partis-bcr 1.0.12.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.13__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (57) hide show
  1. packages/bpp/lib/libbpp-core.a +0 -0
  2. packages/bpp/lib/libbpp-core.so +0 -0
  3. packages/bpp/lib/libbpp-core.so.2 +0 -0
  4. packages/bpp/lib/libbpp-core.so.2.0.3 +0 -0
  5. packages/bpp/lib/libbpp-phyl.a +0 -0
  6. packages/bpp/lib/libbpp-phyl.so +0 -0
  7. packages/bpp/lib/libbpp-phyl.so.9 +0 -0
  8. packages/bpp/lib/libbpp-phyl.so.9.1.3 +0 -0
  9. packages/bpp/lib/libbpp-seq.a +0 -0
  10. packages/bpp/lib/libbpp-seq.so +0 -0
  11. packages/bpp/lib/libbpp-seq.so.9 +0 -0
  12. packages/bpp/lib/libbpp-seq.so.9.1.3 +0 -0
  13. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/METADATA +1 -1
  14. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/RECORD +57 -45
  15. test/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  16. test/new-results/run-times.csv +9 -9
  17. test/new-results/test.log +21 -21
  18. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
  19. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  20. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  21. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  37. test/paired/new-results/run-times.csv +7 -7
  38. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +11 -7
  39. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +12 -8
  40. test/paired/new-results/subset-partition-new-simu/merged-partition.log +8 -4
  41. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  42. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  43. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  44. test/paired/new-results/test.log +99 -90
  45. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/cf-alleles.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/cf-germlines.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/compare-plotdirs.py +0 -0
  48. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py +0 -0
  49. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/gctree-run.py +0 -0
  50. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/get-naive-probabilities.py +0 -0
  51. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/parse-output.py +0 -0
  52. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/partis-test.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/split-loci.py +0 -0
  54. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/WHEEL +0 -0
  55. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/entry_points.txt +0 -0
  56. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/licenses/COPYING +0 -0
  57. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/top_level.txt +0 -0
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test/paired/new-results/run-times.csv CHANGED
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  name,seconds
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- cache-parameters-simu,13.6
3
- partition-new-simu,21.6
4
- subset-partition-new-simu,71.5
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- seed-partition-new-simu,10.8
6
- get-selection-metrics-new-simu,7.1
7
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- simulate,18.8
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3
+ partition-new-simu,22.9
4
+ subset-partition-new-simu,75.3
5
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  reading output
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  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.5 sec)
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+ total time: 3.0
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  cache-parameters igk:
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  run partis cache-parameters --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
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@@ -143,7 +143,7 @@ hmm
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  12 clusters with 1 proc (0.2s)
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@@ -163,7 +163,7 @@ smith-waterman
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  kept 5 (0.278) unproductive
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  water time: 0.0
165
165
  hmm
166
- caching all 18 naive sequences (0.2s)
166
+ caching all 18 naive sequences (0.3s)
167
167
  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
168
168
  reducing n procs to number of clusters: 10 --> 7
169
169
  7 clusters with 7 procs (0.0s)
@@ -217,6 +217,7 @@ cleaning pair info for 52 seqs
217
217
  k 0 0 3
218
218
  merge time 0.0
219
219
  need to get annotations for 1/8 joint igh clusters
220
+ tag: v1.0.13
220
221
  annotate igh+igk: igh
221
222
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh-only-partition.yaml
222
223
  --input-metafnames: added meta info for 16 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml: loci paired-uids
@@ -233,6 +234,7 @@ hmm
233
234
  subcluster annotation time 0.3
234
235
  total time: 0.4
235
236
  need to get annotations for 5/8 joint igk clusters
237
+ tag: v1.0.13
236
238
  annotate igh+igk: igk
237
239
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
238
240
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml: loci paired-uids
@@ -246,7 +248,7 @@ smith-waterman
246
248
  water time: 0.0
247
249
  hmm
248
250
  subcluster annotating 8 clusters with steps: (0.2s) (0.1s)
249
- subcluster annotation time 0.2
251
+ subcluster annotation time 0.3
250
252
  total time: 0.3
251
253
  igh+igl: synchronizing heavy and light chain cluster paths
252
254
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
@@ -263,6 +265,7 @@ hmm
263
265
  h 0 0 0
264
266
  l 0 0 0
265
267
  merge time 0.0
268
+ tag: v1.0.13
266
269
  annotate igh+igl: igh
267
270
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
268
271
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml: loci paired-uids
@@ -278,8 +281,9 @@ smith-waterman
278
281
  hmm
279
282
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s)
280
283
  subcluster annotation time 0.2
281
- total time: 0.2
284
+ total time: 0.3
282
285
  need to get annotations for 2/3 joint igl clusters
286
+ tag: v1.0.13
283
287
  annotate igh+igl: igl
