatFileName)
151 self._obsStatFileName = "%s.annotStatsPerCluster.tab" % self._pathTableName
152
153 iPATEL = PostAnalyzeTELib(analysis=4, clusterFileName=clusterFileName, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize)
154 iPATEL.run()
155
156 self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName))
157
158 iDb.dropTable(self._pathTableName)
159 iDb.dropTable(self._seqTableName)
160 iDb.close()
161 os.remove(clusterFileName)
162
163 def _writeInputFasta_analysis1(self, fileName):
164 with open(fileName, "w") as f:
165 f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
166 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
167 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
168 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
169 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
170 f.write(">DTX-incomp_DmelChr4-B-R10-Map3\n")
171 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
172 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
173 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
174 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
175 f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
176 f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
177 f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
178 f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
179
180 def _writeExpClusterFile_analysis1(self, fileName):
181 with open(fileName, "w") as f:
182 f.write("DTX-incomp_DmelChr4-B-R10-Map3 DTX-incomp_DmelChr4-B-R9-Map3_reversed \n")
183 f.write("PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed \n")
184
185 def _writeExpStatsFile_analysis1(self, fileName):
186 #TODO: header in option ?
187 with open(fileName, "w") as f:
188 f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n")
189 f.write("1\t2\t240\t240\t240\t240\n")
190 f.write("2\t1\t180\t180\t180\t180\n")
191
192 def _writeExpGlobalStats_analysis1(self, fileName):
193 #TODO: file or STDOUT ?
194 with open(fileName, "w") as f:
195 f.write("nb of clusters: 2\n")
196 f.write("nb of clusters with 1 sequence: 1\n")
197 f.write("nb of clusters with 2 sequences: 1\n")
198 f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n")
199 f.write("nb of sequences: 3\n")
200 f.write("nb of sequences in the largest cluster: 2\n")
201 f.write("nb of sequences in the smallest cluster: 1\n")
202 f.write("size of the smallest sequence: 180\n")
203 f.write("size of the largest sequence: 240\n")
204 f.write("average sequences size: 220\n")
205 f.write("median sequences size: 240\n")
206
207 def _writeClusterFile_analysis2(self, fileName):
208 with open(fileName, "w") as f:
209 f.write("DTX-incomp_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tPotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
210 f.write("DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_Blc1_DmelChr4-B-R10-Map3\n")
211 f.write("DXX-comp_DmelChr4-B-R9-Map3\tDTX-comp_DmelChr4-B-R10-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tnoCat_DmelChr4-B-G1-Map3\tnoCat_DmelChr4-B-R1-Map4\n")
212 f.write("RXX-MITE_DmelChr4-B-G7-Map3\tRXX-MITE_DmelChr4-B-G5-Map3\tRXX-MITE_DmelChr4-B-G2-Map3\tRXX-MITE_DmelChr4-B-G23-Map3\tRXX-MITE_DmelChr4-B-G6-Map3\n")
213
214 def _writeExpStatsFile_analysis2(self, fileName):
215 #TODO: header in option ?
216 with open(fileName, "w") as f:
217 f.write("cluster\tnoCat\tPotentialChimeric\tcomp\tincomp\tclassifs (nbTEs)\n")
218 f.write("1\t0\t1\t0\t2\tDTX (2)\tPotentialHostGene (1)\n")
219 f.write("2\t0\t0\t0\t2\tDTX (2)\n")
220 f.write("3\t2\t0\t2\t1\tDTX (2)\tDXX (1)\n")
221 f.write("4\t0\t0\t0\t0\tMITE (5)\n")
222
223 def _writeExpStatsFile_analysis3(self, fileName):
224 #TODO: header in option ?
