partis-bcr 1.0.12.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev3__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.dev3.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.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 +4 -4
  8. test/new-results/test.log +9 -9
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +1 -1
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  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 +6 -6
  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 +3 -3
  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 +64 -64
  36. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  37. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  38. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  39. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/gctree-run.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/parse-output.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/partis-test.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/split-loci.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/WHEEL +0 -0
  46. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/entry_points.txt +0 -0
  47. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/licenses/COPYING +0 -0
  48. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.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
4
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5
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6
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4
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  reading output
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  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.5 sec)
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- infra time: 0.5
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- hmm step time: 1.0
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+ infra time: 0.6
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+ hmm step time: 1.1
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@@ -75,7 +75,7 @@ smith-waterman (new-allele fitting)
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  running 11 procs for 2 seqs
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  kept 5 (0.278) unproductive
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+ water time: 0.1 (ig-sw 0.0 processing 0.0)
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  getting annotations for final partition
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  partition igk:
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  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -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: 24.5
311
+ total time: 24.4
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -43,7 +43,7 @@ smith-waterman (new-allele fitting)
43
43
  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: 0.0 (ig-sw 0.0 processing 0.0)
46
+ water time: 0.1 (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
@@ -53,16 +53,16 @@ smith-waterman (writing parameters)
53
53
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.6 sec)
54
54
  water time: 0.7 (ig-sw 0.6 processing 0.0)
55
55
  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
56
- (0.5 sec)
56
+ (0.6 sec)
57
57
  hmm
58
58
  reading output
59
59
  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
60
60
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.5 sec)
61
61
  infra time: 0.6
62
- hmm step time: 1.2
62
+ hmm step time: 1.3
63
63
  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
64
64
  (0.5 sec)
65
- total time: 3.1
65
+ total time: 3.2
66
66
  cache-parameters igk:
67
67
  run partis cache-parameters --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 --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
68
68
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -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)
@@ -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: 26.1
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
@@ -122,7 +122,7 @@ hmm
122
122
  partition loop time: 0.3
123
123
  getting annotations for final partition
124
124
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s) (0.1s)
125
- subcluster annotation time 0.2
125
+ subcluster annotation time 0.3
126
126
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
127
127
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
128
128
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
@@ -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