partis-bcr 1.0.10__cp312-cp312-manylinux1_x86_64.whl → 1.0.11__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 (43) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/RECORD +43 -43
  5. test/new-results/test.log +3 -3
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +2 -2
  7. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  8. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  9. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  23. test/paired/new-results/run-times.csv +6 -6
  24. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +15 -15
  25. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +12 -12
  26. test/paired/new-results/subset-partition-new-simu/merged-partition.log +8 -8
  27. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  28. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  30. test/paired/new-results/test.log +51 -51
  31. test/phylo-naive-run.py +1 -1
  32. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/cf-alleles.py +0 -0
  33. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/cf-germlines.py +0 -0
  34. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/compare-plotdirs.py +0 -0
  35. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/extract-pairing-info.py +0 -0
  36. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/gctree-run.py +0 -0
  37. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/get-naive-probabilities.py +0 -0
  38. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/partis-test.py +0 -0
  39. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/split-loci.py +0 -0
  40. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/WHEEL +0 -0
  41. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/entry_points.txt +0 -0
  42. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/licenses/COPYING +0 -0
  43. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.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,14.0
3
- partition-new-simu,22.5
4
- subset-partition-new-simu,74.6
5
- seed-partition-new-simu,11.3
6
- get-selection-metrics-new-simu,7.4
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2
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3
+ partition-new-simu,21.2
4
+ subset-partition-new-simu,69.4
5
+ seed-partition-new-simu,10.5
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -51,7 +51,7 @@ smith-waterman (writing parameters)
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  kept 11 (0.458) unproductive
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
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+ water time: 0.6 (ig-sw 0.6 processing 0.0)
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  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-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igl.fa --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
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@@ -150,8 +150,8 @@ hmm
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  getting annotations for final partition
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  subcluster annotating 12 clusters with steps: (0.4s) (0.1s)
153
- subcluster annotation time 0.5
154
- total time: 2.1
153
+ subcluster annotation time 0.4
154
+ total time: 2.0
155
155
  partition igk:
156
156
  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-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/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
157
157
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -163,7 +163,7 @@ smith-waterman
163
163
  kept 5 (0.278) unproductive
164
164
  water time: 0.0
165
165
  hmm
166
- caching all 18 naive sequences (0.3s)
166
+ caching all 18 naive sequences (0.2s)
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)
@@ -217,7 +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: v1.0.10
220
+ tag: v1.0.11
221
221
  annotate igh+igk: igh
222
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
223
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
@@ -234,7 +234,7 @@ hmm
234
234
  subcluster annotation time 0.3
235
235
  total time: 0.4
236
236
  need to get annotations for 5/8 joint igk clusters
237
- tag: v1.0.10
237
+ tag: v1.0.11
238
238
  annotate igh+igk: igk
239
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
240
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
@@ -248,7 +248,7 @@ smith-waterman
248
248
  water time: 0.0
249
249
  hmm
250
250
  subcluster annotating 8 clusters with steps: (0.2s) (0.1s)
251
- subcluster annotation time 0.3
251
+ subcluster annotation time 0.2
252
252
  total time: 0.3
253
253
  igh+igl: synchronizing heavy and light chain cluster paths
254
254
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
@@ -265,7 +265,7 @@ hmm
265
265
  h 0 0 0
266
266
  l 0 0 0
267
267
  merge time 0.0
268
- tag: v1.0.10
268
+ tag: v1.0.11
269
269
  annotate igh+igl: igh
270
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
271
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
@@ -281,9 +281,9 @@ smith-waterman
281
281
  hmm
282
282
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s)
283
283
  subcluster annotation time 0.2
284
- total time: 0.3
284
+ total time: 0.2
285
285
  need to get annotations for 2/3 joint igl clusters
286
- tag: v1.0.10
286
+ tag: v1.0.11
287
287
  annotate igh+igl: igl
288
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
289
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
@@ -312,4 +312,4 @@ hmm
312
312
  h 12 --> 11 -1
313
313
  k 6 --> 8 +2
314
314
  l 3 --> 3
315
- total time: 25.6
315
+ total time: 23.9
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -51,7 +51,7 @@ smith-waterman (writing parameters)
51
51
  kept 14 (0.438) unproductive
52
52
