partis-bcr 1.0.12__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 (47) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/RECORD +47 -46
  5. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  6. test/new-results/run-times.csv +3 -3
  7. test/new-results/test.log +16 -16
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  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-1/log +1 -1
  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 +5 -5
  28. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +1 -5
  29. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -9
  30. test/paired/new-results/subset-partition-new-simu/merged-partition.log +2 -6
  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.log +63 -72
  35. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/cf-alleles.py +0 -0
  36. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/cf-germlines.py +0 -0
  37. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/compare-plotdirs.py +0 -0
  38. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/extract-pairing-info.py +0 -0
  39. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/gctree-run.py +0 -0
  40. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/get-naive-probabilities.py +0 -0
  41. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/parse-output.py +0 -0
  42. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/partis-test.py +0 -0
  43. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev2.data}/scripts/split-loci.py +0 -0
  44. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/WHEEL +0 -0
  45. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/entry_points.txt +0 -0
  46. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/licenses/COPYING +0 -0
  47. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev2.dist-info}/top_level.txt +0 -0
test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg CHANGED
@@ -6,7 +6,7 @@
6
6
  <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
7
7
  <cc:Work>
8
8
  <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
9
- <dc:date>2025-08-25T00:48:43.063269</dc:date>
9
+ <dc:date>2025-08-28T21:06:48.965508</dc:date>
10
10
  <dc:format>image/svg+xml</dc:format>
11
11
  <dc:creator>
12
12
  <cc:Agent>
@@ -41,19 +41,19 @@ z
41
41
  <g id="xtick_1">
42
42
  <g id="line2d_1">
43
43
  <defs>
44
- <path id="mfedd6eedd6" d="M 0 0
44
+ <path id="m57f274e491" d="M 0 0
45
45
  L 0 3.5
46
46
  " style="stroke: #262626; stroke-width: 0.8"/>
47
47
  </defs>
48
48
  <g>
49
- <use xlink:href="#mfedd6eedd6" x="82.944" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
49
+ <use xlink:href="#m57f274e491" x="82.944" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
50
50
  </g>
51
51
  </g>
52
52
  </g>
53
53
  <g id="xtick_2">
54
54
  <g id="line2d_2">
55
55
  <g>
56
- <use xlink:href="#mfedd6eedd6" x="153.9072" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
56
+ <use xlink:href="#m57f274e491" x="153.9072" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
57
57
  </g>
58
58
  </g>
59
59
  <g id="text_1">
@@ -63,7 +63,7 @@ L 0 3.5
63
63
  <g id="xtick_3">
64
64
  <g id="line2d_3">
65
65
  <g>
66
- <use xlink:href="#mfedd6eedd6" x="224.8704" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
66
+ <use xlink:href="#m57f274e491" x="224.8704" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
67
67
  </g>
68
68
  </g>
69
69
  <g id="text_2">
@@ -73,7 +73,7 @@ L 0 3.5
73
73
  <g id="xtick_4">
74
74
  <g id="line2d_4">
75
75
  <g>
76
- <use xlink:href="#mfedd6eedd6" x="295.8336" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
76
+ <use xlink:href="#m57f274e491" x="295.8336" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
77
77
  </g>
78
78
  </g>
79
79
  <g id="text_3">
@@ -83,7 +83,7 @@ L 0 3.5
83
83
  <g id="xtick_5">
84
84
  <g id="line2d_5">
85
85
  <g>
86
- <use xlink:href="#mfedd6eedd6" x="366.7968" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
86
+ <use xlink:href="#m57f274e491" x="366.7968" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
87
87
  </g>
88
88
  </g>
89
89
  <g id="text_4">
@@ -93,7 +93,7 @@ L 0 3.5
93
93
  <g id="xtick_6">
94
94
  <g id="line2d_6">
95
95
  <g>
96
- <use xlink:href="#mfedd6eedd6" x="437.76" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
96
