Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_VarscanFileForGnpSNP.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os
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3
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4 from commons.core.parsing.VarscanFileForGnpSNP import VarscanFileForGnpSNP
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5 from commons.core.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP
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6
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7 class Test_VarscanFileForGnpSNP(unittest.TestCase):
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9 def test__init__(self):
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10 expFastqFileName = "SR.fastq"
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11 expRefFastaFileName = "ref.fasta"
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12 expTaxonName = "Arabidopsis thaliana"
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13 expVarscanFieldSeparator = "\t"
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14 expVarscanHitsList = []
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16 iVarscanFileForGnpSNP = VarscanFileForGnpSNP("", expFastqFileName, expRefFastaFileName, expTaxonName)
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18 obsFastaqFileName = iVarscanFileForGnpSNP.getFastqFileName()
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19 obsRefFastaFileName = iVarscanFileForGnpSNP.getRefFastaFileName()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 obsTaxonName = iVarscanFileForGnpSNP.getTaxonName()
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21 obsVarscanFieldSeparator = iVarscanFileForGnpSNP.getVarscanFieldSeparator()
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22 obsVarscanHitsList = iVarscanFileForGnpSNP.getVarscanHitsList()
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23
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24 self.assertEquals(expFastqFileName, obsFastaqFileName)
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25 self.assertEquals(expRefFastaFileName, obsRefFastaFileName)
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26 self.assertEquals(expTaxonName, obsTaxonName)
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27 self.assertEquals(expVarscanFieldSeparator, obsVarscanFieldSeparator)
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28 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
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29
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30 def test_parse(self):
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31 varscanFileName = "varscan.tab"
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32 self._writeVarscanFile(varscanFileName)
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33
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34 varscanHit1 = VarscanHitForGnpSNP()
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35 varscanHit1.setChrom('C02HBa0291P19_LR48')
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36 varscanHit1.setPosition('32')
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37 varscanHit1.setRef('C')
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38 varscanHit1.setVar('T')
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39 varscanHit1.setReads1('1')
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40 varscanHit1.setReads2('2')
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41 varscanHit1.setVarFreq('66,67%')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 varscanHit1.setStrands1('1')
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43 varscanHit1.setStrands2('1')
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44 varscanHit1.setQual1('37')
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45 varscanHit1.setQual2('35')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 varscanHit1.setPvalue('0.3999999999999999')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 varscanHit1.setGnpSNPRef("C")
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48 varscanHit1.setGnpSNPVar("T")
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49 varscanHit1.setGnpSNPPosition(32)
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50 varscanHit1.setOccurrence(1)
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51 varscanHit1.setPolymType("SNP")
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52 varscanHit1.setPolymLength(1)
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53
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54 varscanHit2 = VarscanHitForGnpSNP()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 varscanHit2.setChrom('C02HBa0291P19_LR48')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 varscanHit2.setPosition('34')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 varscanHit2.setRef('A')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 varscanHit2.setVar('T')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 varscanHit2.setReads1('1')
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60 varscanHit2.setReads2('2')
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61 varscanHit2.setVarFreq('66,67%')
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62 varscanHit2.setStrands1('1')
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63 varscanHit2.setStrands2('1')
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64 varscanHit2.setQual1('40')
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65 varscanHit2.setQual2('34')
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66 varscanHit2.setPvalue('0.3999999999999999')
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67 varscanHit2.setGnpSNPRef("A")
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68 varscanHit2.setGnpSNPVar("T")
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69 varscanHit2.setGnpSNPPosition(34)
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70 varscanHit2.setOccurrence(1)
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71 varscanHit2.setPolymType("SNP")
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72 varscanHit2.setPolymLength(1)
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73 expVarscanHitsList = [varscanHit1, varscanHit2]
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74
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75 iVarscanFileForGnpSNP = VarscanFileForGnpSNP(varscanFileName, '', '', '')
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76 iVarscanFileForGnpSNP.parse()
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77 obsVarscanHitsList = iVarscanFileForGnpSNP.getVarscanHitsList()
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78 os.remove(varscanFileName)
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79
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80 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
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81
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82 def test_parse_with_same_position_and_chr_and_type(self):
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83 varscanFileName = "varscan.tab"
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84 self._writeVarscanFile_2(varscanFileName)
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85
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86 varscanHit1 = VarscanHitForGnpSNP()
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87 varscanHit1.setChrom('C02HBa0291P19_LR48')
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88 varscanHit1.setPosition('32')
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89 varscanHit1.setRef('C')
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90 varscanHit1.setVar('T')
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91 varscanHit1.setReads1('1')
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92 varscanHit1.setReads2('2')
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93 varscanHit1.setVarFreq('66,67%')
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94 varscanHit1.setStrands1('1')
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95 varscanHit1.setStrands2('1')
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96 varscanHit1.setQual1('37')
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97 varscanHit1.setQual2('35')
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98 varscanHit1.setPvalue('0.3999999999999999')
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99 varscanHit1.setOccurrence(1)
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100 varscanHit1._polymType = "SNP"
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101 varscanHit1._gnpSnp_position = 32
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102 varscanHit1._gnpSnp_ref = "C"
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103 varscanHit1._gnpSnp_var = "T"
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104
