Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/test/Test_MrepsToSet.py @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4 from commons.core.parsing.MrepsToSet import MrepsToSet
5
6 class Test_MrepsToSet(unittest.TestCase):
7 def setUp(self):
8 self._mrepsInputFileName = "mrepsInput.fa"
9 self._mrepsOuputFileName = "mrepsOutput.xml"
10 self._obsSetFileName = "obsOuput.set"
11 self._expSetFileName = "expOuput.set"
12
13 self._writeExpSet(self._expSetFileName)
14 self._writeMrepsOutput(self._mrepsOuputFileName)
15
16 def tearDown(self):
17 os.remove(self._expSetFileName)
18 os.remove(self._obsSetFileName)
19 os.remove(self._mrepsOuputFileName)
20
21 def test_convert(self):
22 iMrepsToSet = MrepsToSet(self._mrepsInputFileName, self._mrepsOuputFileName, self._obsSetFileName)
23 iMrepsToSet.run()
24 self.assertTrue(FileUtils.are2FilesIdentical(self._obsSetFileName, self._expSetFileName))
25
26 def _writeExpSet(self, fileName):
27 f = open(fileName, "w")
28 f.write("1\t(tatt)3\tseq1\t4\t16\n")
29 f.write("2\t(tatt)3\tseq1\t23\t35\n")
30 f.write("3\t(tatt)3\tseq1\t42\t54\n")
31 f.close()
32
33 def _writeMrepsOutput(self, fileName):
34 f = open(fileName, "w")
35 f.write("<?xml version='1.0' encoding='UTF-8' ?>\n")
36 f.write("<mreps>\n")
37 f.write("<time>Thu Dec 1 17:25:54 2011\n")
38 f.write("</time>\n")
39 f.write("<parameters>\n")
40 f.write(" <type-of-input>file in fasta format</type-of-input>\n")
41 f.write(" <err>3</err>\n")
42 f.write(" <from>1</from>\n")
43 f.write(" <to>-1</to>\n")
44 f.write(" <win>-1</win>\n")
45 f.write(" <minsize>1</minsize>\n")
46 f.write(" <maxsize>-1</maxsize>\n")
47 f.write(" <minperiod>1</minperiod>\n")
48 f.write(" <maxperiod>-1</maxperiod>\n")
49 f.write(" <minexponent>3.00</minexponent>\n")
50 f.write("</parameters>\n")
51 f.write("<results>\n")
52 f.write("<sequence-name>seq1</sequence-name>\n")
53 f.write("<repetitions>\n")
54 f.write("<window>\n")
55 f.write("<windowstart>1</windowstart>\n")
56 f.write("<windowend>60</windowend>\n")
57 f.write(" <repeat>\n")
58 f.write(" <start>4</start>\n")
59 f.write(" <end>16</end>\n")
60 f.write(" <length>13</length>\n")
61 f.write(" <period>4</period>\n")
62 f.write(" <exponent>3.25</exponent>\n")
63 f.write(" <score>0.000</score>\n")
64 f.write(" <sequence>\n")
65 f.write(" <unit>tatt</unit>\n")
66 f.write(" <unit>tatt</unit>\n")
67 f.write(" <unit>tatt</unit>\n")
68 f.write(" <unit>t</unit>\n")
69 f.write(" </sequence>\n")
70 f.write(" </repeat>\n")
71 f.write(" <repeat>\n")
72 f.write(" <start>23</start>\n")
73 f.write(" <end>35</end>\n")
74 f.write(" <length>13</length>\n")
75 f.write(" <period>4</period>\n")
76 f.write(" <exponent>3.25</exponent>\n")
77 f.write(" <score>0.000</score>\n")
78 f.write(" <sequence>\n")
79 f.write(" <unit>tatt</unit>\n")
80 f.write(" <unit>tatt</unit>\n")
81 f.write(" <unit>tatt</unit>\n")
82 f.write(" <unit>t</unit>\n")
83 f.write(" </sequence>\n")
84 f.write(" </repeat>\n")
85 f.write(" <repeat>\n")
86 f.write(" <start>42</start>\n")
87 f.write(" <end>54</end>\n")
88 f.write(" <length>13</length>\n")
89 f.write(" <period>4</period>\n")
90 f.write(" <exponent>3.25</exponent>\n")
91 f.write(" <score>0.000</score>\n")
92 f.write(" <sequence>\n")
93 f.write(" <unit>tatt</unit>\n")
94 f.write(" <unit>tatt</unit>\n")
95 f.write(" <unit>tatt</unit>\n")
96 f.write(" <unit>t</unit>\n")
97 f.write(" </sequence>\n")
98 f.write(" </repeat>\n")
99 f.write("<nbofreps>3</nbofreps>\n")
100 f.write("</window>\n")
101 f.write("</repetitions>\n")
102 f.write("</results>\n")
103 f.write("<errorcode>0</errorcode>\n")
104 f.write("</mreps>\n")
105 f.close()