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change test data to match code changes
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@sowmyaiyer
sowmyaiyer committed Feb 7, 2018
1 parent bc5eef8 commit c23bc92
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Showing 4 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion test/data/filtered/EMX1_backgroundFiltered.txt
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chr1:236259170-236261754 1473 1486 chr1:236259170-236261754_1486_7 EMX1.sam 8 1:236259170-236261754 1486 ATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGT 7 0 7 0.0 33 0 33 0.0 2 5 3.16227766017 7.11617874986 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
1:236259170-236261754 1473 1486 chr1:236259170-236261754_1486_7 EMX1.sam 1486 ATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGT 7 0 7 0.0 33 0 33 0.0 2 5 3.16227766017 7.116178749862878 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
14 changes: 7 additions & 7 deletions test/data/identified/EMX1_identifiedOfftargets.txt
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#BED Chromosome BED Min.Position BED Max.Position BED Name Filename WindowIndex Chromosome Position Sequence +.mi -.mi bi.sum.mi bi.geometric_mean.mi +.total -.total total.sum total.geometric_mean primer1.mi primer2.mi primer.geometric_mean position.stdev Off-Target Sequence Mismatches Length BED off-target Chromosome BED off-target start BED off-target end BED off-target name BED Score Strand Cells Targetsite Target Sequence Realigned Target Sequence
chr15:44108746-44110769 1007 1025 chr15:44108746-44110769_1017_189 EMX1.sam 1 15:44108746-44110769 1017 GTAGACAAGAGTCTAAGCAGAAGAAGAAGAGAGCCACTACCCAACCATCT 116 73 189 92.0217365626 258 148 406 195.407267009 96 80 87.6356092008 4.93163133804 GAGTCTAAGCAGAAGAAGAAGAG 3 23 chr15:44108746-44110769 1000 1023 chr15:44108746-44110769_1017_189 1 + EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG GAGTCCGAGCAGAAGAAGAANGG
chr1:236259170-236261754 1465 1486 chr1:236259170-236261754_1486_7 EMX1.sam 8 1:236259170-236261754 1486 ATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGT 7 0 7 0.0 33 0 33 0.0 2 5 3.16227766017 7.11617874986 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
chr1:236259170-236261754 1531 1539 chr1:236259170-236261754_1531_5 EMX1.sam 10 1:236259170-236261754 1531 GGGGTGACTCAGAATGGAGCAGGTGACCAGGGGAATAGACGTTAACTACT 0 5 5 0.0 0 5 5 0.0 1 2 1.41421356237 2.94745653064 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
chr2:73159981-73162004 1008 1024 chr2:73159981-73162004_1017_489 EMX1.sam 12 2:73159981-73162004 1017 AAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGG 243 246 489 244.49539873 619 541 1160 578.68730762 236 231 233.486616319 4.71036092035 GAGTCCGAGCAGAAGAAGAAGGG 0 23 chr2:73159981-73162004 1000 1023 chr2:73159981-73162004_1017_489 1 + EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG GAGTCCGAGCAGAAGAAGAANGG
chr3:197899267-197901348 1075 1081 chr3:197899267-197901348_1080_10 EMX1.sam 16 3:197899267-197901348 1080 TTAGGGTTAGGGTTAGGGTTAGGGTTCGGGTTTAGGGTTCAGGTTTATGG 0 10 10 0.0 0 32 32 0.0 9 1 3.0 2.5495097568 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
chr6:9117792-9119815 1007 1007 chr6:9117792-9119815_1007_4 EMX1.sam 18 6:9117792-9119815 1007 ATGTCCTCAGAGTTCTGTCCATTCTTCTTCTGCTCAGACGTTTTGTCTGA 1 3 4 1.73205080757 1 9 10 3.0 2 2 2.0 0.0 ACGTCTGAGCAGAAGAAGAATGG 3 23 chr6:9117792-9119815 1000 1023 chr6:9117792-9119815_1007_4 1 - EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG GAGTCCGAGCAGAAGAAGAANGG
Chromosome Min.Position Max.Position Name Filename Position WindowSequence +.mi -.mi bi.sum.mi bi.geometric_mean.mi +.total -.total total.sum total.geometric_mean primer1.mi primer2.mi primer.geometric_mean position.stdev Site_SubstitutionsOnly.Sequence Site_SubstitutionsOnly.NumSubstitutions Site_SubstitutionsOnly.Strand Site_SubstitutionsOnly.Start Site_SubstitutionsOnly.End Site_GapsAllowed.Sequence Site_GapsAllowed.Length Site_GapsAllowed.Score Site_GapsAllowed.Substitutions Site_GapsAllowed.Insertions Site_GapsAllowed.Deletions Site_GapsAllowed.Strand Site_GapsAllowed.Start Site_GapsAllowed.End Cell Targetsite TargetSequence RealignedTargetSequence
15:44108746-44110769 1007 1025 chr15:44108746-44110769_1017_189 EMX1.sam 1017 GTAGACAAGAGTCTAAGCAGAAGAAGAAGAGAGCCACTACCCAACCATCT 116 73 189 92.0217365626 258 148 406 195.407267009 96 80 87.6356092008 4.931631338038255 GAGTCTAAGCAGAAGAAGAAGAG 3 + 1000 1023 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
