partis-bcr 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__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 (57) hide show
  1. bin/partis-test.py +3 -3
  2. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +3 -3
  3. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +57 -56
  5. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  6. test/new-results/run-times.csv +4 -4
  7. test/new-results/test/simu.yaml +1 -1
  8. test/new-results/test.log +24 -24
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  27. test/paired/new-results/run-times.csv +7 -7
  28. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +2 -2
  29. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +2 -2
  30. test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  34. test/paired/new-results/test/simu/all-seqs.fa +168 -212
  35. test/paired/new-results/test/simu/igh+igk/igh.yaml +1 -1
  36. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -1
  37. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -1
  38. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -1
  39. test/paired/new-results/test/simu/igh.yaml +1 -1
  40. test/paired/new-results/test/simu/igk.yaml +1 -1
  41. test/paired/new-results/test/simu/igl.yaml +1 -1
  42. test/paired/new-results/test/simu/meta.yaml +1 -1
  43. test/paired/new-results/test.log +97 -109
  44. test/test.py +3 -3
  45. test/trees.nwk +100 -0
  46. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  47. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  48. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  49. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  50. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  51. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  52. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  53. {partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  54. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  55. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  56. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  57. {partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.11.post1.dev7.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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3
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4
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6
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2
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3
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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
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  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.3 sec)
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+ total time: 23.9
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
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  kept 9 (0.500) unproductive
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test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -32,7 +32,7 @@ hmm
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  23 clusters with 5 procs (0.3s)
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33
  22 clusters with 3 procs (0.3s)
34
34
  21 clusters with 2 procs (0.1s)
35
- 21 clusters with 1 proc (0.4s)
35
+ 21 clusters with 1 proc (0.5s)
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: 2.9
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']
@@ -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: 15.3
275
+ total time: 15.2