Mercurial > repos > yufei-luo > s_mart
diff commons/tools/tests/Test_F_GameXmlMaker.py @ 18:94ab73e8a190
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/tools/tests/Test_F_GameXmlMaker.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,281 @@ +import unittest +import os +import glob +from commons.core.utils.FileUtils import FileUtils +from commons.core.sql.DbFactory import DbFactory +from commons.tools.GameXmlMaker import GameXmlMaker + + +class Test_F_GameXmlMaker(unittest.TestCase): + + def setUp(self): + pass + + + def tearDown(self): + FileUtils.removeFilesByPattern("*gamexml") + + + def test_run_as_script_step1(self): + fastaFileName = "input.fa" + self._writeFastaFile(fastaFileName) + + cmd = "GameXmlMaker.py -f %s " % fastaFileName + os.system(cmd) + + lObsGameXmlNew = glob.glob("*.gamexml") + self._writeStep1ExpectedXmls() + self.assertTrue(len(lObsGameXmlNew) > 0) + for obsGameXmlNew in lObsGameXmlNew: + expGameXmlNew = "exp_%s" % obsGameXmlNew + self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) + + os.remove(fastaFileName) + + def test_run_as_script_step2(self): + self._tableFileName = "annotation_tables.txt" + + self._writeStep2InputTableFile() + self._writeStep2InputXmls() + self._writeStep2InputPathFile() + self._writeStep2InputSetFile() + self._writeStep2InputMapFile() + self._createStep2Tables() + + lObsGameXmlNew = glob.glob("*.gamexml") + + cmd = "GameXmlMaker.py -t %s " % self._tableFileName + os.system(cmd) + + self._writeStep2ExpXmls() + + self.assertTrue(len(lObsGameXmlNew) > 0) + for obsGameXmlNew in lObsGameXmlNew: + expGameXmlNew = "exp_%s" % obsGameXmlNew + self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) + + os.remove("Test_F_GameXmlMaker_path.path") + os.remove("Test_F_GameXmlMaker_set.set") + os.remove("Test_F_GameXmlMaker_chk_map.map") + + os.remove(self._tableFileName) + os.system("ListAndDropTables.py -d Test_F_GameXmlMaker") + + def test_run_step2(self): + self._tableFileName = "annotation_tables.txt" + + self._writeStep2InputTableFile() + self._writeStep2InputXmls() + self._writeStep2InputPathFile() + self._writeStep2InputSetFile() + self._writeStep2InputMapFile() + self._createStep2Tables() + + lObsGameXmlNew = glob.glob("*.gamexml") + + iGameXmlMaker = GameXmlMaker(tablesFileName = self._tableFileName) + iGameXmlMaker.run() + self._writeStep2ExpXmls() + self.assertTrue(len(lObsGameXmlNew) > 0) + for obsGameXmlNew in lObsGameXmlNew: + expGameXmlNew = "exp_%s" % obsGameXmlNew + self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) + + os.remove("Test_F_GameXmlMaker_path.path") + os.remove("Test_F_GameXmlMaker_set.set") + os.remove("Test_F_GameXmlMaker_chk_map.map") + + os.remove(self._tableFileName) + os.system("ListAndDropTables.py -d Test_F_GameXmlMaker") + + def _writeFastaFile(self, inFileName): + f = open(inFileName,'w') + f.write('>seq1\n') + f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') + f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') + f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA\n') + f.write('>seq2\n') + f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') + f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') + f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') + f.write('>seq3\n') + f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n') + f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n') + f.write('>seq4\n') + f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') + f.write('CAGGAATCATGAAGGGTACGACTGTTCG\n') + f.close() + + def _writeStep1ExpectedXmls(self): + f = open("exp_seq1.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>') + f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>') + f.close() + f = open("exp_seq2.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>') + f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>') + f.close() + f = open("exp_seq3.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>') + f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>') + f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>') + f.close() + f = open("exp_seq4.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>') + f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>') + f.close() + + def _createStep2Tables(self): + iDb = DbFactory.createInstance() + iDb.createTable("Test_F_GameXmlMaker_set", "set", "Test_F_GameXmlMaker_set.set", True) + iDb.createTable("Test_F_GameXmlMaker_chk_map", "map", "Test_F_GameXmlMaker_chk_map.map", True) + iDb.createTable("Test_F_GameXmlMaker_path", "path", "Test_F_GameXmlMaker_path.path", True) + iDb.close() + + def _writeStep2InputXmls(self): + f = open("seq1.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>') + f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>') + f.close() + f = open("seq2.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>') + f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>') + f.close() + f = open("seq3.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>') + f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>') + f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>') + f.close() + f = open("seq4.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>') + f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>') + f.close() + + def _writeStep2InputPathFile(self): + f = open("Test_F_GameXmlMaker_path.path", 'w') + f.write("1\tseq1\t1\t10\tTE1\t1\t10\t0\t550\t80.7\n") + f.write("2\tseq1\t15\t50\tTE1\t12\t47\t0\t770\t90.8\n") + f.write("2\tseq1\t55\t70\tTE1\t50\t65\t0\t5410\t97.7\n") + f.write("3\tseq1\t75\t80\tTE2\t10\t15\t0\t8710\t60.0\n") + f.write("4\tseq2\t1\t10\tTE2\t20\t30\t0\t5410\t75.7\n") + f.write("5\tseq3\t1\t120\tTE2\t450\t550\t0\t5410\t75.7\n") + f.close() + + def _writeStep2InputSetFile(self): + f = open("Test_F_GameXmlMaker_set.set", 'w') + f.write("1\tseq1\tseq1\t1\t10\n") + f.write("2\tseq1\tseq1\t15\t50\n") + f.write("3\tseq1\tseq1\t75\t80\n") + f.write("4\tseq2\tseq2\t1\t10\n") + f.write("5\tseq3\tseq3\t1\t120\n") + f.close() + + def _writeStep2InputMapFile(self): + f = open("Test_F_GameXmlMaker_chk_map.map", 'w') + f.write("chunk1\tseq1\t1\t200000\n") + f.write("chunk2\tseq1\t190001\t390000\n") + f.write("chunk3\tseq3\t380001\t580000\n") + f.write("chunk4\tseq4\t570001\t770000\n") + f.write("chunk5\tseq5\t760001\t960000\n") + f.write("chunk6\tseq6\t950001\t1150000\n") + f.write("chunk7\tseq7\t1140001\t1281640\n") + f.close() + + def _writeStep2ExpXmls(self): + f = open("exp_seq1.