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view commons/core/parsing/test/Test_F_VarscanToVCF.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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import unittest
import os
from commons.core.parsing.VarscanToVCF import VarscanToVCF
from commons.core.utils.FileUtils import FileUtils

class Test_F_VarscanToVCF(unittest.TestCase):
    
    def setUp(self):
        self.emptyVarscanFileName = "emptyfile.varscan"
        self.varscanFileName = "%s/commons/core/parsing/test/data/sampleForTestVarscanToVCF.varscan" % os.environ["REPET_PATH"]
        self.expVCFFileName = "expVCF.vcf"
        self.obsVCFFileName = "obsVCF.vcf"
        
    def tearDown(self):
        if os.path.exists(self.emptyVarscanFileName):
            os.remove(self.emptyVarscanFileName)
        os.remove(self.expVCFFileName)
        os.remove(self.obsVCFFileName)
        
    def test_VarscanToVCF(self):
        self._writeExpOutputFile()
        iVarscanFile = VarscanToVCF(self.varscanFileName, self.obsVCFFileName, doClean = True)
        iVarscanFile.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self.expVCFFileName, self.obsVCFFileName))
       
    def test_VarscanToVCF_empty(self):
        self._writeInputFile_empty()
        self._writeExpOutputFile_empty()
        iVarscanFile = VarscanToVCF(self.emptyVarscanFileName, self.obsVCFFileName, doClean = True)
        iVarscanFile.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self.expVCFFileName, self.obsVCFFileName))
           
    def _writeInputFile_empty(self):
        with open(self.emptyVarscanFileName, "w") as varscanFileName:
            varscanFileName.write("Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n")
            
    def _writeExpOutputFile_empty(self):
        with open(self.expVCFFileName, "w") as vcfFileName:   
            vcfFileName.write("##fileformat=VCFv4.1\n")
            vcfFileName.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
   
