Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.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 subprocess
2 import unittest
3 import os
4 from commons.core.utils.FileUtils import FileUtils
5 from commons.core.sql.DbMySql import DbMySql
6 from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
7 from shutil import rmtree
8 from glob import glob
9
10 class Test_F_GetMultAlignAndPhylogenyPerTErefSeq(unittest.TestCase):
11
12 def setUp(self):
13 self._verbosity = 3
14
15 self._testPrefix = 'Test_GMAAPperTErefSeq_'
16 self._configFileName = "%sConfig.cfg" % self._testPrefix
17 self._iDb = DbMySql()
18
19 self.inPathTableName = "%sDmelChr4_chr_allTEs_nr_noSSR_join_path" % (self._testPrefix)
20 self.inPathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
21 self._iDb.createTable(self.inPathTableName, "path", self.inPathFileName, True)
22
23 self.RefTETableName = "%sDmelChr4_refTEs" % (self._testPrefix)
24 self.RefTEFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
25 self._iDb.createTable(self.RefTETableName, "seq", self.RefTEFileName, True)
26
27 self.genomeTableName = "%sDmelChr4_chr" % (self._testPrefix)
28 self.genomeFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
29 self._iDb.createTable(self.genomeTableName, "seq", self.genomeFileName, True)
30
31 try:
32 os.makedirs(self._testPrefix)
33 except:pass
34 os.chdir(self._testPrefix)
35 self._writeConfigFile()
36
37 # self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"]
38 # self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"]
39 # self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"]
40 # self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"]
41 # self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"]
42 # self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"]
43
44
45 # inputFastaFileName = "input_TEannot_refTEs.fa"
46 # os.symlink(self._expFastaFileName_Copy, inputFastaFileName)
47
48 # self._tableName = "Dummy_Atha_refTEs_seq"
49 # self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True)
50 # os.remove(inputFastaFileName)
51 #
52 # self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
53 # self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
54 # self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
55 # self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0]
56 # self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0]
57 # self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0]
58
59 def tearDown(self):
60 # self._iDb.dropTable(self.inPathTableName)
61 # self._iDb.dropTable(self.RefTETableName)
62 # self._iDb.dropTable(self.genomeTableName)
63 # self._iDb.close()
64
65 os.chdir("..")
66 # try:
67 # rmtree(self._testPrefix)
68 # except:pass
69
70
71 # def test_run_step1(self):
72 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, configFileName=self._configFileName, step=1, verbosity=self._verbosity)
73 # iGMAAPperTErefSeq.run()
74 #
75 # copiesFiles = glob("*_copies.fa")
76 # self.assertTrue(len(copiesFiles) > 0)
77 # self.assertTrue(os.stat("DmelChr4-B-R9-Map3_NoCat_copies.fa")[6] != 0)#check if file is empty
78 #
79 # def test_run_step1Step2Map(self):
80 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
81 # iGMAAPperTErefSeq.run()
82 # iGMAAPperTErefSeq.step = 2
83 # iGMAAPperTErefSeq.run()
84 #
85 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
86 #
87 # def test_run_step1Step2RefAlign(self):
88 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="RefAlign", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
89 # iGMAAPperTErefSeq.run()
90 # iGMAAPperTErefSeq.step = 2
91 # iGMAAPperTErefSeq.run()
92 #
93 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_refalign.fa_aln")[6] != 0)
94
95 def test_run_step1Step2Step3Map(self):
96 iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
97 iGMAAPperTErefSeq.run()
98 iGMAAPperTErefSeq.step = 2
99 iGMAAPperTErefSeq.run()
100 iGMAAPperTErefSeq.step = 3
101 iGMAAPperTErefSeq.run()
102
103 self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
104
105 def _writeConfigFile(self):
106 f = open(self._configFileName, "w")
107 f.write("[repet_env]\n")
108 f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
109 f.write("repet_user: %s\n" % os.environ["REPET_USER"])
110 f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
111 f.write("repet_db: %s\n" % os.environ["REPET_DB"])
112 f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
113 f.write("repet_job_manager: SGE\n")
114 f.close()
115
116
117 # def test_run_as_script_step1Step2Map(self):
118 # #cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -m 'Map' -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
119 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
120 # subprocess.call(cmd, shell = True)
121 #
122 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 2 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
123 # subprocess.call(cmd, shell = True)
124 #
125 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
126
127
128 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
129 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
130 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
131 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
132 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
133 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
134
135 # def test_run_as_script_step2(self):
136 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
137 # print cmd
138 # subprocess.call(cmd, shell = True)
139 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
140 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
141 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
142 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
143 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
144 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
145
146 if __name__ == "__main__":
147 unittest.main()