Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchRepeatMasker.py @ 18:94ab73e8a190

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents
children
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4 from commons.launcher.LaunchRepeatMasker import LaunchRepeatMasker
5
6
7 class Test_F_RepeatMasker(unittest.TestCase):
8
9 def setUp(self):
10 self._queryFastaFileName = "query.fa"
11 self._libFastaFileName = "lib.fa"
12 self._expMaskedQueryFileName = "expMaskedQuery.fa"
13 self._obsMaskedQueryFileName = "%s.masked" % self._queryFastaFileName
14
15 self._expCatFileName = "expCat.fa"
16 self._obsCatFileName = "%s.cat" % self._queryFastaFileName
17
18 self._writeInputFastaFiles()
19 self._writeExpMaskedQueryFile()
20 self._writeExpCatFile()
21
22 def tearDown(self):
23 os.remove(self._queryFastaFileName)
24 os.remove(self._libFastaFileName)
25 os.remove(self._expMaskedQueryFileName)
26 os.remove(self._obsMaskedQueryFileName)
27 os.remove(self._expCatFileName)
28 os.remove(self._obsCatFileName)
29 os.remove("%s.tbl" % self._queryFastaFileName)
30 os.remove("%s.out" % self._queryFastaFileName)
31 os.remove("%s.ori.out" % self._queryFastaFileName)
32
33 def test_run(self):
34 ilauncher = LaunchRepeatMasker(self._queryFastaFileName, self._libFastaFileName,verbosity=1 )
35 ilauncher.run()
36 self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
37
38 def test_run_as_script(self):
39 #FIXME : change path to launcher
40 cmd = 'python %s/commons/launcher/LaunchRepeatMasker.py -q %s -l %s' % (os.environ["REPET_PATH"],self._queryFastaFileName, self._libFastaFileName)
41 os.system(cmd)
42 self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
43
44 def _writeInputFastaFiles(self):
45 InputFile = open(self._queryFastaFileName, 'w')
46 InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
47 InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
48 InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
49 InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
50 InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
51 InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
52 InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTACCTCCTTCCA\n')
53 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
54 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
55 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
56 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
57 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
58 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
59 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
60 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
61 InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
62 InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
63 InputFile.write('AAAAAAA\n')
64 InputFile.close()
65
66 InputFile = open(self._libFastaFileName, 'w')
67 InputFile.write('>RefLib\n')
68 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
69 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
70 InputFile.close()
71
72 def _writeExpMaskedQueryFile(self):
73 f = open(self._expMaskedQueryFileName, 'w')
74 f.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
75 f.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAG\n')
76 f.write('ACCCCGGTTCGATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGC\n')
77 f.write('TACCCACTCCAGTATTCTTGGGCTTCCCTGGTGGCTCAGACGGTAAAGAA\n')
78 f.write('TCCGCCTGCAATGCGGGAGACCTGGGTTCGATCCCTGGGTTGGGAAGATC\n')
79 f.write('CCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATC\n')
80 f.write('CCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
81 f.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTA\n')
82 f.write('CCTCCTTCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
83 f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
84 f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCTGCGTGGGTTCTCTCCG\n')
85 f.write('GGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGATTGGGGATTA\n')
86 f.write('GGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
87 f.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCC\n')
88 f.write('AGGGTGTACCCTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCC\n')
89 f.write('CGCGACCCTCAGTGGAGGAAGGGCAGCCTGGGTGGCTCAGCGGTTTAGCG\n')
90 f.write('CCTGCCTTTGGCCCAGGGCGTGATCCTGGAGACCCGGGATCGAGTCCCAC\n')
91 f.write('ATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTGGGGGAGGGTA\n')
92 f.write('TAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
93 f.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTC\n')
94 f.write('CCCCACCAAAAAAAAAA\n')
95 f.close()
96
97 def _writeExpCatFile(self):
98 f = open(self._expCatFileName, 'w')
99 f.write('958 0.00 0.00 0.00 Bovc-tA2:classI:SINE:SINE2/tRNA 361 480 (487) RefLib 1 120 (0) 5\n')
100 f.write('## Total Sequences: 1\n')
101 f.write('## Total Length: 967\n')
102 f.write('## Total NonMask ( excluding >20bp runs of N/X bases ): 967\n')
103 f.write('## Total NonSub ( excluding all non ACGT bases ):967\n')
104 f.write('RepeatMasker version open-3.2.6 , default mode\n')
105 f.write('run with blastp version 2.0MP-WashU\n')
106 f.write('RepBase Update 20080801, RM database version 20080801\n')
107 f.close()
108
109 if __name__ == "__main__":
110 unittest.main()