partis-bcr 1.0.12.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev2__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 (48) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/RECORD +48 -47
  5. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  6. test/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
  7. test/new-results/run-times.csv +5 -5
  8. test/new-results/test.log +15 -15
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  28. test/paired/new-results/run-times.csv +7 -7
  29. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +2 -2
  30. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +6 -6
  31. test/paired/new-results/subset-partition-new-simu/merged-partition.log +2 -2
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  34. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  35. test/paired/new-results/test.log +76 -76
  36. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/cf-alleles.py +0 -0
  37. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/cf-germlines.py +0 -0
  38. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/compare-plotdirs.py +0 -0
  39. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/extract-pairing-info.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/gctree-run.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/get-naive-probabilities.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/parse-output.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/partis-test.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/split-loci.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/WHEEL +0 -0
  46. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/entry_points.txt +0 -0
  47. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/licenses/COPYING +0 -0
  48. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev2.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,13.4
3
- partition-new-simu,21.5
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5
- seed-partition-new-simu,10.5
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3
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  getting annotations for final partition
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  subcluster annotating 12 clusters with steps: (0.4s) (0.1s)
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- total time: 2.0
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  partition igk:
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  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
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@@ -308,4 +308,4 @@ hmm
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+ total time: 24.6
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
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  running 10 procs for 32 seqs
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  kept 14 (0.438) unproductive
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+ water time: 0.1 (ig-sw 0.0 processing 0.0)
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+ caching all 32 naive sequences (0.7s)
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  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: 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
@@ -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: 25.4
309
+ total time: 26.0
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: 1.7
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)
39
39
  subcluster annotation time 1.0
@@ -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: 15.2
275
+ total time: 15.6