+ <use xlink:href="#m57f274e491" x="437.76" y="276.48" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
97
97
  </g>
98
98
  </g>
99
99
  </g>
@@ -102,12 +102,12 @@ L 0 3.5
102
102
  <g id="ytick_1">
103
103
  <g id="line2d_7">
104
104
  <defs>
105
- <path id="m01d9c4b91e" d="M 0 0
105
+ <path id="mc2ac2625f5" d="M 0 0
106
106
  L -3.5 0
107
107
  " style="stroke: #262626; stroke-width: 0.8"/>
108
108
  </defs>
109
109
  <g>
110
- <use xlink:href="#m01d9c4b91e" x="82.944" y="265.169455" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
110
+ <use xlink:href="#mc2ac2625f5" x="82.944" y="265.169455" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
111
111
  </g>
112
112
  </g>
113
113
  <g id="text_5">
@@ -117,7 +117,7 @@ L -3.5 0
117
117
  <g id="ytick_2">
118
118
  <g id="line2d_8">
119
119
  <g>
120
- <use xlink:href="#m01d9c4b91e" x="82.944" y="215.483012" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
120
+ <use xlink:href="#mc2ac2625f5" x="82.944" y="215.483012" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
121
121
  </g>
122
122
  </g>
123
123
  <g id="text_6">
@@ -127,7 +127,7 @@ L -3.5 0
127
127
  <g id="ytick_3">
128
128
  <g id="line2d_9">
129
129
  <g>
130
- <use xlink:href="#m01d9c4b91e" x="82.944" y="165.796569" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
130
+ <use xlink:href="#mc2ac2625f5" x="82.944" y="165.796569" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
131
131
  </g>
132
132
  </g>
133
133
  <g id="text_7">
@@ -137,7 +137,7 @@ L -3.5 0
137
137
  <g id="ytick_4">
138
138
  <g id="line2d_10">
139
139
  <g>
140
- <use xlink:href="#m01d9c4b91e" x="82.944" y="116.110126" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
140
+ <use xlink:href="#mc2ac2625f5" x="82.944" y="116.110126" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
141
141
  </g>
142
142
  </g>
143
143
  <g id="text_8">
@@ -147,7 +147,7 @@ L -3.5 0
147
147
  <g id="ytick_5">
148
148
  <g id="line2d_11">
149
149
  <g>
150
- <use xlink:href="#m01d9c4b91e" x="82.944" y="66.423683" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
150
+ <use xlink:href="#mc2ac2625f5" x="82.944" y="66.423683" style="fill: #262626; stroke: #262626; stroke-width: 0.8"/>
151
151
  </g>
152
152
  </g>
153
153
  <g id="text_9">
@@ -161,25 +161,25 @@ L -3.5 0
161
161
  <g id="LineCollection_1">
162
162
  <path d="M 153.9072 83.951533
163
163
  L 153.9072 38.958545
164
- " clip-path="url(#p9a90c2a0ce)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
164
+ " clip-path="url(#p6daf56a11f)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
165
165
  <path d="M 224.8704 235.357589
166
166
  L 224.8704 215.483012
167
- " clip-path="url(#p9a90c2a0ce)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
167
+ " clip-path="url(#p6daf56a11f)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
168
168
  <path d="M 295.8336 265.169455
169
169
  L 295.8336 265.169455
170
- " clip-path="url(#p9a90c2a0ce)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
170
+ " clip-path="url(#p6daf56a11f)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
171
171
  <path d="M 366.7968 237.526361
172
172
  L 366.7968 218.282884
173
- " clip-path="url(#p9a90c2a0ce)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
173
+ " clip-path="url(#p6daf56a11f)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3"/>
174
174
  </g>
175
175
  <g id="line2d_12">
176
176
  <path d="M 153.9072 61.455039
177
177
  L 224.8704 225.4203
178
178
  L 295.8336 265.169455
179
179
  L 366.7968 227.904622
180
- " clip-path="url(#p9a90c2a0ce)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3; stroke-linecap: round"/>
180
+ " clip-path="url(#p6daf56a11f)" style="fill: none; stroke: #000000; stroke-opacity: 0.6; stroke-width: 3; stroke-linecap: round"/>
181
181
  <defs>
182
- <path id="mc07063287b" d="M 0 3.25
182
+ <path id="m1d73d729b2" d="M 0 3.25
183
183
  C 0.86191 3.25 1.688635 2.907559 2.298097 2.298097
184
184
  C 2.907559 1.688635 3.25 0.86191 3.25 0
185
185
  C 3.25 -0.86191 2.907559 -1.688635 2.298097 -2.298097
@@ -191,11 +191,11 @@ C -1.688635 2.907559 -0.86191 3.25 0 3.25
191
191
  z
192
192
  " style="stroke: #000000; stroke-opacity: 0.6"/>
193
193
  </defs>
194
- <g clip-path="url(#p9a90c2a0ce)">
195
- <use xlink:href="#mc07063287b" x="153.9072" y="61.455039" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
