partis-bcr 1.0.12.post1.dev2__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev4__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 (56) 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.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/METADATA +1 -1
  14. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/RECORD +56 -44
  15. test/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
  16. test/new-results/run-times.csv +6 -6
  17. test/new-results/test.log +17 -17
  18. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  19. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  20. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  36. test/paired/new-results/run-times.csv +7 -7
  37. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -5
  38. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  39. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -4
  40. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  41. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  42. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  43. test/paired/new-results/test.log +74 -74
  44. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  48. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/gctree-run.py +0 -0
  49. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  50. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/parse-output.py +0 -0
  51. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/partis-test.py +0 -0
  52. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/split-loci.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/WHEEL +0 -0
  54. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/entry_points.txt +0 -0
  55. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/licenses/COPYING +0 -0
  56. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.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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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  partition igk:
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@@ -163,7 +163,7 @@ smith-waterman
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  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)
@@ -246,7 +246,7 @@ smith-waterman
246
246
  water time: 0.0
247
247
  hmm
248
248
  subcluster annotating 8 clusters with steps: (0.2s) (0.1s)
249
- subcluster annotation time 0.3
249
+ subcluster annotation time 0.2
250
250
  total time: 0.3
251
251
  igh+igl: synchronizing heavy and light chain cluster paths
252
252
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
@@ -308,4 +308,4 @@ hmm
308
308
  h 12 --> 11 -1
309
309
  k 6 --> 8 +2
310
310
  l 3 --> 3
311
- total time: 24.6
311
+ total time: 23.9
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -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: 2.9
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
@@ -229,7 +229,7 @@ smith-waterman
229
229
  hmm
230
230
  subcluster annotating 11 clusters with steps: (0.3s) (0.1s)
231
231
  subcluster annotation time 0.4
232
- total time: 0.4
232
+ total time: 0.5
233
233
  need to get annotations for 6/11 joint igk clusters
234
234
  annotate igh+igk: igk
235
235
  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
@@ -306,4 +306,4 @@ hmm
306
306
  h 16 --> 16
307
307
  k 6 --> 11 +5
308
308
  l 3 --> 5 +2
309
- total time: 26.0
309
+ total time: 25.0
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -33,7 +33,7 @@ hmm
33
33
  22 clusters with 3 procs (0.3s)
34
34
  21 clusters with 2 procs (0.1s)
35
35
  21 clusters with 1 proc (0.4s)
36
- partition loop time: 1.8
36
+ partition loop time: 1.7
37
37
  getting annotations for final partition
38
38
  subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
39
39
  subcluster annotation time 1.0
@@ -47,7 +47,7 @@ getting annotations for final partition
47
47
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
48
48
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
49
49
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
50
- total time: 2.9
50
+ total time: 2.8
51
51
  partition igk:
52
52
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igk.yaml --continue-from-input-partition --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/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
53
53
  warning replacing 'paired-uids'/'paired-uids' value for 'bc11af4843-igk' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['bc11af4843-igh', 'eee6809ad6-igh', 'eee6809ad6-igl'] --> ['eee6809ad6-igh']
@@ -179,7 +179,7 @@ smith-waterman
179
179
  water time: 0.0
180
180
  hmm
181
181
  subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
182
- subcluster annotation time 0.5
182
+ subcluster annotation time 0.6
183
183
  total time: 0.6
184
184
  need to get annotations for 13/15 joint igk clusters
185
185
  annotate igh+igk: igk
@@ -272,4 +272,4 @@ hmm
272
272
  h 18 --> 21 +3
273
273
  k 6 --> 15 +9
274
274
  l 3 --> 6 +3
275
- total time: 15.6
275
+ total time: 15.1