Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_F_LaunchBlasterInParallel.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 from commons.core.utils.FileUtils import FileUtils
2 import unittest
3 import os
4 import shutil
5 from commons.tools.LaunchBlasterInParallel import LaunchBlasterInParallel
6
7 class Test_F_LaunchBlasterInParallel(unittest.TestCase):
8
9 CLUSTER_HOST = "compute-2-46.local"
10
11 def setUp(self):
12 self._inFilePath = "%s/Tools/DmelChr4_chunks.fa" % os.environ["REPET_DATA"]
13 self._configFileName = "TE.cfg"
14 self._outputFileName = "out.align.not_over"
15
16 def tearDown(self):
17 try:
18 os.remove(self._outputFileName)
19 os.remove(self._configFileName)
20 except:
21 pass
22
23 def test_run_as_script_1bank_1file_withoutABA(self):
24 self._outputFileName = "out.align"
25 os.mkdir("tmp")
26 os.chdir("tmp")
27 queryFileName = "chunks.fa"
28 with open(queryFileName, "w") as f:
29 f.write(">chunk1\n")
30 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
31 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
32 os.chdir("..")
33 subjectFileName = "genome.fa"
34 with open(subjectFileName, "w") as f:
35 f.write(">chunk1\n")
36 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
37 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
38 f.write(">chunk2\n")
39 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
40 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
41 expFileName = "expected"
42 with open(expFileName, "w") as f:
43 f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
44 f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
45 self._writeConfig(0.1)
46
47 cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s/%s -C %s -o %s" % (os.getcwd(), os.getcwd(), subjectFileName, self._configFileName, self._outputFileName)
48 os.system(cmd)
49
50 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
51 FileUtils.removeFilesByPattern("*.param")
52 shutil.rmtree("tmp")
53 os.remove(subjectFileName)
54 os.remove(expFileName)
55
56 def test_run_as_script_1bank_2_batches(self):
57 os.mkdir("tmp")
58 os.chdir("tmp")
59 os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
60 os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
61 os.chdir("..")
62
63 expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
64 self._writeConfig()
65
66 cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s -a -o %s -C %s" % (os.getcwd(), self._inFilePath, self._outputFileName, self._configFileName)
67 os.system(cmd)
68
69 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
70 FileUtils.removeFilesByPattern("*.param")
71 shutil.rmtree("tmp")
72
73 def test_run_1bank_1bank_2_batches(self):
74 os.mkdir("tmp")
75 os.chdir("tmp")
76 os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
77 os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
78 os.chdir("..")
79
80 expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
81 self._writeConfig()
82
83 iLaunchBlaster = LaunchBlasterInParallel(configFileName = self._configFileName, outFileName = self._outputFileName)
84 iLaunchBlaster.setDoAllByall(True)
85 iLaunchBlaster.setVerbosity(4)
86 iLaunchBlaster.setQueryDirectory("%s/tmp" % os.getcwd())
87 iLaunchBlaster.setSubjectFilePath(self._inFilePath)
88 iLaunchBlaster.run()
89
90 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
91 FileUtils.removeFilesByPattern("*.param")
92 shutil.rmtree("tmp")
93
94 def _writeConfig(self, eValue = 1e-300):
95 with open(self._configFileName, "w") as fh:
96 fh.write("[jobs]\n")
97 if os.getenv("HOSTNAME") == self.CLUSTER_HOST:
98 fh.write("resources: test\n")
99 else:
100 fh.write("resources:\n")
101 fh.write("tmpDir:\n")
102 fh.write("copy: no\n")
103 fh.write("clean: yes\n")
104 fh.write("\n")
105 fh.write("[prepare_data]\n")
106 fh.write("chunk_length: 200000\n")
107 fh.write("chunk_overlap: 10000\n")
108 fh.write("\n")
109 fh.write("[alignment]\n")
110 fh.write("blast: ncbi\n")
111 fh.write("Evalue: %s\n" % eValue)
112 fh.write("length: 100\n")
113 fh.write("identity: 90\n")
114
115 if __name__ == "__main__":
116 unittest.main()