196
- <use xlink:href="#mc07063287b" x="224.8704" y="225.4203" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
197
- <use xlink:href="#mc07063287b" x="295.8336" y="265.169455" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
198
- <use xlink:href="#mc07063287b" x="366.7968" y="227.904622" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
194
+ <g clip-path="url(#p6daf56a11f)">
195
+ <use xlink:href="#m1d73d729b2" x="153.9072" y="61.455039" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
196
+ <use xlink:href="#m1d73d729b2" x="224.8704" y="225.4203" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
197
+ <use xlink:href="#m1d73d729b2" x="295.8336" y="265.169455" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
198
+ <use xlink:href="#m1d73d729b2" x="366.7968" y="227.904622" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
199
199
  </g>
200
200
  </g>
201
201
  <g id="patch_3">
@@ -234,7 +234,7 @@ L 145.13664 108.8308
234
234
  </g>
235
235
  <g id="line2d_14">
236
236
  <g>
237
- <use xlink:href="#mc07063287b" x="125.13664" y="108.8308" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
237
+ <use xlink:href="#m1d73d729b2" x="125.13664" y="108.8308" style="fill-opacity: 0.6; stroke: #000000; stroke-opacity: 0.6"/>
238
238
  </g>
239
239
  </g>
240
240
  <g id="text_11">
@@ -244,7 +244,7 @@ L 145.13664 108.8308
244
244
  </g>
245
245
  </g>
246
246
  <defs>
247
- <clipPath id="p9a90c2a0ce">
247
+ <clipPath id="p6daf56a11f">
248
248
  <rect x="82.944" y="27.648" width="354.816" height="248.832"/>
249
249
  </clipPath>
250
250
  </defs>
test/paired/new-results/run-times.csv CHANGED
@@ -1,8 +1,8 @@
1
1
  name,seconds
2
- cache-parameters-simu,13.8
2
+ cache-parameters-simu,13.7
3
3
  partition-new-simu,21.9
4
- subset-partition-new-simu,70.8
5
- seed-partition-new-simu,10.7
6
- get-selection-metrics-new-simu,7.2
4
+ subset-partition-new-simu,71.6
5
+ seed-partition-new-simu,10.9
6
+ get-selection-metrics-new-simu,7.1
7
7
  cache-parameters-data,23.4
8
- simulate,18.9
8
+ simulate,19.1
test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -217,7 +217,6 @@ cleaning pair info for 52 seqs
217
217
  k 0 0 3
218
218
  merge time 0.0
219
219
  need to get annotations for 1/8 joint igh clusters
220
- tag: v1.0.12
221
220
  annotate igh+igk: igh
222
221
  run partis annotate --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-0/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh-only-partition.yaml
223
222
  --input-metafnames: added meta info for 16 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml: loci paired-uids
@@ -234,7 +233,6 @@ hmm
234
233
  subcluster annotation time 0.3
235
234
  total time: 0.4
236
235
  need to get annotations for 5/8 joint igk clusters
237
- tag: v1.0.12
238
236
  annotate igh+igk: igk
239
237
  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-0/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/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 --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
240
238
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml: loci paired-uids
@@ -265,7 +263,6 @@ hmm
265
263
  h 0 0 0
266
264
  l 0 0 0
267
265
  merge time 0.0
268
- tag: v1.0.12
269
266
  annotate igh+igl: igh
270
267
  run partis annotate --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-0/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
271
268
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml: loci paired-uids
@@ -283,7 +280,6 @@ hmm
283
280
  subcluster annotation time 0.2
284
281
  total time: 0.2
285
282
  need to get annotations for 2/3 joint igl clusters
286
- tag: v1.0.12
287
283
  annotate igh+igl: igl
288
284
  run partis annotate --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-0/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
289
285
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml: loci paired-uids
@@ -312,4 +308,4 @@ hmm
312
308
  h 12 --> 11 -1
313
309
  k 6 --> 8 +2
314
310
  l 3 --> 3
315
- total time: 24.5
311
+ total time: 24.6
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -136,7 +136,7 @@ smith-waterman
136
136
  kept 14 (0.438) unproductive
137
137
  water time: 0.0
138
138
  hmm
139
- caching all 32 naive sequences (0.6s)
139