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105 varscanHit2 = VarscanHitForGnpSNP()
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106 varscanHit2.setChrom('C02HBa0291P19_LR48')
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107 varscanHit2.setPosition('32')
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108 varscanHit2.setRef('C')
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109 varscanHit2.setVar('A')
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110 varscanHit2.setReads1('1')
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111 varscanHit2.setReads2('2')
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112 varscanHit2.setVarFreq('66,67%')
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113 varscanHit2.setStrands1('1')
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114 varscanHit2.setStrands2('1')
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115 varscanHit2.setQual1('37')
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116 varscanHit2.setQual2('35')
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117 varscanHit2.setPvalue('0.3999999999999999')
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118 varscanHit2.setOccurrence(2)
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119 varscanHit2._polymType = "SNP"
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120 varscanHit2._gnpSnp_position = 32
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121 varscanHit2._gnpSnp_ref = "C"
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122 varscanHit2._gnpSnp_var = "T"
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123
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124 expVarscanHitsOccurence = varscanHit2._occurrence
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125
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
126 iVarscanFileForGnpSNP = VarscanFileForGnpSNP(varscanFileName, '', '', '')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
127 iVarscanFileForGnpSNP.parse()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
128 obsVarscanHitsList = iVarscanFileForGnpSNP.getVarscanHitsList()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
129 obsVarscanHitsOccurence = obsVarscanHitsList[1]._occurrence
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
130 os.remove(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
131
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
132 self.assertEquals(expVarscanHitsOccurence, obsVarscanHitsOccurence)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
133
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
134 def test_parse_with_same_position_and_chr_and_different_type(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
135 varscanFileName = "varscan.tab"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
136 self._writeVarscanFile_3(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
137
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
138 varscanHit1 = VarscanHitForGnpSNP()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
139 varscanHit1.setChrom('C02HBa0291P19_LR48')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
140 varscanHit1.setPosition('32')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
141 varscanHit1.setRef('C')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
142 varscanHit1.setVar('T')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
143 varscanHit1.setReads1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
144 varscanHit1.setReads2('2')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
145 varscanHit1.setVarFreq('66,67%')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
146 varscanHit1.setStrands1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
147 varscanHit1.setStrands2('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
148 varscanHit1.setQual1('37')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
149 varscanHit1.setQual2('35')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
150 varscanHit1.setPvalue('0.3999999999999999')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
151 varscanHit1.setOccurrence(1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
152 varscanHit1._polymType = "SNP"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
153 varscanHit1._gnpSnp_position = 32
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
154 varscanHit1._gnpSnp_ref = "C"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
155 varscanHit1._gnpSnp_var = "T"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
156
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
157 varscanHit2 = VarscanHitForGnpSNP()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
158 varscanHit2.setChrom('C02HBa0291P19_LR48')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
159 varscanHit2.setPosition('32')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
160 varscanHit2.setRef('C')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
161 varscanHit2.setVar('+A')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
162 varscanHit2.setReads1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
163 varscanHit2.setReads2('2')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
164 varscanHit2.setVarFreq('66,67%')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
165 varscanHit2.setStrands1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
166 varscanHit2.setStrands2('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
167 varscanHit2.setQual1('37')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
168 varscanHit2.setQual2('35')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
169 varscanHit2.setPvalue('0.3999999999999999')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
170 varscanHit2.setOccurrence(1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
171 varscanHit2._polymType = "SNP"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
172 varscanHit2._gnpSnp_position = 32
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
173 varscanHit2._gnpSnp_ref = "C"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
174 varscanHit2._gnpSnp_var = "T"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
175
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
176 expVarscanHitsOccurence = varscanHit2._occurrence
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
177
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
178 iVarscanFileForGnpSNP = VarscanFileForGnpSNP(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
179 iVarscanFileForGnpSNP.parse()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
180 obsVarscanHitsList = iVarscanFileForGnpSNP.getVarscanHitsList()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
181 obsVarscanHitsOccurence = obsVarscanHitsList[1].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
182 os.remove(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
183
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
184 self.assertEquals(expVarscanHitsOccurence, obsVarscanHitsOccurence)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
185
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
186 def test_parse_on_occurence(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
187 varscanFileName = "varscan.tab"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
188 self._writeVarscanFile_4(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
189
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
190 expOccurrence1 = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
191 expOccurrence2 = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
192 expOccurrence3 = 2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
193 expOccurrence4 = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
194 expOccurrence5 = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
195 expOccurrence6 = 2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
196
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
197 iVarscanFileForGnpSNP = VarscanFileForGnpSNP(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
198 iVarscanFileForGnpSNP.parse()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
199 obsVarscanHitsList = iVarscanFileForGnpSNP.getVarscanHitsList()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
200 obsOccurrence1 = obsVarscanHitsList[0].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
201 obsOccurrence2 = obsVarscanHitsList[1].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
202 obsOccurrence3 = obsVarscanHitsList[2].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
203 obsOccurrence4 = obsVarscanHitsList[3].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
204 obsOccurrence5 = obsVarscanHitsList[4].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
205 obsOccurrence6 = obsVarscanHitsList[5].getOccurrence()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
206 os.remove(varscanFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
207
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
