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makes umi_tools deterministic with --random-seed #550

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merged 7 commits into from
Oct 1, 2024
Merged

makes umi_tools deterministic with --random-seed #550

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6db7f76
makes umi_tools deterministic with --random-seed
TomSmithCGAT Aug 4, 2022
726ac72
git commit to re-trigger tests
TomSmithCGAT Mar 2, 2023
9ccf700
another test re-trigger (output from previous was lost)
TomSmithCGAT Jun 13, 2023
5c0d427
Remove py3.6 from testing
TomSmithCGAT Jun 13, 2023
03b42b8
merge with master
TomSmithCGAT Oct 1, 2024
a045356
Updates test files for deterministic output
TomSmithCGAT Oct 1, 2024
4a74d5b
removes final dependency on pythonhashseed
TomSmithCGAT Oct 1, 2024
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1 change: 0 additions & 1 deletion .github/workflows/nosetests.yml
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Expand Up @@ -33,5 +33,4 @@ jobs:
python setup.py install
- name: Test with nosetests
run: |
export PYTHONHASHSEED=0
nosetests -v tests/test_umi_tools.py
1 change: 0 additions & 1 deletion README.rst
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Expand Up @@ -121,4 +121,3 @@ Dependencies
------------
umi_tools is dependent on `python>=3.5`, `numpy`, `pandas`, `scipy`, `cython`, `pysam`,
`future`, `regex` and `matplotlib`

97,560 changes: 48,780 additions & 48,780 deletions tests/group_adj_py3.sam
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97,560 changes: 48,780 additions & 48,780 deletions tests/group_adj_py3.tsv
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50 changes: 25 additions & 25 deletions tests/group_cluster_py3.sam
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52 changes: 26 additions & 26 deletions tests/group_cluster_py3.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -667,8 +667,8 @@ SRR2057595.13442648_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13549325_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13587544_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13626788_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.7273343_ATTGG chr19 3571762 NA ATTGG 1 ATCGG 188 3
SRR2057595.10958947_ATCGA chr19 3571762 NA ATCGA 1 ATCGG 188 3
SRR2057595.7273343_ATTGG chr19 3571762 NA ATTGG 1 ATCGG 188 3
SRR2057595.7803605_TCGGC chr19 3571763 NA TCGGC 2 TCGGC 2 4
SRR2057595.8458115_TCGGC chr19 3571763 NA TCGGC 2 TCGGC 2 4
SRR2057595.40212_ATTCT chr19 3576313 NA ATTCT 90 ATTCT 90 5
Expand Down Expand Up @@ -1317,9 +1317,9 @@ SRR2057595.13499597_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.13502818_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.13563255_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.6047279_ACAAA chr19 4078320 NA ACAAA 1 ACAGA 237 13
SRR2057595.8461380_GCAGA chr19 4078320 NA GCAGA 1 ACAGA 237 13
SRR2057595.11830696_ACATA chr19 4078320 NA ACATA 1 ACAGA 237 13
SRR2057595.12503000_ACAGC chr19 4078320 NA ACAGC 1 ACAGA 237 13
SRR2057595.11830696_ACATA chr19 4078320 NA ACATA 1 ACAGA 237 13
SRR2057595.8461380_GCAGA chr19 4078320 NA GCAGA 1 ACAGA 237 13
SRR2057595.11891309_TAACC chr19 4078320 NA TAACC 1 TAACC 1 14
SRR2057595.12261872_GGGCC chr19 4078320 NA GGGCC 1 GGGCC 1 15
SRR2057595.327916_GTACC chr19 4078324 NA GTACC 7 GTACC 7 16
Expand Down Expand Up @@ -1667,8 +1667,8 @@ SRR2057595.9452803_GTGGC chr19 4078333 NA GTGGC 3 GTGGC 3 46
SRR2057595.2846379_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.4116943_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.9653749_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.4627616_TAGAC chr19 4078333 NA TAGAC 1 TAGAC 2 48
SRR2057595.7183987_GAGAC chr19 4078333 NA GAGAC 1 TAGAC 2 48
SRR2057595.7183987_GAGAC chr19 4078333 NA GAGAC 1 GAGAC 2 48
SRR2057595.4627616_TAGAC chr19 4078333 NA TAGAC 1 GAGAC 2 48
SRR2057595.13080756_CTGCC chr19 4078333 NA CTGCC 1 CTGCC 1 49
SRR2057595.59150_AGCCG chr19 4078334 NA AGCCG 586 AGCCG 967 50
SRR2057595.61132_AGCCG chr19 4078334 NA AGCCG 586 AGCCG 967 50
Expand Down Expand Up @@ -2635,8 +2635,8 @@ SRR2057595.9512923_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.12027381_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.6570489_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.254072_AACCG chr19 4078334 NA AACCG 1 AGCCG 967 50
SRR2057595.12445458_AGTCG chr19 4078334 NA AGTCG 1 AGCCG 967 50
SRR2057595.13571873_AGCAG chr19 4078334 NA AGCAG 1 AGCCG 967 50
SRR2057595.12445458_AGTCG chr19 4078334 NA AGTCG 1 AGCCG 967 50
SRR2057595.11597812_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
SRR2057595.10788_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