+ caching all 32 naive sequences (0.7s)
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)
@@ -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
@@ -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)
@@ -215,7 +215,6 @@ cleaning pair info for 61 seqs
215
215
  k 0 0 1
216
216
  merge time 0.0
217
217
  need to get annotations for 2/11 joint igh clusters
218
- tag: v1.0.12
219
218
  annotate igh+igk: igh
220
219
  run partis annotate --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/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/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 --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
221
220
  --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
@@ -230,9 +229,8 @@ smith-waterman
230
229
  hmm
231
230
  subcluster annotating 11 clusters with steps: (0.3s) (0.1s)
232
231
  subcluster annotation time 0.4
233
- total time: 0.5
232
+ total time: 0.4
234
233
  need to get annotations for 6/11 joint igk clusters
235
- tag: v1.0.12
236
234
  annotate igh+igk: igk
237
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
238
236
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -265,7 +263,6 @@ hmm
265
263
  l 0 0 1
266
264
  merge time 0.0
267
265
  need to get annotations for 2/5 joint igh clusters
268
- tag: v1.0.12
269
266
  annotate igh+igl: igh
270
267
  run partis annotate --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/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/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 --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
271
268
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -282,7 +279,6 @@ hmm
282
279
  subcluster annotation time 0.3
283
280
  total time: 0.4
284
281
  need to get annotations for 5/5 joint igl clusters
285
- tag: v1.0.12
286
282
  annotate igh+igl: igl
287
283
  run partis annotate --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/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --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 --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
288
284
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
@@ -310,4 +306,4 @@ hmm
310
306
  h 16 --> 16
311
307
  k 6 --> 11 +5
312
308
  l 3 --> 5 +2
313
- total time: 25.7
309
+ total time: 26.0
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -165,7 +165,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
165
165
  joint 0.963 0.594
166
166
  merge time 0.0
167
167
  need to get annotations for 6/15 joint igh clusters
168
- tag: v1.0.12
169
168
  annotate igh+igk: igh
170
169
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
170
  run partis annotate --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/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -180,10 +179,9 @@ smith-waterman
180
179
  water time: 0.0
181
180
  hmm
182
181
  subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
183
- subcluster annotation time 0.6
182
+ subcluster annotation time 0.5
184
183
  total time: 0.6
185
184
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.12
187
185
  annotate igh+igk: igk
188
186
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
187
  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/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --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/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -228,7 +226,6 @@ hmm
228
226
  joint 1.000 0.787
229
227
  merge time 0.0
230
228
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.12
232
229
  annotate igh+igl: igh
233
230
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
231
  run partis annotate --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/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -246,7 +243,6 @@ hmm
246
243
  subcluster annotation time 0.5
247
244
  total time: 0.6
248
245
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.12
250
246
  annotate igh+igl: igl
251
247
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
252
248
  run partis annotate --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/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -276,4 +272,4 @@ hmm
276
272
  h 18 --> 21 +3
277
273
  k 6 --> 15 +9
278
274
  l 3 --> 6 +3
279
- total time: 15.5
275
+ total time: 15.6