view commons/tools/tests/Test_F_GameXmlMaker.py @ 18:94ab73e8a190

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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()