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
  27     def setUp(self):
  28         pass
  29
  30
  31     def tearDown(self):
  32         pass
  33
  34
  35     def testChkSNPFile(self):
  36         inputFileName = "testChkSNP_input.txt"
  37         infile = open(inputFileName, "w")
  38         infile.write("# header line\n")
  39         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
  40         infile.write("%s\n" % snpEntry)
  41         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
  42         infile.write("%s\n" % snpEntry)
  43         infile.close()
  44
  45         outputFileName = "testChkSNP_output.txt"
  46
  47         chksnp.chkSNPFile(self.snpDB, inputFileName, outputFileName)
  48         outfile = open(outputFileName, "r")
  49         line = outfile.readline()
  50         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  51         self.assertEquals(result, line)
  52         result = "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A\n"
  53         line = outfile.readline()
  54         self.assertEquals(result, line)
  55         outfile.close()
  56         os.remove(outputFileName)
  57
  58         chksnp.chkSNPFile(self.snpDB, inputFileName, outputFileName, snpDBList=[self.altSnpDB])
  59         outfile = open(outputFileName, "r")
  60         line = outfile.readline()
  61         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  62         self.assertEquals(result, line)
  63         result = "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown\n"
  64         line = outfile.readline()
  65         self.assertEquals(result, line)
  66         outfile.close()
  67
  68         os.remove(inputFileName)
  69         os.remove(outputFileName)
  70
  71
  72     def testMain(self):
  73         inputFileName = "testChkSNP_input.txt"
  74         infile = open(inputFileName, "w")
  75         infile.write("# header line\n")
  76         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
  77         infile.write("%s\n" % snpEntry)
  78         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
  79         infile.write("%s\n" % snpEntry)
  80         infile.close()
  81
  82         outputFileName = "testChkSNP_output.txt"
  83
  84         argv = ["chksnp", self.snpDB, inputFileName, outputFileName]
  85         chksnp.main(argv)
  86         outfile = open(outputFileName, "r")
  87         line = outfile.readline()
  88         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
  89         self.assertEquals(result, line)
  90         result = "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A\n"
  91         line = outfile.readline()
  92         self.assertEquals(result, line)
  93         outfile.close()
  94         os.remove(outputFileName)
  95
  96     def testChkSNP(self):
  97         snpPropertiesList = []
  98         dbList = [self.snpDB]
  99         self.assertEquals({}, chksnp.chkSNP(dbList, snpPropertiesList))
 100
 101         snpPropertiesList = ["# header line"]
 102         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
 103         snpPropertiesList.append(snpEntry)
 104         snpEntry = string.join(["foo2", "foo2", "chr1", "81752"], "\t")
 105         snpPropertiesList.append(snpEntry)
 106         dbList = [self.snpDB, self.altSnpDB]
 107         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 108                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 109         self.assertEquals(result, chksnp.chkSNP(dbList, snpPropertiesList))
 110
 111
 112     def testGetSNPLocationInfo(self):
 113         snpPropertiesList = []
 114         snpEntry = string.join(["foo", "foo", "chr1", "20"], "\t")
 115         snpPropertiesList.append(snpEntry)
 116         snpLocationList, snpDict = chksnp.getSNPLocationInfo(snpPropertiesList)
 117         self.assertEquals([("1", 20)], snpLocationList)
 118         self.assertEquals({("1", 20): "foo\tfoo\tchr1\t20"}, snpDict)
 119
 120         snpPropertiesList = ["# header line"]
 121         snpEntry = string.join(["foo", "foo", "chr1", "20"], "\t")
 122         snpPropertiesList.append(snpEntry)
 123         snpLocationList, snpDict = chksnp.getSNPLocationInfo(snpPropertiesList)
 124         self.assertEquals([("1", 20)], snpLocationList)
 125         self.assertEquals({("1", 20): "foo\tfoo\tchr1\t20"}, snpDict)
 126
 127
 128     def testDoNotProcessLine(self):
 129         self.assertTrue(chksnp.doNotProcessLine("#anything"))
 130         self.assertFalse(chksnp.doNotProcessLine("line to process"))
 131
 132
 133     def testAnnotateSNPFromDB(self):
 134         snpLocationList = [("1", 691), ("1", 81752)]
 135         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 136                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 137         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 138                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A"}
 139         self.assertEquals(result, chksnp.annotateSNPFromDB(snpLocationList, snpDict, self.snpDB))
 140
 141         snpLocationList = [("1", 691), ("1", 81752)]
 142         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 143                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 144         result = {("1", 691): "foo\tfoo\tchr1\t691\tN\\A\tN\\A",
 145                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 146         self.assertEquals(result, chksnp.annotateSNPFromDB(snpLocationList, snpDict, self.altSnpDB))
 147
 148
 149     def testAnnotateSNPFromDBList(self):
 150         snpLocationList = []
 151         snpDict = {}
 152         dbList = [self.snpDB]
 153         self.assertEquals({}, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 154
 155         snpLocationList = [("1", 21)]
 156         snpDict = {("1", 21): "foo\tfoo\tchr1\t21"}
 157         dbList = [self.snpDB]
 158         result = {("1", 21): "foo\tfoo\tchr1\t21\tN\\A\tN\\A"}
 159         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 160
 161         snpLocationList = [("1", 21)]
 162         snpDict = {("1", 21): "foo\tfoo\tchr1\t21"}
 163         dbList = [self.snpDB]
 164         result = {("1", 21): "foo\tfoo\tchr1\t21\tN\\A\tN\\A"}
 165         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList, cachePages=10000))
 166
 167         snpLocationList = [("1", 691)]
 168         snpDict = {("1", 691): "foo\tfoo\tchr1\t691"}
 169         dbList = [self.snpDB]
 170         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown"}
 171         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 172
 173         snpLocationList = [("1", 691), ("1", 81752)]
 174         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 175                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 176         dbList = [self.snpDB]
 177         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 178                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\tN\\A\tN\\A"}
 179         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 180
 181         snpLocationList = [("1", 691), ("1", 81752)]
 182         snpDict = {("1", 691): "foo\tfoo\tchr1\t691",
 183                    ("1", 81752): "foo2\tfoo2\tchr1\t81752"}
 184         dbList = [self.snpDB, self.altSnpDB]
 185         result = {("1", 691): "foo\tfoo\tchr1\t691\trs10218492\tunknown",
 186                   ("1", 81752): "foo2\tfoo2\tchr1\t81752\trs17160650\tunknown"}
 187         self.assertEquals(result, chksnp.annotateSNPFromDBList(snpLocationList, snpDict, dbList))
 188
 189
 190 def suite():
 191     suite = unittest.TestSuite()
 192     suite.addTest(unittest.makeSuite(TestChksnp))
 193
 194     return suite
 195
 196
 197 if __name__ == "__main__":
 198     #import sys;sys.argv = ['', 'Test.testName']
 199     unittest.main()