    def _writeExpOutputFile(self):
        with open(self.expVCFFileName, "w") as vcfFileName:
            vcfFileName.write("##fileformat=VCFv4.1\n")
            vcfFileName.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
            vcfFileName.write("chr1\t10759\t.\tC\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=47\n")
            vcfFileName.write("chr1\t12438\t.\tC\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=62;ABQ=42\n")
            vcfFileName.write("chr1\t17432\t.\tA\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=55;ABQ=37\n")
            vcfFileName.write("chr1\t20391\t.\tA\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=56;ABQ=37\n")
            vcfFileName.write("chr1\t21207\t.\tT\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=55;ABQ=41\n")
            vcfFileName.write("chr1\t26057\t.\tT\tG\t0.087739243\t.\tAF=0.1538;DP=13;RBQ=60;ABQ=37\n")
            vcfFileName.write("chr1\t36838\t.\tT\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=61;ABQ=36\n")
            vcfFileName.write("chr1\t37751\t.\tA\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=42\n")
            vcfFileName.write("chr1\t43500\t.\tC\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t50481\t.\tA\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=60;ABQ=40\n")
            vcfFileName.write("chr1\t106849\t.\tC\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t108726\t.\tT\tA\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=50;ABQ=41\n")
            vcfFileName.write("chr1\t114204\t.\tG\tC\t0.087739243\t.\tAF=0.3333;DP=6;RBQ=60;ABQ=39\n")
            vcfFileName.write("chr1\t115030\t.\tA\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=57;ABQ=41\n")
            vcfFileName.write("chr1\t116173\t.\tA\tG\t0.087739243\t.\tAF=0.2222;DP=9;RBQ=58;ABQ=39\n")
            vcfFileName.write("chr1\t118433\t.\tG\tC\t0.087739243\t.\tAF=0.1429;DP=7;RBQ=64;ABQ=50\n")
            vcfFileName.write("chr1\t119042\t.\tA\tG\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=55;ABQ=51\n")
            vcfFileName.write("chr1\t139219\t.\tA\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=46\n")
            vcfFileName.write("chr1\t140710\t.\tA\tG\t0.087739243\t.\tAF=0.1818;DP=11;RBQ=63;ABQ=41\n")
            vcfFileName.write("chr1\t144419\t.\tT\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=63;ABQ=39\n")
            vcfFileName.write("chr1\t146099\t.\tG\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=64;ABQ=38\n")
            vcfFileName.write("chr1\t146435\t.\tT\tC\t0.087739243\t.\tAF=0.3889;DP=18;RBQ=60;ABQ=24\n")
            vcfFileName.write("chr1\t147232\t.\tA\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=64;ABQ=39\n")
            vcfFileName.write("chr1\t158703\t.\tA\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=60;ABQ=55\n")
            vcfFileName.write("chr1\t166732\t.\tA\tT\t0.087739243\t.\tAF=0.3333;DP=6;RBQ=62;ABQ=24\n")
            vcfFileName.write("chr1\t179887\t.\tC\tA\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=39\n")
            vcfFileName.write("chr1\t185971\t.\tA\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=55;ABQ=40\n")
            vcfFileName.write("chr1\t211074\t.\tA\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t219573\t.\tG\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=61;ABQ=41\n")
            vcfFileName.write("chr1\t229396\t.\tC\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=57;ABQ=39\n")
            vcfFileName.write("chr1\t236388\t.\tT\tG\t0.087739243\t.\tAF=0.2000;DP=10;RBQ=52;ABQ=32\n")
            vcfFileName.write("chr1\t245990\t.\tG\tC\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=61;ABQ=46\n")
            vcfFileName.write("chr1\t249155\t.\tC\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=62;ABQ=37\n")
            vcfFileName.write("chr1\t261257\t.\tT\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=60;ABQ=39\n")
            vcfFileName.write("chr1\t274692\t.\tA\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=63;ABQ=39\n")
            vcfFileName.write("chr1\t283468\t.\tG\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=63;ABQ=45\n")
            vcfFileName.write("chr1\t284288\t.\tT\tA\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=39\n")
            vcfFileName.write("chr1\t286983\t.\tT\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=64;ABQ=37\n")
            vcfFileName.write("chr1\t287378\t.\tC\tA\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=37\n")
            vcfFileName.write("chr1\t302928\t.\tA\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=64;ABQ=38\n")
            vcfFileName.write("chr1\t305952\t.\tC\tA\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=38\n")
            vcfFileName.write("chr1\t307932\t.\tT\tC\t0.087739243\t.\tAF=0.2000;DP=5;RBQ=65;ABQ=42\n")
            vcfFileName.write("chr1\t317422\t.\tG\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=57;ABQ=40\n")
            vcfFileName.write("chr1\t321480\t.\tA\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=64;ABQ=38\n")
            vcfFileName.write("chr1\t322307\t.\tA\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=37\n")
            vcfFileName.write("chr1\t328326\t.\tG\tC\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=62;ABQ=52\n")
            vcfFileName.write("chr1\t333138\t.\tT\tG\t0.087739243\t.\tAF=0.4000;DP=5;RBQ=63;ABQ=24\n")
            vcfFileName.write("chr1\t333388\t.\tT\tC\t0.087739243\t.\tAF=0.2000;DP=5;RBQ=64;ABQ=43\n")
            vcfFileName.write("chr1\t335592\t.\tT\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=58;ABQ=39\n")
            vcfFileName.write("chr1\t336572\t.\tC\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=58;ABQ=38\n")
            vcfFileName.write("chr1\t347396\t.\tT\tG\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=62;ABQ=52\n")
            vcfFileName.write("chr1\t359080\t.\tT\tG\t0.087739243\t.\tAF=0.2000;DP=5;RBQ=61;ABQ=42\n")
            vcfFileName.write("chr1\t360223\t.\tA\tT\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=54;ABQ=52\n")
            vcfFileName.write("chr1\t361047\t.\tT\tG\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=62;ABQ=50\n")
