Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_LaunchTallymer.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 from commons.core.utils.FileUtils import FileUtils
2 import os
3 import unittest
4 from commons.launcher.LaunchTallymer import ConvertUtils
5
6 class Test_ConvertUtils(unittest.TestCase):
7
8 def test_convertTallymerFormatIntoMapFormatAndGenerateData(self):
9 inputFastaFileName = "input.fa"
10 inputTallymerSearchFileName = "input.tallymer"
11 expMapFileName = "exp.map"
12 obsMapFileName = "obs.map"
13 self._writeInputFasta(inputFastaFileName)
14 self._writeInputTallymerSearch(inputTallymerSearchFileName)
15 self._writeExpMap(expMapFileName)
16
17 expOccNb = 4
18 expDKmer2Occ = {"caagatgcgtaacggccata":1,
19 "aagatgcgtaacggccatac":1,
20 "agatgcgtaacggccataca":1,
21 "gatgcgtaacggccatacat":1}
22 expPlotData = {4379: 17,
23 4380: 17,
24 4381: 16,
25 4382: 16}
26
27 obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
28
29 self.assertEquals(expOccNb, obsOccNb)
30 self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
31 self.assertEquals(expPlotData, obsPlotData)
32 self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
33
34 os.remove(inputFastaFileName)
35 os.remove(inputTallymerSearchFileName)
36 os.remove(expMapFileName)
37 os.remove(obsMapFileName)
38
39 def test_convertTallymerFormatIntoMapFormatAndGenerateDataMultiFasta(self):
40 inputFastaFileName = "input.fa"
41 inputTallymerSearchFileName = "input.tallymer"
42 expMapFileName = "exp.map"
43 obsMapFileName = "obs.map"
44 self._writeInputMultiFasta(inputFastaFileName)
45 self._writeInputTallymerSearchMultiFasta(inputTallymerSearchFileName)
46 self._writeExpMapMultiFasta(expMapFileName)
47
48 expOccNb = 6
49 expDKmer2Occ = {"caagatgcgtaacggccata":1,
50 "aagatgcgtaacggccatac":1,
51 "agatgcgtaacggccataca":1,
52 "gatgcgtaacggccatacat":1,
53 "agatgcgtaacggccataca":2,
54 "gatgcgtaacggccatacat":2}
55 expPlotData = {4379: 17, 4380: 17, 4381: 16, 4382: 35}
56
57 obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
58
59 self.assertEquals(expOccNb, obsOccNb)
60 self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
61 self.assertEquals(expPlotData, obsPlotData)
62 self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
63
64 os.remove(inputFastaFileName)
65 os.remove(inputTallymerSearchFileName)
66 os.remove(expMapFileName)
67 os.remove(obsMapFileName)
68
69 def _writeInputTallymerSearch(self, tallymerFormatFileName):
70 with open(tallymerFormatFileName, 'w') as f:
71 f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
72 f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
73 f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
74 f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
75
76 def _writeInputFasta(self, fastaFileName):
77 with open(fastaFileName, 'w') as f:
78 f.write(">Seq1\n")
79 f.write("caagatgcgtaacggccata\n")
80 f.write("aagatgcgtaacggccatac\n")
81 f.write("agatgcgtaacggccataca\n")
82 f.write("gatgcgtaacggccatacat\n")
83
84 def _writeExpMap(self, mapFileName):
85 with open(mapFileName, 'w') as f:
86 f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
87 f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
88 f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
89 f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
90
91 def _writeInputTallymerSearchMultiFasta(self, tallymerFormatFileName):
92 with open(tallymerFormatFileName, 'w') as f:
93 f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
94 f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
95 f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
96 f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
97 f.write("1\t+4380\t16\tagatgcgtaacggccataca\n")
98 f.write("1\t+4381\t35\tgatgcgtaacggccatacat\n")
99
100 def _writeInputMultiFasta(self, fastaFileName):
101 with open(fastaFileName, 'w') as f:
102 f.write(">Seq1\n")
103 f.write("caagatgcgtaacggccata\n")
104 f.write("aagatgcgtaacggccatac\n")
105 f.write("agatgcgtaacggccataca\n")
106 f.write("gatgcgtaacggccatacat\n")
107 f.write(">Seq2\n")
108 f.write("agatgcgtaacggccataca\n")
109 f.write("gatgcgtaacggccatacat\n")
110
111 def _writeExpMapMultiFasta(self, mapFileName):
112 with open(mapFileName, 'w') as f:
113 f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
114 f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
115 f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
116 f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
117 f.write("agatgcgtaacggccataca_16\tSeq2\t4381\t4401\t16\n")
118 f.write("gatgcgtaacggccatacat_35\tSeq2\t4382\t4402\t35\n")
119
120 if __name__ == "__main__":
121 unittest.main()