test/testChksnp.py

   1 '''
   2 Created on Aug 25, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import string
   8 import os
   9 from erange import chksnp
  10
  11 dbPath = "/Users/sau/work/snpdb/hg18"
  12
  13 class TestChksnp(unittest.TestCase):
  14     """ First entries from snpDB using select func, name, start, stop from snp where chrom="1" limit 4;
  15         unknown|rs10218492|690|691
  16         unknown|rs10218493|766|767
  17         unknown|rs10218527|789|790
  18         unknown|rs28853987|800|801
  19
  20         Entry from altSnpDB not in sndDB
  21         unknown|rs17160650|81751|81752
  22     """
  23
  24     snpDB = "%s/dbSNP128.db" % dbPath
  25     altSnpDB = "%s/snp129cDNA.db" % dbPath
  26     inputFileName = "testChkSNP_input.txt"
  27     outputFileName = "testChkSNP_output.txt"
  28
  29     def setUp(self):
  30         pass
  31
  32
  33     def tearDown(self):
  34         pass
  35
  36
  37     def testChkSNPFile(self):
  38         infile = open(self.inputFileName, "w")
  39         infile.write("# header line\n")
  40         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
  41         infile.write("%s\n" % snpEntry)
  42         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
  43         infile.write("%s\n" % snpEntry)
  44         infile.close()
  45
  46         chksnp.chkSNPFile(self.snpDB, self.inputFileName, self.outputFileName)
  47         outfile = open(self.outputFileName, "r")
  48         line = outfile.readline()
  49         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  50         self.assertEquals(result, line)
  51         result = "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A\n"
  52         line = outfile.readline()
  53         self.assertEquals(result, line)
  54         outfile.close()
  55         os.remove(self.outputFileName)
  56
  57         chksnp.chkSNPFile(self.snpDB, self.inputFileName, self.outputFileName, snpDBList=[self.altSnpDB])
  58         outfile = open(self.outputFileName, "r")
  59         line = outfile.readline()
  60         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  61         self.assertEquals(result, line)
  62         result = "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown\n"
  63         line = outfile.readline()
  64         self.assertEquals(result, line)
  65         outfile.close()
  66
  67         os.remove(self.inputFileName)
  68         os.remove(self.outputFileName)
  69
  70
  71     def testMain(self):
  72         infile = open(self.inputFileName, "w")
  73         infile.write("# header line\n")
  74         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
  75         infile.write("%s\n" % snpEntry)
  76         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
  77         infile.write("%s\n" % snpEntry)
  78         infile.close()
  79
  80         argv = ["chksnp", self.snpDB, self.inputFileName, self.outputFileName]
  81         chksnp.main(argv)
  82         outfile = open(self.outputFileName, "r")
  83         line = outfile.readline()
  84         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  85         self.assertEquals(result, line)
  86         result = "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A\n"
  87         line = outfile.readline()
  88         self.assertEquals(result, line)
  89         outfile.close()
  90
  91         os.remove(self.inputFileName)
  92         os.remove(self.outputFileName)
  93
  94
  95     def testChkSNP(self):
  96         snpPropertiesList = []
  97         dbList = [self.snpDB]
  98         self.assertEquals({}, chksnp.chkSNP(dbList, snpPropertiesList))
  99
 100         snpPropertiesList = ["# header line"]
 101         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
 102         snpPropertiesList.append(snpEntry)
 103         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
 104         snpPropertiesList.append(snpEntry)
 105         dbList = [self.snpDB, self.altSnpDB]
 106         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 107                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 108         self.assertEquals(result, chksnp.chkSNP(dbList, snpPropertiesList))
 109
 110
 111     def testGetSNPLocationInfo(self):
 112         snpPropertiesList = []
 113         snpEntry = string.join(["foo", "foo", "chr1", "20"], "\t")
 114         snpPropertiesList.append(snpEntry)
 115         snpLocationList, snpDict = chksnp.getSNPLocationInfo(snpPropertiesList)
 116         self.assertEquals([("1", 20)], snpLocationList)
 117         self.assertEquals({("1", 20): "foo\tfoo\tchr1\t20"}, snpDict)
 118
 119         snpPropertiesList = ["# header line"]
 120         snpEntry = string.join(["foo", "foo", "chr1", "20"], "\t")
 121         snpPropertiesList.append(snpEntry)
 122         snpLocationList, snpDict = chksnp.getSNPLocationInfo(snpPropertiesList)
 123         self.assertEquals([("1", 20)], snpLocationList)
 124         self.assertEquals({("1", 20): "foo\tfoo\tchr1\t20"}, snpDict)
 125
 126
 127     def testDoNotProcessLine(self):
 128         self.assertTrue(chksnp.doNotProcessLine("#anything"))
 129         self.assertFalse(chksnp.doNotProcessLine("line to process"))
 130
 131
 132     def testAnnotateSNPFromDB(self):
 133         snpLocationList = [("1", 691), ("1", 81752)]
 134         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 135                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 136         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 137                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A"}
 138         self.assertEquals(result, chksnp.annotateSNPFromDB(snpLocationList, snpDict, self.snpDB))
 139
 140         snpLocationList = [("1", 691), ("1", 81752)]
 141         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 142                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 143         result = {("1", 691): "foo\tfoo\tchr1\t691\tN\\A\tN\\A",
 144                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 145         self.assertEquals(result, chksnp.annotateSNPFromDB(snpLocationList, snpDict, self.altSnpDB))
 146
 147
 148     def testAnnotateSNPFromDBList(self):
 149         snpLocationList = []
 150         snpDict = {}
 151         dbList = [self.snpDB]
 152         self.assertEquals({}, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 153
 154         snpLocationList = [("1", 21)]
 155         snpDict = {("1", 21): "foo\tfoo\tchr1\t21"}
 156         dbList = [self.snpDB]
 157         result = {("1", 21): "foo\tfoo\tchr1\t21\tN\\A\tN\\A"}
 158         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 159
 160         snpLocationList = [("1", 21)]
 161         snpDict = {("1", 21): "foo\tfoo\tchr1\t21"}
 162         dbList = [self.snpDB]
 163         result = {("1", 21): "foo\tfoo\tchr1\t21\tN\\A\tN\\A"}
 164         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList, cachePages=10000))
 165
 166         snpLocationList = [("1", 691)]
 167         snpDict = {("1", 691): "foo\tfoo\tchr1\t691"}
 168         dbList = [self.snpDB]
 169         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown"}
 170         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 171
 172         snpLocationList = [("1", 691), ("1", 81752)]
 173         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 174                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 175         dbList = [self.snpDB]
 176         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 177                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A"}
 178         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 179
 180         snpLocationList = [("1", 691), ("1", 81752)]
 181         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 182                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 183         dbList = [self.snpDB, self.altSnpDB]
 184         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 185                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 186         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 187
 188
 189 def suite():
 190     suite = unittest.TestSuite()
 191     suite.addTest(unittest.makeSuite(TestChksnp))
 192
 193     return suite
 194
 195
 196 if __name__ == "__main__":
 197     #import sys;sys.argv = ['', 'Test.testName']
 198     unittest.main()