Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchNucmer.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 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4 from commons.launcher.LaunchNucmer import LaunchNucmer
5
6 class Test_F_LaunchNucmer(unittest.TestCase):
7
8 def setUp(self):
9 self._queryFastaFileName = "query.fa"
10 self._refFastaFileName = "ref.fa"
11 self._writeInputFastaFiles()
12 self._expDeltaFileName = "expNucmer.delta"
13 self._writeExpDeltaFile()
14 self._obsDeltaFileName = "obsNucmer.delta"
15 self._obsCoordFileName= "obsNucmer.coords"
16 self._expCoordFileName= "expNucmer.coords"
17
18 def tearDown(self):
19 try:
20 os.remove(self._queryFastaFileName)
21 except:pass
22 try:
23 os.remove(self._refFastaFileName)
24 except:pass
25 try:
26 os.remove(self._expDeltaFileName)
27 except:pass
28 try:
29 os.remove(self._obsDeltaFileName)
30 except:pass
31
32 def test_run(self):
33 ilauncher = LaunchNucmer(self._refFastaFileName, self._queryFastaFileName,"obsNucmer",verbosity=1)
34 ilauncher.run()
35 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
36
37 def test_run_as_script(self):
38 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
39 os.system(cmd)
40 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
41
42 def test_run_as_script_gencoords_output(self):
43 self._writeExpGenCoordsFile()
44 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
45 os.system(cmd)
46 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
47 os.remove(self._obsCoordFileName)
48 os.remove(self._expCoordFileName)
49
50 def test_run_as_script_with_mincluster(self):
51 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
52 os.system(cmd)
53 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
54
55 def test_run_as_script_showcoords_output(self):
56 self._writeExpShowCoordsFile()
57 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
58 os.system(cmd)
59 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
60 os.remove(self._obsCoordFileName)
61 os.remove(self._expCoordFileName)
62
63 def _writeInputFastaFiles(self):
64 InputFile = open(self._queryFastaFileName, 'w')
65 InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
66 InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
67 InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
68 InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
69 InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
70 InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
71 InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
72 InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
73 InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
74 InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
75 InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
76 InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
77 InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
78 InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
79 InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
80 InputFile.write('CCAAAAAAAAA\n')
81 InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
82 InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
83 InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
84 InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
85 InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
86 InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
87 InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
88 InputFile.write('>SINE_FR2:classI:SINE:?\n')
89 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
90 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
91 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
92 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
93 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
94 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
95 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
96 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
97 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
98 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
99 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
100 InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
101 InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
102 InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
103 InputFile.write('AAAAAAA\n')
104 InputFile.close()
105
106 InputFile = open(self._refFastaFileName, 'w')
107 InputFile.write('>SINE_FR2:classI:SINE:?\n')
108 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
109 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
110 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
111 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
112 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
113 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
114 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
115 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
116 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
117 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
118 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
119 InputFile.close()
120
121 def _writeExpDeltaFile(self):
122 f = open(self._expDeltaFileName, 'w')
123 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
124 f.write('NUCMER\n')
125 f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
126 f.write('1 343 1 343 0 0 0\n')
127 f.write('0\n')
128 f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
129 f.write('1 161 1 161 0 0 0\n')
130 f.write('0\n')
131 f.close()
132
133 def _writeExpGenCoordsFile(self):
134 f = open(self._expCoordFileName, 'w')
135 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
136 f.write('NUCMER\n\n')
137 f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS]\n')
138 f.write('=====================================================================================\n')
139 f.write(' 1 161 | 1 161 | 161 161 | 100.00 | SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
140 f.write(' 1 343 | 1 343 | 343 343 | 100.00 | SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
141 f.close()
142
143 def _writeExpShowCoordsFile(self):
144 f = open(self._expCoordFileName, 'w')
145 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
146 f.write('NUCMER\n\n')
147 f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
148 f.write('1\t161\t1\t161\t161\t161\t100.00\t164\t161\t98.17\t100.00\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
149 f.write('1\t343\t1\t343\t343\t343\t100.00\t389\t371\t88.17\t92.45\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
150 f.close()
151
152 if __name__ == "__main__":
153 unittest.main()