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
53
53
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.6 sec)
54
- water time: 0.7 (ig-sw 0.7 processing 0.0)
54
+ water time: 0.7 (ig-sw 0.6 processing 0.0)
55
55
  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
56
56
  (0.5 sec)
57
57
  hmm
@@ -62,7 +62,7 @@ hmm
62
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
- total time: 3.2
65
+ total time: 3.1
66
66
  cache-parameters igk:
67
67
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --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
68
68
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -136,11 +136,11 @@ smith-waterman
136
136
  kept 14 (0.438) unproductive
137
137
  water time: 0.0
138
138
  hmm
139
- caching all 32 naive sequences (0.7s)
139
+ caching all 32 naive sequences (0.6s)
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)
143
- 28 clusters with 5 procs (0.3s)
143
+ 28 clusters with 5 procs (0.2s)
144
144
  28 clusters with 3 procs (0.3s)
145
145
  23 clusters with 2 procs (0.3s)
146
146
  20 clusters with 1 proc (0.5s)
@@ -149,7 +149,7 @@ hmm
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: 3.1
152
+ total time: 3.0
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 (0.3s)
164
+ caching all 18 naive sequences (0.2s)
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: 1.0
176
+ total time: 0.9
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
@@ -215,7 +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: v1.0.10
218
+ tag: v1.0.11
219
219
  annotate igh+igk: igh
220
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
221
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
@@ -232,7 +232,7 @@ hmm
232
232
  subcluster annotation time 0.4
233
233
  total time: 0.5
234
234
  need to get annotations for 6/11 joint igk clusters
235
- tag: v1.0.10
235
+ tag: v1.0.11
236
236
  annotate igh+igk: igk
237
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
238
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
@@ -265,7 +265,7 @@ hmm
265
265
  l 0 0 1
266
266
  merge time 0.0
267
267
  need to get annotations for 2/5 joint igh clusters
268
- tag: v1.0.10
268
+ tag: v1.0.11
269
269
  annotate igh+igl: igh
270
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
271
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
@@ -282,7 +282,7 @@ hmm
282
282
  subcluster annotation time 0.3
283
283
  total time: 0.4
284
284
  need to get annotations for 5/5 joint igl clusters
285
- tag: v1.0.10
285
+ tag: v1.0.11
286
286
  annotate igh+igl: igl
287
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
288
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
@@ -310,4 +310,4 @@ hmm
310
310
  h 16 --> 16
311
311
  k 6 --> 11 +5
312
312
  l 3 --> 5 +2
313
- total time: 27.2
313
+ total time: 25.3
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -32,10 +32,10 @@ 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 (0.5s)
35
+ 21 clusters with 1 proc (0.4s)
36
36
  partition loop time: 1.8
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.7s) (0.2s) (0.1s)
38
+ subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
39
39
  subcluster annotation time 1.0
40
40
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
41
41
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -122,7 +122,7 @@ hmm
122
122
  partition loop time: 0.3
123
123
  getting annotations for final partition
124
124
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s) (0.1s)
125
- subcluster annotation time 0.3
125
+ subcluster annotation time 0.2
126
126
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
127
127
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
128
128
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
@@ -165,7 +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: v1.0.10
168
+ tag: v1.0.11
169
169
  annotate igh+igk: igh
170
170
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
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
@@ -183,7 +183,7 @@ hmm
183
183
  subcluster annotation time 0.6
184
184
  total time: 0.6
185
185
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.10
186
+ tag: v1.0.11
187
187
  annotate igh+igk: igk
188
188
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
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
@@ -228,7 +228,7 @@ hmm
228
228
  joint 1.000 0.787
229
229
  merge time 0.0
230
230
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.10
231
+ tag: v1.0.11
232
232
  annotate igh+igl: igh
233
233
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
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  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
@@ -246,7 +246,7 @@ hmm
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  subcluster annotation time 0.5
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  total time: 0.6
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  need to get annotations for 6/6 joint igl clusters
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- tag: v1.0.10
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+ tag: v1.0.11
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  annotate igh+igl: igl
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  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
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  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
@@ -276,4 +276,4 @@ hmm
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  h 18 --> 21 +3
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  k 6 --> 15 +9
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  l 3 --> 6 +3
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- total time: 16.2
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+ total time: 15.2