Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_findTss.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os, os.path
3 from SMART.Java.Python.misc import Utils
4
5
6 TestF_PATH = os.environ['REPET_PATH'] + '/SMART/Java/Python/TestFiles'
7
8
9 class Test_F_findTss(unittest.TestCase):
10
11 def setUp(self):
12 self._outputFileName = 'output.gff3'
13 self._expOutputFileName = 'expOutput.gff3'
14
15 def tearDown(self):
16 os.remove(self._outputFileName)
17 os.remove(self._expOutputFileName)
18
19 def test_run_default_option(self):
20 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -v 0" % TestF_PATH
21 os.system(cmd)
22 self._writeExpDefaultOption(self._expOutputFileName)
23 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
24
25 def test_run_normalize_option(self):
26 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -n -v 0" % TestF_PATH
27 os.system(cmd)
28 self._writeExpNormalizeOption(self._expOutputFileName)
29 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
30
31 def test_run_distance_option(self):
32 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -d 20 -v 0" % TestF_PATH
33 os.system(cmd)
34 self._writeExpDistance_option(self._expOutputFileName)
35 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
36
37 def test_run_colinear_option(self):
38 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -e -v 0" % TestF_PATH
39 os.system(cmd)
40 self._writeExpColinearOption(self._expOutputFileName)
41 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
42
43 def test_run_excel_option(self):
44 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -c output.csv -v 0" % TestF_PATH
45 os.system(cmd)
46 obsCsv = 'output.csv'
47 self.assertTrue(os.path.exists(obsCsv))
48 os.remove(obsCsv)
49 self._writeExpExcelOption(self._expOutputFileName)
50 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
51
52 def _writeExpDefaultOption(self, fileName):
53 f = open(fileName, 'w')
54 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
55 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
56 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
57 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
58 f.close()
59
60 def _writeExpNormalizeOption(self, fileName):
61 f = open(fileName, 'w')
62 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
63 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
64 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
65 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
66 f.close()
67
68 def _writeExpDistance_option(self, fileName):
69 f = open(fileName, 'w')
70 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
71 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
72 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
73 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
74 f.close()
75
76 def _writeExpColinearOption(self, fileName):
77 f = open(fileName, 'w')
78 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
79 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
80 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
81 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
82 f.close()
83
84 def _writeExpExcelOption(self, fileName):
85 f = open(fileName, 'w')
86 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
87 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
88 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
89 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
90 f.close()
91
92 if __name__ == "__main__":
93 unittest.main()