208 self.assertEquals(expOccurrence1, obsOccurrence1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
209 self.assertEquals(expOccurrence2, obsOccurrence2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
210 self.assertEquals(expOccurrence3, obsOccurrence3)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
211 self.assertEquals(expOccurrence4, obsOccurrence4)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
212 self.assertEquals(expOccurrence5, obsOccurrence5)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
213 self.assertEquals(expOccurrence6, obsOccurrence6)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
214
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
215 def test__eq__notEqual(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 fastqFileName = "SR.fastq"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
217 refFastaFileName = "ref.fasta"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
218 taxonName = "Arabidopsis thaliana"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
219
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 iVarscanFileForGnpSNP1 = VarscanFileForGnpSNP("", fastqFileName, refFastaFileName, taxonName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
222 fastqFileName = "SR.fastq2"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
223 refFastaFileName = "ref.fasta"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 taxonName = "Arabidopsis thaliana"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
225
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
226 iVarscanFileForGnpSNP2 = VarscanFileForGnpSNP("", fastqFileName, refFastaFileName, taxonName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
227
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228 self.assertFalse(iVarscanFileForGnpSNP1 == iVarscanFileForGnpSNP2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
230 def test__eq__equal(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231 fastqFileName = "SR.fastq"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232 refFastaFileName = "ref.fasta"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
233 taxonName = "Arabidopsis thaliana"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
234
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235 varscanHit1 = VarscanHitForGnpSNP()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236 varscanHit1.setChrom('C02HBa0291P19_LR48')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
237 varscanHit1.setPosition('34')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
238 varscanHit1.setRef('A')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 varscanHit1.setVar('T')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
240 varscanHit1.setReads1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241 varscanHit1.setReads2('2')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
242 varscanHit1.setVarFreq('66,67%')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
243 varscanHit1.setStrands1('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
244 varscanHit1.setStrands2('1')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
245 varscanHit1.setQual1('40')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 varscanHit1.setQual2('34')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 varscanHit1.setPvalue('0.3999999999999999')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248 lVarscanHits1 = [varscanHit1]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250 iVarscanFileForGnpSNP1 = VarscanFileForGnpSNP("", fastqFileName, refFastaFileName, taxonName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
251 iVarscanFileForGnpSNP1.setVarscanHitsList(lVarscanHits1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
252
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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253 varscanHit2 = VarscanHitForGnpSNP()
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254 varscanHit2.setChrom('C02HBa0291P19_LR48')
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255 varscanHit2.setPosition('34')
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256 varscanHit2.setRef('A')
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257 varscanHit2.setVar('T')
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258 varscanHit2.setReads1('1')
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259 varscanHit2.setReads2('2')
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260 varscanHit2.setVarFreq('66,67%')
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261 varscanHit2.setStrands1('1')
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262 varscanHit2.setStrands2('1')
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263 varscanHit2.setQual1('40')
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264 varscanHit2.setQual2('34')
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265 varscanHit2.setPvalue('0.3999999999999999')
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266 lVarscanHits2 = [varscanHit2]
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267
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268 iVarscanFileForGnpSNP2 = VarscanFileForGnpSNP("", fastqFileName, refFastaFileName, taxonName)
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269 iVarscanFileForGnpSNP2.setVarscanHitsList(lVarscanHits2)
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270
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271 self.assertTrue(iVarscanFileForGnpSNP1 == iVarscanFileForGnpSNP2)
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272
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273 def _writeVarscanFile(self, varscanFileName):
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274 varscanFile = open(varscanFileName, 'w')
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275 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
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276 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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277 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
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278 varscanFile.close()
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279
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280 def _writeVarscanFile_2(self, varscanFileName):
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281 varscanFile = open(varscanFileName, 'w')
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282 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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283 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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284 varscanFile.write("C02HBa0291P19_LR48\t32\tA\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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285 varscanFile.close()
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286
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287 def _writeVarscanFile_3(self, varscanFileName):
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288 varscanFile = open(varscanFileName, 'w')
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289 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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291 varscanFile.write("C02HBa0291P19_LR48\t32\tC\t+A\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 varscanFile.close()
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293
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294 def _writeVarscanFile_4(self, varscanFileName):
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295 varscanFile = open(varscanFileName, 'w')
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296 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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297 varscanFile.write("seqname\t2\tA\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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298 varscanFile.write("seqname\t4\tC\tG\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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299 varscanFile.write("seqname\t4\tC\tA\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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300 varscanFile.write("seqname\t8\tT\tA\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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301 varscanFile.write("chrom\t4\tC\tG\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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302 varscanFile.write("chrom\t4\tC\tA\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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303 varscanFile.close()
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304 if __name__ == "__main__":
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305 unittest.main()