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code changes to (1) move key field to end of line because it was mess…
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…ing up the filter step (2) change identified reference data to match code changes and (3) change filter reference data to add additional key that tagged along from identify step
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@sowmyaiyer
sowmyaiyer committed Apr 10, 2018
1 parent d98432e commit 12609a0
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Showing 4 changed files with 15 additions and 15 deletions.
6 changes: 3 additions & 3 deletions guideseq/identifyOfftargetSites.py
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Original file line number Diff line number Diff line change
Expand Up @@ -329,15 +329,15 @@ def analyze(sam_filename, reference_genome, outfile, annotations, search_radius,

with open(outfile, 'w') as f, open(outfile_unmerged, 'w') as f_unmerged:
# Write header
print('Window.key','Chromosome', 'Min.Position', 'Max.Position', 'Name', 'Filename', 'Position', 'WindowSequence', # 0:6
print('Chromosome', 'Min.Position', 'Max.Position', 'Name', 'Filename', 'Position', 'WindowSequence', # 0:6
'+.mi', '-.mi', 'bi.sum.mi', 'bi.geometric_mean.mi', '+.total', '-.total', 'total.sum', 'total.geometric_mean', # 7:14
'primer1.mi', 'primer2.mi', 'primer.geometric_mean', 'position.stdev', # 15:18
'Site_SubstitutionsOnly.Sequence', 'Site_SubstitutionsOnly.NumSubstitutions', # 19:20
'Site_SubstitutionsOnly.Strand', 'Site_SubstitutionsOnly.Start', 'Site_SubstitutionsOnly.End', # 21:23
'Site_GapsAllowed.Sequence', 'Site_GapsAllowed.Length', 'Site_GapsAllowed.Score', # 24:26
'Site_GapsAllowed.Substitutions', 'Site_GapsAllowed.Insertions', 'Site_GapsAllowed.Deletions', # 27:29
'Site_GapsAllowed.Strand', 'Site_GapsAllowed.Start', 'Site_GapsAllowed.End', # 30:32
'Cell', 'Targetsite', 'TargetSequence', 'RealignedTargetSequence', sep='\t', file=f) # 33:36
'Cell', 'Targetsite', 'TargetSequence', 'RealignedTargetSequence', 'Window.key',sep='\t', file=f) # 33:36

print('Window.key','Chromosome', 'Min.Position', 'Max.Position', 'Name', 'Filename', 'Position', 'WindowSequence', # 0:6
'+.mi', '-.mi', 'bi.sum.mi', 'bi.geometric_mean.mi', '+.total', '-.total', 'total.sum', 'total.geometric_mean', # 7:14
Expand Down Expand Up @@ -418,7 +418,7 @@ def analyze(sam_filename, reference_genome, outfile, annotations, search_radius,
print(*output_row_with_key, sep='\t', file=f_unmerged)

for key in sorted(output_dict.keys()):
output_dict[key].insert(0, key)
output_dict[key].append(key)
print(*output_dict[key], sep='\t', file=f)

def assignPrimerstoReads(read_sequence, sam_flag):
Expand Down
2 changes: 1 addition & 1 deletion test/data/filtered/EMX1_backgroundFiltered.txt
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@@ -1 +1 @@
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
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 chr1:236259170-236261754_1465_1486
14 changes: 7 additions & 7 deletions test/data/identified/EMX1_identifiedOfftargets.txt
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@@ -1,7 +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
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 Window.key
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 chr15:44108746-44110769_1000_1023
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_1465_1486
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 chr1:236259170-236261754_1531_1539
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 chr2:73159981-73162004_1000_1023
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 chr3:197899267-197901348_1075_1081
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 chr6:9117792-9119815_1000_1023
8 changes: 4 additions & 4 deletions test/data/identified/control_identifiedOfftargets.txt
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@@ -1,4 +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
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 Window.key
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_1473_1490
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 chr1:236259170-236261754_1521_1531
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 chr3:197899267-197901348_1035_1040

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