partis-bcr 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.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-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/RECORD +46 -46
  3. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  4. test/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
  5. test/new-results/run-times.csv +4 -4
  6. test/new-results/test.log +8 -8
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +1 -1
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-2/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 +107 -107
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  26. test/paired/new-results/run-times.csv +3 -3
  27. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -5
  28. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +4 -4
  29. test/paired/new-results/subset-partition-new-simu/merged-partition.log +2 -2
  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 +63 -63
  34. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  35. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  36. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  37. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  38. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/gctree-run.py +0 -0
  39. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  40. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/parse-output.py +0 -0
  41. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/partis-test.py +0 -0
  42. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.post1.dev1.data}/scripts/split-loci.py +0 -0
  43. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/WHEEL +0 -0
  44. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/entry_points.txt +0 -0
  45. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/licenses/COPYING +0 -0
  46. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.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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- partition-new-simu,21.1
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- subset-partition-new-simu,69.6
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+ partition-new-simu,21.5
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+ subset-partition-new-simu,70.3
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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@@ -123,7 +123,7 @@ hmm
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test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -43,7 +43,7 @@ smith-waterman (new-allele fitting)
43
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  running 10 procs for 32 seqs
44
44
  info for 32 / 32 = 1.000 (removed: 0 failed)
45
45
  kept 14 (0.438) unproductive
46
- water time: 0.1 (ig-sw 0.0 processing 0.0)
46
+ water time: 0.0 (ig-sw 0.0 processing 0.0)
47
47
  smith-waterman (writing parameters)
48
48
  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.0 sec
49
49
  running 10 procs for 32 seqs
@@ -138,9 +138,9 @@ smith-waterman
138
138
  hmm
139
139
  caching all 32 naive sequences (0.6s)
140
140
  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
141
- 30 clusters with 10 procs (0.2s)
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)
@@ -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: 25.3
309
+ total time: 25.4
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 (0.5s)
35
+ 21 clusters with 1 proc (0.4s)
36
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)
@@ -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: 2.8
50
+ total time: 2.9
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']