SRR2057595.42646_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
Expand Down Expand Up @@ -5948,14 +5948,14 @@ SRR2057595.11741654_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.12192177_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.12959733_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.13565871_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.2949476_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.5134248_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.12286012_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.8560272_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.11481316_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.12911150_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.5483821_CTGAT chr19 4078346 NA CTGAT 2 ATGAT 8 86
SRR2057595.12468205_CTGAT chr19 4078346 NA CTGAT 2 ATGAT 8 86
SRR2057595.8560272_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.11481316_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.12911150_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.2949476_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.5134248_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.12286012_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.5483821_CTGAT chr19 4078346 NA CTGAT 2 AAGAT 8 86
SRR2057595.12468205_CTGAT chr19 4078346 NA CTGAT 2 AAGAT 8 86
SRR2057595.4318931_TCGAT chr19 4078346 NA TCGAT 1 TCGAT 1 87
SRR2057595.19310_TAACA chr19 4078347 NA TAACA 462 TAACA 832 88
SRR2057595.24047_TAACA chr19 4078347 NA TAACA 462 TAACA 832 88
Expand Down Expand Up @@ -9904,8 +9904,8 @@ SRR2057595.2210298_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.5394707_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.5779297_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.13496292_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.12229826_GTCGA chr19 4078354 NA GTCGA 1 GTCAA 556 107
SRR2057595.1408002_GCCAA chr19 4078354 NA GCCAA 1 GTCAA 556 107
SRR2057595.12229826_GTCGA chr19 4078354 NA GTCGA 1 GTCAA 556 107
SRR2057595.2688_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
SRR2057595.37339_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
SRR2057595.41440_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
Expand Down Expand Up @@ -11233,8 +11233,8 @@ SRR2057595.12896743_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.12492803_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.13007419_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.8484200_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.7487423_GTAGC chr19 4078359 NA GTAGC 1 CTAGC 319 116
SRR2057595.13443839_CTAAC chr19 4078359 NA CTAAC 1 CTAGC 319 116
SRR2057595.7487423_GTAGC chr19 4078359 NA GTAGC 1 CTAGC 319 116
SRR2057595.8085966_CCGAG chr19 4078360 NA CCGAG 1 CCGAG 1 117
SRR2057595.4460250_AAAAT chr19 4078360 NA AAAAT 1 AAAAT 1 118
SRR2057595.8722606_GCCGA chr19 4078361 NA GCCGA 152 GCCGA 154 119
Expand Down Expand Up @@ -13231,8 +13231,8 @@ SRR2057595.13489373_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.3566252_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.12978364_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.6463453_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.2878355_AATTT chr19 4078483 NA AATTT 1 AACTT 238 159
SRR2057595.13442879_AACGT chr19 4078483 NA AACGT 1 AACTT 238 159
SRR2057595.2878355_AATTT chr19 4078483 NA AATTT 1 AACTT 238 159
SRR2057595.7790483_CTCTC chr19 4078483 NA CTCTC 1 CTCTC 1 160
SRR2057595.3284641_GGGCA chr19 4078484 NA GGGCA 1 GGGCA 1 161
SRR2057595.83632_TGGTC chr19 4078485 NA TGGTC 149 TGGTC 149 162
Expand Down Expand Up @@ -16368,8 +16368,8 @@ SRR2057595.13442648_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13549325_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13587544_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13626788_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.7273343_ATTGG chr19 4379011 NA ATTGG 1 ATCGG 187 188
SRR2057595.10958947_ATCGA chr19 4379011 NA ATCGA 1 ATCGG 187 188
SRR2057595.7273343_ATTGG chr19 4379011 NA ATTGG 1 ATCGG 187 188
SRR2057595.7803605_TCGGC chr19 4379012 NA TCGGC 2 TCGGC 2 189
SRR2057595.8458115_TCGGC chr19 4379012 NA TCGGC 2 TCGGC 2 189
SRR2057595.479300_ACAGC chr19 4641015 NA ACAGC 8 ACAGC 8 190
Expand Down Expand Up @@ -17556,8 +17556,8 @@ SRR2057595.13479955_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13491625_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13499957_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13618555_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.1260332_TATAC chr19 5038318 NA TATAC 1 TATTC 482 202
SRR2057595.8460968_GATTC chr19 5038318 NA GATTC 1 TATTC 482 202
