Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchMummerPlot.py @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4 from commons.launcher.LaunchMummerPlot import LaunchMummerPlot
5
6 class Test_F_LaunchMummerPlot(unittest.TestCase):
7
8 def setUp(self):
9 self._queryFastaFileName = "query.fa"
10 self._refFastaFileName = "ref.fa"
11 self._writeInputFastaFiles()
12
13 self._inputDeltaFileName = "inputNucmer.delta"
14 self._writeInputDeltaFileName()
15
16 self._expGpFileName = "expMummerPlot.gp"
17 self._obsGpFileName = "obsMummerPlot.gp"
18 self._obsPngFileName = "obsMummerPlot.png"
19
20 def tearDown(self):
21 try:
22 os.remove(self._queryFastaFileName)
23 except:pass
24 try:
25 os.remove(self._refFastaFileName)
26 except:pass
27 try:
28 os.remove(self._inputDeltaFileName)
29 except:pass
30 try:
31 os.remove(self._expGpFileName)
32 except:pass
33 try:
34 os.remove(self._obsGpFileName)
35 except:pass
36 try:
37 os.remove(self._obsPngFileName)
38 except:pass
39
40
41 def test_run(self):
42 self._writeExpGpFile()
43 ilaunchMummerPlot = LaunchMummerPlot(self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName,"obsMummerPlot",fat=True, filter=True, clean=True, verbosity=1)
44 ilaunchMummerPlot.run()
45 self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName))
46
47 def test_run_as_script(self):
48 self._writeExpGpFile()
49 cmd = 'LaunchMummerPlot.py --input %s --Qfile %s --Rfile %s --prefix %s --fat --filter --clean' % (self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName, "obsMummerPlot")
50 os.system(cmd)
51 self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName))
52
53 def _writeInputFastaFiles(self):
54 InputFile = open(self._queryFastaFileName, 'w')
55 InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
56 InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
57 InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
58 InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
59 InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
60 InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
61 InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
62 InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
63 InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
64 InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
65 InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
66 InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
67 InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
68 InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
69 InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
70 InputFile.write('CCAAAAAAAAA\n')
71 InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
72 InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
73 InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
74 InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
75 InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
76 InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
77 InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
78 InputFile.write('>SINE_FR2:classI:SINE:?\n')
79 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
80 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
81 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
82 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
83 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
84 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
85 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
86 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
87 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
88 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
89 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
90 InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
91 InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
92 InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
93 InputFile.write('AAAAAAA\n')
94 InputFile.close()
95
96 InputFile = open(self._refFastaFileName, 'w')
97 InputFile.write('>SINE_FR2:classI:SINE:?\n')
98 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
99 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
100 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
101 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
102 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
103 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
104 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
105 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
106 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
107 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
108 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
109 InputFile.close()
110
111 def _writeExpGpFile(self):
112 f = open(self._expGpFileName, 'w')
113 f.write('set terminal png tiny size 800,800\n')
114 f.write('set output "obsMummerPlot.png"\n')
115 f.write('set xtics rotate ( \\\n')
116 f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n')
117 f.write(' "SINEC1B2_CF:classI:SINE:?" 389, \\\n')
118 f.write(' "SINE1A_SS:classI:SINE:SINE2/tRNA" 552, \\\n')
119 f.write(' "SUSINE2:classI:SINE:SINE2/tRNA" 682, \\\n')
120 f.write(' "Bovc-tA2:classI:SINE:SINE2/tRNA" 891, \\\n')
121 f.write(' "ALPINE1:classI:SINE:SINE2/tRNA" 1223, \\\n')
122 f.write(' "SINE2-1_Pca:classI:SINE:SINE2/tRNA" 1349, \\\n')
123 f.write(' "" 1694 \\\n')
124 f.write(')\n')
125 f.write('set ytics ( \\\n')
126 f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n')
127 f.write(' "SINEC1B2_CF:classI:SINE:?" 371, \\\n')
128 f.write(' "" 532 \\\n')
129 f.write(')\n')
130 f.write('set size 1,1\n')
131 f.write('set grid\n')
132 f.write('unset key\n')
133 f.write('set border 0\n')
134 f.write('set tics scale 0\n')
135 f.write('set xlabel "REF"\n')
136 f.write('set ylabel "QRY"\n')
137 f.write('set format "%.0f"\n')
138 f.write('set mouse format "%.0f"\n')
139 f.write('set mouse mouseformat "[%.0f, %.0f]"\n')
140 f.write('set mouse clipboardformat "[%.0f, %.0f]"\n')
141 f.write('set xrange [1:1694]\n')
142 f.write('set yrange [1:532]\n')
143 f.write('set style line 1 lt 1 lw 3 pt 6 ps 1\n')
144 f.write('set style line 2 lt 3 lw 3 pt 6 ps 1\n')
145 f.write('set style line 3 lt 2 lw 3 pt 6 ps 1\n')
146 f.write('plot \\\n')
147 f.write(' "obsMummerPlot.fplot" title "FWD" w lp ls 1, \\\n')
148 f.write(' "obsMummerPlot.rplot" title "REV" w lp ls 2\n')
149 f.write('')
150 f.close()
151
152 def _writeInputDeltaFileName(self):
153 f = open(self._inputDeltaFileName, 'w')
154 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
155 f.write('NUCMER\n')
156 f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
157 f.write('1 343 1 343 0 0 0\n')
158 f.write('0\n')
159 f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
160 f.write('1 161 1 161 0 0 0\n')
161 f.write('0\n')
162 f.close()
163
164 if __name__ == "__main__":
165 unittest.main()
166