            vcfFileName.write("chr1\t366048\t.\tA\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=39\n")
            vcfFileName.write("chr1\t368105\t.\tA\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=55;ABQ=40\n")
            vcfFileName.write("chr1\t373782\t.\tT\tA\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=41\n")
            vcfFileName.write("chr1\t378159\t.\tG\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=63;ABQ=41\n")
            vcfFileName.write("chr1\t383945\t.\tC\tG\t0.087739243\t.\tAF=0.1111;DP=9;RBQ=58;ABQ=57\n")
            vcfFileName.write("chr1\t389461\t.\tA\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=36\n")
            vcfFileName.write("chr1\t396860\t.\tG\tT\t0.087739243\t.\tAF=0.2000;DP=5;RBQ=65;ABQ=43\n")
            vcfFileName.write("chr1\t397170\t.\tA\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=36\n")
            vcfFileName.write("chr1\t399939\t.\tA\tC\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=63;ABQ=46\n")
            vcfFileName.write("chr1\t400733\t.\tG\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=41\n")
            vcfFileName.write("chr1\t401165\t.\tA\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=41\n")
            vcfFileName.write("chr1\t406774\t.\tT\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=58;ABQ=39\n")
            vcfFileName.write("chr1\t417293\t.\tC\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=55\n")
            vcfFileName.write("chr1\t417723\t.\tG\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=49\n")
            vcfFileName.write("chr1\t420308\t.\tC\tA\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=36\n")
            vcfFileName.write("chr1\t435579\t.\tC\tT\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=40\n")
            vcfFileName.write("chr1\t437183\t.\tG\tA\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=39\n")
            vcfFileName.write("chr1\t437194\t.\tA\tT\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=41\n")
            vcfFileName.write("chr1\t438866\t.\tG\tC\t0.087739243\t.\tAF=0.1429;DP=7;RBQ=62;ABQ=52\n")
            vcfFileName.write("chr1\t446237\t.\tT\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=39\n")
            vcfFileName.write("chr1\t446308\t.\tA\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=50;ABQ=38\n")
            vcfFileName.write("chr1\t452322\t.\tA\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=36\n")
            vcfFileName.write("chr1\t462721\t.\tT\tG\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=58;ABQ=41\n")
            vcfFileName.write("chr1\t477145\t.\tC\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=64;ABQ=39\n")
            vcfFileName.write("chr1\t493772\t.\tG\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t498962\t.\tC\tA\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=41\n")
            vcfFileName.write("chr1\t510532\t.\tT\tC\t0.087739243\t.\tAF=0.2000;DP=5;RBQ=64;ABQ=53\n")
            vcfFileName.write("chr1\t516369\t.\tT\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=34;ABQ=40\n")
            vcfFileName.write("chr1\t523631\t.\tG\tT\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=64;ABQ=40\n")
            vcfFileName.write("chr1\t524680\t.\tC\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=41\n")
            vcfFileName.write("chr1\t525898\t.\tT\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=62;ABQ=49\n")
            vcfFileName.write("chr1\t526118\t.\tA\tC\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=61;ABQ=50\n")
            vcfFileName.write("chr1\t535762\t.\tC\tT\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=42\n")
            vcfFileName.write("chr1\t543235\t.\tG\tT\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=45;ABQ=41\n")
            vcfFileName.write("chr1\t550086\t.\tT\tC\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=50;ABQ=41\n")
            vcfFileName.write("chr1\t550508\t.\tA\tG\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=55;ABQ=40\n")
            vcfFileName.write("chr1\t551143\t.\tG\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=39\n")
            vcfFileName.write("chr1\t552924\t.\tA\tG\t0.087739243\t.\tAF=0.2500;DP=8;RBQ=62;ABQ=38\n")
            vcfFileName.write("chr1\t553541\t.\tA\tG\t0.087739243\t.\tAF=0.1250;DP=8;RBQ=65;ABQ=52\n")
            vcfFileName.write("chr1\t560806\t.\tT\tC\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=65;ABQ=49\n")
            vcfFileName.write("chr1\t562736\t.\tC\tG\t0.087739243\t.\tAF=0.1667;DP=6;RBQ=64;ABQ=52\n")
            vcfFileName.write("chr1\t563224\t.\tT\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=51;ABQ=39\n")
            vcfFileName.write("chr1\t564217\t.\tT\tA\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=62;ABQ=40\n")
            vcfFileName.write("chr1\t567288\t.\tC\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t569652\t.\tT\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=48;ABQ=42\n")
            vcfFileName.write("chr1\t570280\t.\tG\tT\t0.087739243\t.\tAF=0.1250;DP=8;RBQ=60;ABQ=53\n")
            vcfFileName.write("chr1\t582185\t.\tT\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=63;ABQ=40\n")
            vcfFileName.write("chr1\t582453\t.\tG\tC\t0.087739243\t.\tAF=0.5000;DP=2;RBQ=65;ABQ=38\n")
            vcfFileName.write("chr1\t583477\t.\tT\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=62;ABQ=39\n")
            vcfFileName.write("chr1\t584179\t.\tG\tT\t0.087739243\t.\tAF=0.2500;DP=4;RBQ=65;ABQ=41\n")
            vcfFileName.write("chr1\t589074\t.\tG\tC\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=36\n")
            vcfFileName.write("chr1\t596641\t.\tC\tG\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=65;ABQ=40\n")
            vcfFileName.write("chr1\t599263\t.\tG\tT\t0.087739243\t.\tAF=0.3333;DP=3;RBQ=60;ABQ=38\n")
                     
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000Gchr1    10759    .    C    T    0.087739243    .    AF=33.33%;DP=3enomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
            
if __name__ == "__main__":
    unittest.main()