SRR2057595.1260332_TATAC chr19 5038318 NA TATAC 1 TATTC 482 202
SRR2057595.9269865_TATCC chr19 5038318 NA TATCC 1 TATTC 482 202
SRR2057595.35589_GGAGA chr19 5104716 NA GGAGA 12 GGAGA 12 203
SRR2057595.477494_GGAGA chr19 5104716 NA GGAGA 12 GGAGA 12 203
Expand Down Expand Up @@ -21725,9 +21725,9 @@ SRR2057595.13609810_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.13610242_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.13648468_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.2019660_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.8637529_GGCGA chr19 7390041 NA GGCGA 1 GCCGA 665 270
SRR2057595.8139214_GCTGA chr19 7390041 NA GCTGA 1 GCCGA 665 270
SRR2057595.13256411_CCCGA chr19 7390041 NA CCCGA 1 GCCGA 665 270
SRR2057595.8139214_GCTGA chr19 7390041 NA GCTGA 1 GCCGA 665 270
SRR2057595.8637529_GGCGA chr19 7390041 NA GGCGA 1 GCCGA 665 270
SRR2057595.9119459_ACGCA chr19 7507313 NA ACGCA 1 ACGCA 1 271
SRR2057595.46326_CAGTA chr19 7545895 NA CAGTA 157 CAGTA 157 272
SRR2057595.52336_CAGTA chr19 7545895 NA CAGTA 157 CAGTA 157 272
Expand Down Expand Up @@ -32781,8 +32781,8 @@ SRR2057595.13597841_TATGG chr19 13129321 NA TATGG 245 TATTG 521 391
SRR2057595.13626245_TATGG chr19 13129321 NA TATGG 245 TATTG 521 391
SRR2057595.2931220_TACGG chr19 13129321 NA TACGG 2 TATTG 521 391
SRR2057595.4971514_TACGG chr19 13129321 NA TACGG 2 TATTG 521 391
SRR2057595.2867945_CATTG chr19 13129321 NA CATTG 1 TATTG 521 391
SRR2057595.13255450_AATGG chr19 13129321 NA AATGG 1 TATTG 521 391
SRR2057595.2867945_CATTG chr19 13129321 NA CATTG 1 TATTG 521 391
SRR2057595.11618608_TAATG chr19 13129321 NA TAATG 1 TATTG 521 391
SRR2057595.116977_CGCTT chr19 13129321 NA CGCTT 254 CGCTT 254 392
SRR2057595.223450_CGCTT chr19 13129321 NA CGCTT 254 CGCTT 254 392
Expand Down Expand Up @@ -39738,8 +39738,8 @@ SRR2057595.13421676_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.13463857_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.13584467_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.12488286_GCAAA chr19 32596081 NA GCAAA 1 GCTAA 224 512
SRR2057595.13441427_GCTGA chr19 32596081 NA GCTGA 1 GCTAA 224 512
SRR2057595.9833878_GCCAA chr19 32596081 NA GCCAA 1 GCTAA 224 512
SRR2057595.13441427_GCTGA chr19 32596081 NA GCTGA 1 GCTAA 224 512
SRR2057595.1134582_GATGT chr19 32850823 NA GATGT 2 GATGT 2 513
SRR2057595.8708447_GATGT chr19 32850823 NA GATGT 2 GATGT 2 513
SRR2057595.965130_GACAG chr19 32981872 NA GACAG 1 GACAG 1 514
Expand Down Expand Up @@ -40219,8 +40219,8 @@ SRR2057595.13290815_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13313064_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13322565_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13476968_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.6413612_ATCCC chr19 35673172 NA ATCCC 1 ATACC 263 529
SRR2057595.4829989_ACACC chr19 35673172 NA ACACC 1 ATACC 263 529
SRR2057595.6413612_ATCCC chr19 35673172 NA ATCCC 1 ATACC 263 529
SRR2057595.308008_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
SRR2057595.311184_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
SRR2057595.360154_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
Expand Down Expand Up @@ -50799,8 +50799,8 @@ SRR2057595.13594861_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13595630_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13601460_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13640428_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.4392906_ATGAT chr19 56007799 NA ATGAT 1 ATGAA 457 659
SRR2057595.11588152_ATGAG chr19 56007799 NA ATGAG 1 ATGAA 457 659
SRR2057595.4392906_ATGAT chr19 56007799 NA ATGAT 1 ATGAA 457 659
SRR2057595.9339337_TGGAA chr19 56007800 NA TGGAA 2 TGGAA 2 660
SRR2057595.9424164_TGGAA chr19 56007800 NA TGGAA 2 TGGAA 2 660
SRR2057595.1122774_ATGAA chr19 56007800 NA ATGAA 1 ATGAA 1 661
Expand Down Expand Up @@ -54724,9 +54724,9 @@ SRR2057595.13443130_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13576443_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13581746_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13623055_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.4284087_CTGTG chr19 61240340 NA CTGTG 1 CTGCG 240 707
SRR2057595.8361213_AAGCG chr19 61240340 NA AAGCG 1 CTGCG 240 707
SRR2057595.10713055_CAGCG chr19 61240340 NA CAGCG 1 CTGCG 240 707
SRR2057595.4284087_CTGTG chr19 61240340 NA CTGTG 1 CTGCG 240 707
SRR2057595.2364090_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
SRR2057595.2489631_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
SRR2057595.9327159_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
Expand Down
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