225 with open(fileName, "w") as f:
226 f.write("TE\tlength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tmeanLgth\tmeanLgthPerc\n")
227 f.write("DmelChr4-B-G1-Map3_NoCat\t542\t3701\t12\t4\t10\t4\t95.72\t370.10\t68.28\n")
228 f.write("DmelChr4-B-G11-Map20_classII-TIR-incomp\t1240\t8216\t27\t0\t22\t0\t88.80\t375.00\t30.24\n")
229 f.write("DmelChr4-B-G7-Map3_classII-TIR-incomp\t1944\t15212\t49\t1\t42\t1\t89.44\t382.36\t19.67\n")
230 f.write("DmelChr4-B-G9-Map3_NoCat\t1590\t11564\t24\t0\t21\t1\t92.03\t550.67\t34.63\n")
231 f.write("DmelChr4-B-P0.0-Map3_classII-TIR-incomp\t1042\t4001\t13\t3\t11\t3\t85.11\t366.36\t35.16\n")
232 f.write("DmelChr4-B-R1-Map4_NoCat\t2367\t66031\t484\t0\t361\t0\t77.84\t182.91\t7.73\n")
233 f.write("DmelChr4-B-R12-Map3_NoCat\t2284\t4938\t3\t2\t3\t2\t99.26\t1646.00\t72.07\n")
234 f.write("DmelChr4-B-R19-Map4_NoCat\t705\t3328\t10\t3\t10\t3\t88.51\t332.80\t47.21\n")
235 f.write("DmelChr4-B-R2-Map6_NoCat\t4638\t20539\t34\t2\t29\t3\t80.93\t708.24\t15.27\n")
236 f.write("DmelChr4-B-R4-Map5_NoCat\t1067\t7292\t35\t1\t28\t1\t86.50\t260.54\t24.42\n")
237 f.write("DmelChr4-B-R9-Map3_NoCat\t714\t5453\t19\t2\t16\t2\t81.18\t340.81\t47.73\n")
238
239 def _writeExpGlobalStats_analysis3(self, fileName):
240 with open(fileName, "w") as f:
241 f.write("nb of sequences: 11\n")
242 f.write("nb of matched sequences: 11\n")
243 f.write("cumulative coverage: 150275 bp\n")
244 f.write("coverage percentage: 11.73%\n")
245 f.write("\n")
246 f.write("total nb of TE fragments: 710\n")
247 f.write("total nb full-length fragments: 18 (2.54%)\n")
248 f.write("total nb of TE copies: 553\n")
249 f.write("total nb full-length copies: 20 (3.62%)\n")
250 f.write("families with full-length fragments: 8 (72.73%)\n")
251 f.write(" with only one full-length fragment: 2\n")
252 f.write(" with only two full-length fragments: 3\n")
253 f.write(" with only three full-length fragments: 2\n")
254 f.write(" with more than three full-length fragments: 1\n")
255 f.write("families with full-length copies: 9 (81.82%)\n")
256 f.write(" with only one full-length copy: 3\n")
257 f.write(" with only two full-length copies: 2\n")
258 f.write(" with only three full-length copies: 3\n")
259 f.write(" with more than three full-length copies: 1\n")
260 f.write("mean of median identity of all families: 88.30 +- 8.33\n")
261 f.write("mean of median length percentage of all families: 30.83 +- 32.30\n")
262
263 def _writeClusterFile_analysis4(self, fileName):
264 with open(fileName, "w") as f:
265 f.write("1\tDmelChr4-B-R1-Map4_NoCat\tDmelChr4-B-R2-Map6_NoCat\tDmelChr4-B-R4-Map5_NoCat\n")
266 f.write("2\tDmelChr4-B-G7-Map3_classII-TIR-incomp\tDmelChr4-B-P0.0-Map3_classII-TIR-incomp\n")
267
268 def _writeExpStatsFile_analysis4(self, fileName):
269 with open(fileName, "w") as f:
270 f.write("Cluster\tcovg\tfrags\tcopies\n")
271 f.write("1\t93862\t553\t418\n")
272 f.write("2\t19213\t62\t53\n")
273
274 def _writeConfigFile(self, configFileName):
275 with open(configFileName, "w") as fHandle:
276 fHandle.write("[repet_env]\n")
277 fHandle.write("repet_host: %s\n" % os.environ["REPET_HOST"])
278 fHandle.write("repet_user: %s\n" % os.environ["REPET_USER"])
279 fHandle.write("repet_pw: %s\n" % os.environ["REPET_PW"])
280 fHandle.write("repet_db: %s\n" % os.environ["REPET_DB"])
281 fHandle.write("repet_port: 3306\n")
282 fHandle.write("[analysis1]\n")
283 fHandle.write("fasta_name: %s\n" % self._expStatFileName)
284
285 fHandle.write("[analysis2]\n")
286 fHandle.write("clusterFileName: %s\n" % self._expStatFileName)
287
288 fHandle.write("[analysis3]\n")
289 fHandle.write("pathTableName: %s\n" % self._pathTableName)
290 fHandle.write("seqTableName: %s\n" % self._seqTableName)
291 fHandle.write("genomeSize: %s\n" % self._genomeSize)
292
293 if __name__ == "__main__":
294 unittest.main()