1:236259170-236261754 1465 1486 chr1:236259170-236261754_1486_7 EMX1.sam 1486 ATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGT 7 0 7 0.0 33 0 33 0.0 2 5 3.16227766017 7.116178749862878 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
1:236259170-236261754 1531 1539 chr1:236259170-236261754_1531_5 EMX1.sam 1531 GGGGTGACTCAGAATGGAGCAGGTGACCAGGGGAATAGACGTTAACTACT 0 5 5 0.0 0 5 5 0.0 1 2 1.41421356237 2.947456530637899 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
2:73159981-73162004 1008 1024 chr2:73159981-73162004_1017_489 EMX1.sam 1017 AAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGG 243 246 489 244.49539873 619 541 1160 578.68730762 236 231 233.486616319 4.710360920354193 GAGTCCGAGCAGAAGAAGAAGGG 0 + 1000 1023 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
3:197899267-197901348 1075 1081 chr3:197899267-197901348_1080_10 EMX1.sam 1080 TTAGGGTTAGGGTTAGGGTTAGGGTTCGGGTTTAGGGTTCAGGTTTATGG 0 10 10 0.0 0 32 32 0.0 9 1 3.0 2.5495097567963922 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
6:9117792-9119815 1007 1007 chr6:9117792-9119815_1007_4 EMX1.sam 1007 ATGTCCTCAGAGTTCTGTCCATTCTTCTTCTGCTCAGACGTTTTGTCTGA 1 3 4 1.73205080757 1 9 10 3.0 2 2 2.0 0.0 ACGTCTGAGCAGAAGAAGAATGG 3 - 1000 1023 EMX_site1 EMX1 GAGTCCGAGCAGAAGAAGAANGG none
8 changes: 4 additions & 4 deletions test/data/identified/control_identifiedOfftargets.txt
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#BED Chromosome BED Min.Position BED Max.Position BED Name Filename WindowIndex Chromosome Position Sequence +.mi -.mi bi.sum.mi bi.geometric_mean.mi +.total -.total total.sum total.geometric_mean primer1.mi primer2.mi primer.geometric_mean position.stdev Off-Target Sequence Mismatches Length BED off-target Chromosome BED off-target start BED off-target end BED off-target name BED Score Strand Cells Targetsite Target Sequence Realigned Target Sequence
chr1:236259170-236261754 1473 1490 chr1:236259170-236261754_1481_7 control.sam 10 1:236259170-236261754 1481 TCAGAATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCA 1 6 7 2.44948974278 1 9 10 3.0 2 5 3.16227766017 5.53534100124 Control control None none
chr1:236259170-236261754 1521 1531 chr1:236259170-236261754_1523_14 control.sam 11 1:236259170-236261754 1523 GGTGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGAATAGACGT 0 14 14 0.0 0 18 18 0.0 7 7 7.0 3.7094473982 Control control None none
chr3:197899267-197901348 1035 1040 chr3:197899267-197901348_1040_3 control.sam 15 3:197899267-197901348 1040 TAGGGTTGGGTTAGGGTTAGGGTTCGGGTTAGGGTTAGGGTTAGGGTTAG 3 0 3 0.0 5 0 5 0.0 1 1 1.0 2.05480466766 Control control None none
Chromosome Min.Position Max.Position Name Filename Position WindowSequence +.mi -.mi bi.sum.mi bi.geometric_mean.mi +.total -.total total.sum total.geometric_mean primer1.mi primer2.mi primer.geometric_mean position.stdev Site_SubstitutionsOnly.Sequence Site_SubstitutionsOnly.NumSubstitutions Site_SubstitutionsOnly.Strand Site_SubstitutionsOnly.Start Site_SubstitutionsOnly.End Site_GapsAllowed.Sequence Site_GapsAllowed.Length Site_GapsAllowed.Score Site_GapsAllowed.Substitutions Site_GapsAllowed.Insertions Site_GapsAllowed.Deletions Site_GapsAllowed.Strand Site_GapsAllowed.Start Site_GapsAllowed.End Cell Targetsite TargetSequence RealignedTargetSequence
1:236259170-236261754 1473 1490 chr1:236259170-236261754_1481_7 control.sam 1481 TCAGAATGGAGCAGGCGACCAGGGGTGACTCAGAATGGAGCAGGTGACCA 1 6 7 2.44948974278 1 9 10 3.0 2 5 3.16227766017 5.535341001239219 Control control None none
1:236259170-236261754 1521 1531 chr1:236259170-236261754_1523_14 control.sam 1523 GGTGACCAGGGGTGACTCAGAATGGAGCAGGTGACCAGGGGAATAGACGT 0 14 14 0.0 0 18 18 0.0 7 7 7.0 3.7094473981982814 Control control None none
3:197899267-197901348 1035 1040 chr3:197899267-197901348_1040_3 control.sam 1040 TAGGGTTGGGTTAGGGTTAGGGTTCGGGTTAGGGTTAGGGTTAGGGTTAG 3 0 3 0.0 5 0 5 0.0 1 1 1.0 2.0548046676563256 Control control None none
2 changes: 1 addition & 1 deletion test/test_guideseq.py
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Expand Up @@ -110,7 +110,7 @@ def testFullPipeline(self):

def tearDown(self):
# Delete temp output
shutil.rmtree(TEST_OUTPUT_PATH)
#shutil.rmtree(TEST_OUTPUT_PATH)
pass

if __name__ == '__main__':
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