284
288
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
285
289
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml: loci paired-uids
@@ -308,4 +312,4 @@ hmm
308
312
  h 12 --> 11 -1
309
313
  k 6 --> 8 +2
310
314
  l 3 --> 3
311
- total time: 24.4
315
+ total time: 25.9
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -59,7 +59,7 @@ hmm
59
59
  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
60
60
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.5 sec)
61
61
  infra time: 0.6
62
- hmm step time: 1.3
62
+ hmm step time: 1.2
63
63
  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
64
64
  (0.5 sec)
65
65
  total time: 3.2
@@ -93,7 +93,7 @@ hmm
93
93
  hmm step time: 0.7
94
94
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
95
95
  (0.2 sec)
96
- total time: 1.8
96
+ total time: 1.9
97
97
  cache-parameters igl:
98
98
  run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
99
99
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -136,7 +136,7 @@ smith-waterman
136
136
  kept 14 (0.438) unproductive
137
137
  water time: 0.0
138
138
  hmm
139
- caching all 32 naive sequences (0.6s)
139
+ caching all 32 naive sequences (0.7s)
140
140
  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
141
141
  30 clusters with 10 procs (0.1s)
142
142
  29 clusters with 7 procs (0.2s)
@@ -145,11 +145,11 @@ hmm
145
145
  23 clusters with 2 procs (0.3s)
146
146
  20 clusters with 1 proc (0.5s)
147
147
  note not merging entire cpath history
148
- partition loop time: 1.7
148
+ partition loop time: 1.8
149
149
  getting annotations for final partition
150
150
  subcluster annotating 16 clusters with steps: (0.5s) (0.1s)
151
151
  subcluster annotation time 0.6
152
- total time: 3.0
152
+ total time: 3.1
153
153
  partition igk:
154
154
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
155
155
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -161,7 +161,7 @@ smith-waterman
161
161
  kept 9 (0.500) unproductive
162
162
  water time: 0.0
163
163
  hmm
164
- caching all 18 naive sequences (0.2s)
164
+ caching all 18 naive sequences (0.3s)
165
165
  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
166
166
  reducing n procs to number of clusters: 10 --> 7
167
167
  7 clusters with 7 procs (0.0s)
@@ -173,7 +173,7 @@ hmm
173
173
  getting annotations for final partition
174
174
  subcluster annotating 6 clusters with steps: (0.2s) (0.1s)
175
175
  subcluster annotation time 0.2
176
- total time: 0.9
176
+ total time: 1.0
177
177
  partition igl:
178
178
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
179
179
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -215,6 +215,7 @@ cleaning pair info for 61 seqs
215
215
  k 0 0 1
216
216
  merge time 0.0
217
217
  need to get annotations for 2/11 joint igh clusters
218
+ tag: v1.0.13
218
219
  annotate igh+igk: igh
219
220
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
220
221
  --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
@@ -231,6 +232,7 @@ hmm
231
232
  subcluster annotation time 0.4
232
233
  total time: 0.5
233
234
  need to get annotations for 6/11 joint igk clusters
235
+ tag: v1.0.13
234
236
  annotate igh+igk: igk
235
237
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
236
238
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -263,6 +265,7 @@ hmm
263
265
  l 0 0 1
264
266
  merge time 0.0
265
267
  need to get annotations for 2/5 joint igh clusters
268
+ tag: v1.0.13
266
269
  annotate igh+igl: igh
267
270
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
268
271
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -279,6 +282,7 @@ hmm
279
282
  subcluster annotation time 0.3
280
283
  total time: 0.4
281
284
  need to get annotations for 5/5 joint igl clusters
285
+ tag: v1.0.13
282
286
  annotate igh+igl: igl
283
287
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
284
288
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
@@ -306,4 +310,4 @@ hmm
306
310
  h 16 --> 16
307
311
  k 6 --> 11 +5
308
312
  l 3 --> 5 +2
309
- total time: 26.1
313
+ total time: 27.6
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -32,7 +32,7 @@ hmm
32
32
  23 clusters with 5 procs (0.3s)
33
33
  22 clusters with 3 procs (0.3s)
34
34
  21 clusters with 2 procs (0.1s)
35
- 21 clusters with 1 proc (0.4s)
35
+ 21 clusters with 1 proc (0.5s)
36
36
  partition loop time: 1.8
37
37
  getting annotations for final partition
38
38
  subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
@@ -165,6 +165,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
165
165
  joint 0.963 0.594
166
166
  merge time 0.0
167
167
  need to get annotations for 6/15 joint igh clusters
168
+ tag: v1.0.13
168
169
  annotate igh+igk: igh
169
170
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
170
171
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -178,10 +179,11 @@ smith-waterman
178
179
  kept 13 (0.371) unproductive
179
180
  water time: 0.0
180
181
  hmm
181
- subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
182
- subcluster annotation time 0.5
182
+ subcluster annotating 15 clusters with steps: (0.5s) (0.1s)
183
+ subcluster annotation time 0.6
183
184
  total time: 0.6
184
185
  need to get annotations for 13/15 joint igk clusters
186
+ tag: v1.0.13
185
187
  annotate igh+igk: igk
186
188
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
187
189
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -226,6 +228,7 @@ hmm
226
228
  joint 1.000 0.787
227
229
  merge time 0.0
228
230
  need to get annotations for 2/6 joint igh clusters
231
+ tag: v1.0.13
229
232
  annotate igh+igl: igh
230
233
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
231
234
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -243,6 +246,7 @@ hmm
243
246
  subcluster annotation time 0.5
244
247
  total time: 0.6
245
248
  need to get annotations for 6/6 joint igl clusters
249
+ tag: v1.0.13
246
250
  annotate igh+igl: igl
247
251
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
248
252
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -272,4 +276,4 @@ hmm
272
276
  h 18 --> 21 +3
273
277
  k 6 --> 15 +9
274
278
  l 3 --> 6 +3
275
- total time: 15.6
279
+ total time: 16.3