partis-bcr 1.0.12.post1.dev4__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev1__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 (46) hide show
  1. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.dist-info}/RECORD +46 -46
  3. python/processargs.py +3 -0
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +1 -1
  5. test/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  6. test/new-results/run-times.csv +4 -4
  7. test/new-results/test.log +12 -12
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  9. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +108 -108
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
  26. test/paired/new-results/run-times.csv +7 -7
  27. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +4 -4
  28. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  29. test/paired/new-results/subset-partition-new-simu/merged-partition.log +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  33. test/paired/new-results/test.log +65 -65
  34. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  35. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  36. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  37. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  38. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/gctree-run.py +0 -0
  39. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/parse-output.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/partis-test.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.post1.dev1.data}/scripts/split-loci.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.dist-info}/WHEEL +0 -0
  44. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.dist-info}/entry_points.txt +0 -0
  45. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.dist-info}/licenses/COPYING +0 -0
  46. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.post1.dev1.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,13.2
3
- partition-new-simu,20.9
4
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4
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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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+ water time: 0.6 (ig-sw 0.6 processing 0.0)
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+ total time: 2.8
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  total time: 1.2
@@ -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: 23.9
311
+ total time: 24.0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -140,7 +140,7 @@ hmm
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 (0.2s)
143
+ 28 clusters with 5 procs (0.3s)
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: 2.9
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 (0.2s)
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)
@@ -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: 0.5
232
+ total time: 0.4
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: 25.0
309
+ total time: 25.4
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -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: 15.1
275
+ total time: 15.2