From d98432ee84ec6f8350036092bffb22829444d8b0 Mon Sep 17 00:00:00 2001 From: Sowmya Iyer Date: Mon, 9 Apr 2018 21:54:04 -0400 Subject: [PATCH] update test data to match new 'Window.key' column name added in code --- test/data/identified/EMX1_identifiedOfftargets.txt | 14 +++++++------- .../EMX1_identifiedOfftargets.txt.unmerged | 7 +++++++ .../identified/control_identifiedOfftargets.txt | 8 ++++---- .../control_identifiedOfftargets.txt.unmerged | 4 ++++ 4 files changed, 22 insertions(+), 11 deletions(-) create mode 100644 test/data/identified/EMX1_identifiedOfftargets.txt.unmerged create mode 100644 test/data/identified/control_identifiedOfftargets.txt.unmerged diff --git a/test/data/identified/EMX1_identifiedOfftargets.txt b/test/data/identified/EMX1_identifiedOfftargets.txt index 9022658..130bfdc 100644 --- a/test/data/identified/EMX1_identifiedOfftargets.txt +++ b/test/data/identified/EMX1_identifiedOfftargets.txt @@ -1,7 +1,7 @@ -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 +Window.key 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 +chr15:44108746-44110769_1000_1023 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 +chr1:236259170-236261754_1465_1486 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 +chr1:236259170-236261754_1531_1539 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 +chr2:73159981-73162004_1000_1023 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 +chr3:197899267-197901348_1075_1081 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 +chr6:9117792-9119815_1000_1023 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 diff --git a/test/data/identified/EMX1_identifiedOfftargets.txt.unmerged b/test/data/identified/EMX1_identifiedOfftargets.txt.unmerged new file mode 100644 index 0000000..130bfdc --- /dev/null +++ b/test/data/identified/EMX1_identifiedOfftargets.txt.unmerged @@ -0,0 +1,7 @@ +Window.key 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 +chr15:44108746-44110769_1000_1023 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 +chr1:236259170-236261754_1465_1486 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 +chr1:236259170-236261754_1531_1539 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 +chr2:73159981-73162004_1000_1023 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 +chr3:197899267-197901348_1075_1081 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 +chr6:9117792-9119815_1000_1023 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 diff --git a/test/data/identified/control_identifiedOfftargets.txt b/test/data/identified/control_identifiedOfftargets.txt index e021690..933bca8 100644 --- a/test/data/identified/control_identifiedOfftargets.txt +++ b/test/data/identified/control_identifiedOfftargets.txt @@ -1,4 +1,4 @@ -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 +Window.key 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 +chr1:236259170-236261754_1473_1490 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 +chr1:236259170-236261754_1521_1531 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 +chr3:197899267-197901348_1035_1040 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 diff --git a/test/data/identified/control_identifiedOfftargets.txt.unmerged b/test/data/identified/control_identifiedOfftargets.txt.unmerged new file mode 100644 index 0000000..933bca8 --- /dev/null +++ b/test/data/identified/control_identifiedOfftargets.txt.unmerged @@ -0,0 +1,4 @@ +Window.key 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 +chr1:236259170-236261754_1473_1490 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 +chr1:236259170-236261754_1521_1531 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 +chr3:197899267-197901348_1035_1040 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