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>') + f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="1"><name>TE1::1</name>') + f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship><seq_relationship seq="TE1::1" type="subject"><span>') + f.write('<start>1</start><end>10</end></span></seq_relationship><score>80.7</score></result_span></result_set><result_set id="2"><name>TE1::2</name><result_span>') + f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship><seq_relationship seq="TE1::2" type="subject"><span><start>12</start>') + f.write('<end>47</end></span></seq_relationship><score>90.8</score></result_span><result_span><seq_relationship seq="seq1" type="query"><span><start>55</start><end>70</end></span></seq_relationship>') + f.write('<seq_relationship seq="TE1::2" type="subject"><span><start>50</start><end>65</end></span></seq_relationship><score>97.7</score></result_span></result_set><result_set id="3"><name>TE2::3</name>') + f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship><seq_relationship seq="TE2::3" type="subject"><span><start>10</start><end>15</end></span></seq_relationship>') + f.write('<score>60.0</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database>') + f.write('<result_set id="1"><name>seq1::1</name><result_span>') + f.write('<seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship>') + f.write('<seq_relationship seq="seq1::1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set>') + f.write('<result_set id="2"><name>seq1::2</name><result_span>') + f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship>') + f.write('<seq_relationship seq="seq1::2" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set>') + f.write('<result_set id="3"><name>seq1::3</name><result_span>') + f.write('<seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship>') + f.write('<seq_relationship seq="seq1::3" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>') + f.write('<result_set id="-1"><name>chunk1::-1</name>') + f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>200000</end></span></seq_relationship>') + f.write('<seq_relationship seq="chunk1::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set>') + f.write('<result_set id="-1"><name>chunk2::-1</name>') + f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>190001</start><end>390000</end></span></seq_relationship>') + f.write('<seq_relationship seq="chunk2::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship><score>0</score></result_span></result_set></computational_analysis></game>') + f.close() + + f = open("exp_seq2.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>') + f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="4"><name>TE2::4</name>') + f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span>') + f.write('</seq_relationship><seq_relationship seq="TE2::4" type="subject"><span><start>20</start><end>30</end></span></seq_relationship>') + f.write('<score>75.7</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="4"><name>seq2::4</name>') + f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span></seq_relationship>') + f.write('<seq_relationship seq="seq2::4" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database></computational_analysis></game>') + f.close() + + f = open("exp_seq3.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>') + f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>') + f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="5"><name>TE2::5</name>') + f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span>') + f.write('</seq_relationship><seq_relationship seq="TE2::5" type="subject"><span><start>450</start><end>550</end></span></seq_relationship>') + f.write('<score>75.7</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="5"><name>seq3::5</name>') + f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span></seq_relationship>') + f.write('<seq_relationship seq="seq3::5" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>') + f.write('<result_set id="-1"><name>chunk3::-1</name>') + f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>380001</start><end>580000</end></span></seq_relationship>') + f.write('<seq_relationship seq="chunk3::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set></computational_analysis></game>') + f.close() + + f = open("exp_seq4.gamexml", 'w') + f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>') + f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>') + f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database></computational_analysis>') + f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>') + f.write('<result_set id="-1"><name>chunk4::-1</name>') + f.write('<result_span><seq_relationship seq="seq4" type="query"><span><start>570001</start><end>770000</end></span></seq_relationship>') + f.write('<seq_relationship seq="chunk4::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>') + f.write('<score>0</score></result_span></result_set></computational_analysis></game>') + f.close() + + def _writeStep2InputTableFile(self): + f = open(self._tableFileName,'w') + f.write("Test_F_GameXmlMaker_path\tpath\tTest_F_GameXmlMaker_path\n") + f.write("Test_F_GameXmlMaker_set\tset\tTest_F_GameXmlMaker_set\n") + f.write("Test_F_GameXmlMaker_chk_map\tmap\tTest_F_GameXmlMaker_chk_map") + f.close() + +if __name__ == "__main__": + unittest.main() \ No newline at end of file