partis-bcr 1.0.9.post1.dev4__cp312-cp312-manylinux1_x86_64.whl → 1.0.10.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 (45) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/RECORD +45 -45
  5. test/new-results/test.log +3 -3
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  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-annotation-performance/plots/flcount-matrix.svg +107 -107
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  25. test/paired/new-results/run-times.csv +5 -5
  26. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -5
  27. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +10 -10
  28. test/paired/new-results/subset-partition-new-simu/merged-partition.log +7 -7
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  32. test/paired/new-results/test.log +50 -50
  33. test/phylo-naive-run.py +1 -1
  34. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  35. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  36. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  37. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  38. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/gctree-run.py +0 -0
  39. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  40. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/partis-test.py +0 -0
  41. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/split-loci.py +0 -0
  42. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/WHEEL +0 -0
  43. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/entry_points.txt +0 -0
  44. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/licenses/COPYING +0 -0
  45. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.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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- partition-new-simu,21.2
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- subset-partition-new-simu,70.5
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- seed-partition-new-simu,10.6
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3
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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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  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-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --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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@@ -75,7 +75,7 @@ smith-waterman (new-allele fitting)
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+ water time: 0.1 (ig-sw 0.0 processing 0.0)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.5 sec)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.4 sec)
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  getting annotations for final partition
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156
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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
157
157
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -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: 24.2
311
+ total time: 25.5
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
@@ -57,7 +57,7 @@ smith-waterman (writing parameters)
57
57
  hmm
58
58
  reading output
59
59
  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
60
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.6 sec)
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
62
  hmm step time: 1.2
63
63
  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
@@ -82,18 +82,18 @@ smith-waterman (writing parameters)
82
82
  kept 9 (0.500) unproductive
83
83
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
84
84
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.5 sec)
85
- water time: 0.6 (ig-sw 0.5 processing 0.0)
85
+ water time: 0.5 (ig-sw 0.5 processing 0.0)
86
86
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
87
87
  (0.2 sec)
88
88
  hmm
89
89
  reading output
90
90
  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
91
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.5 sec)
91
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.4 sec)
92
92
  infra time: 0.5
93
93
  hmm step time: 0.7
94
94
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
95
95
  (0.2 sec)
96
- total time: 1.9
96
+ total time: 1.8
97
97
  cache-parameters igl:
98
98
  run partis cache-parameters --locus igl --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/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
99
99
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -113,7 +113,7 @@ smith-waterman (writing parameters)
113
113
  kept 7 (0.636) unproductive
114
114
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
115
115
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.3 sec)
116
- water time: 0.4 (ig-sw 0.4 processing 0.0)
116
+ water time: 0.4 (ig-sw 0.3 processing 0.0)
117
117
  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
118
118
  (0.1 sec)
119
119
  hmm
@@ -124,7 +124,7 @@ hmm
124
124
  hmm step time: 0.5
125
125
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
126
126
  (0.1 sec)
127
- total time: 1.3
127
+ total time: 1.2
128
128
  partition igh:
129
129
  run partis partition --locus igh --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/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
130
130
  --input-metafnames: added meta info for 32 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)
@@ -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 (0.3s)
164
+ caching all 18 naive sequences (0.2s)
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)
@@ -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: 25.8
309
+ total time: 25.9
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -32,10 +32,10 @@ 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 (0.4s)
36
- partition loop time: 1.7
35
+ 21 clusters with 1 proc (0.5s)
36
+ partition loop time: 1.8
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
38
+ subcluster annotating 18 clusters with steps: (0.6s) (0.3s) (0.1s)
39
39
  subcluster annotation time 1.0
40
40
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
41
41
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -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']
@@ -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
@@ -179,7 +179,7 @@ smith-waterman
179
179
  water time: 0.0
180
180
  hmm
181
181
  subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
182
- subcluster annotation time 0.6
182
+ subcluster annotation time 0.5
183
183
  total time: 0.6
184
184
  need to get annotations for 13/15 joint igk clusters
185
185
  annotate igh+igk: igk
@@ -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: 15.5