partis-bcr 1.0.8.post1.dev1__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

{partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.8.post1.dev1
+Version: 1.0.9.post1.dev1
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph

{partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD

@@ -303,16 +303,16 @@ data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
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 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
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 python/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -372,8 +372,8 @@ test/phylo-naive-run.py,sha256=pTyXPv0CBddu0CVPetORRazoYyKzYa427Cwtpcuq7DE,5282
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@@ -456,8 +456,8 @@ test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ6_star_02.csv,sha256=-nv
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@@ -472,13 +472,13 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=qnyJc6r4fEij37iP8yKvwXdXa6oz1GlprIABjBvEac4,5954
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@@ -488,7 +488,7 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust
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@@ -504,7 +504,7 @@ test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.csv,sha256=tzXelx5oSqhgkstNA-6DGK027GYT-M4TXrFGDEWNEcg,405
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 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_3p_del.csv,sha256=P0iNxvqMk9z8jTIYcGjxfKa-T2JIi3eOSh3eXPEnBvM,318
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_5p_del.csv,sha256=G4CoyPjc1MSkQnVijOv2ysz56zGYG4i-QYelQU-un10,635
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/dj_insertion.csv,sha256=kLzxSn3wfZysDk4IhTlgvEsvdNbLWYOJgMTz_nqRJHU,233
@@ -1182,7 +1182,7 @@ test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igh.yaml,sha256=9Pxnw0p8Ug9ZMVcg7X7RMHURhxpWtpj4h93WuuVS-NY,31446
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml,sha256=ZPuU2MYn7BLZmOJ6jUiH-oCa3SaZAr0jVMEAePScKxA,14687
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml,sha256=Ls3u67M8CfP5yaBnfud78p7L9uwH1B0BXGkFwHf48to,6542
-test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=Ky5YM8mpCQX3oOqHV6IYQCZAAGpmXFx2enApkFx_z9o,30272
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 test/paired/new-results/subset-partition-new-simu/partition-igh.yaml,sha256=HgoqpG1_ChEuLNouoAGTWOJTKXDR9TP6y_TFxIMmprI,66188
 test/paired/new-results/subset-partition-new-simu/partition-igk.yaml,sha256=Mwg9UfLe-e0sYsvxNgiepogOj0DxuIUECIktiMu_f-A,46690
 test/paired/new-results/subset-partition-new-simu/partition-igl.yaml,sha256=Wi-WCJfj2dWt0E0eSbKaSnY9zajo9lzpZnIVw7mF9OY,19395
@@ -1206,7 +1206,7 @@ test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml,sha256=ZUaFW7
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igh.yaml,sha256=AcC85PCqK8Epm4ICu4B8q5eUjtsmlFTQwTkmMhZqQ5I,30562
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igk.yaml,sha256=TrjOFEnyjqRB1mIbZaG2dDUg0BB7h_YMn7P7NJ4siRA,24486
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igl.yaml,sha256=fc2SzIWy51agwAZcCTJZAfZW_-ddT-g0celyJsbelgY,7960
-test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=RLEDDZ7WOKXqyTYj47wGYxJYW8-S_24cbUH92JPRbAQ,24021
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 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igh.fa,sha256=vR3IfQGVf6SVv6ls-ebrcQmDTDxNu0nhjizzNbitup4,5852
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igk.fa,sha256=_fxa0GOLuWDb0sfWeO4YbSmIcKwuG4F_4fMxte4dYLE,5107
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml,sha256=FjL_OaOcNDHHamp3ehFMyAuU4sO4_TMXgEAPlI1kBdw,22125
@@ -1557,7 +1557,7 @@ test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml,sha256=J_IVfe
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml,sha256=BiuYTVEBQq5uK6kM1ywk5H5q_ebrK7YJ_38iBuRi2eU,45209
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igk.yaml,sha256=93vPGzB3jaCjPPBEUEvqSqf2axzmd1Ry0P6-YoN7OTg,28793
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igl.yaml,sha256=rzwVZ9JijOgNZAWVW5MaiYTNW6HtQvsrqKPV_y9NT30,14925
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@@ -1926,7 +1926,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partiti
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igk.yaml,sha256=Ybr2uxzr0wzPyEwrxDWDYif2gFk4UlHNPsXmufeFZhg,50990
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@@ -1960,7 +1960,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-33_star_01.yaml,sha256=FU4oDYBlqRgZwlQrbG23AEZneBh-icKPaswTKnXojUI,103996
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-7_star_01.yaml,sha256=GLt0fNZJsArlWs95oE7v2E-ZKciqmRa6plG-AWAxaCg,104240
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV4-39_star_01.yaml,sha256=GGUYeGeP3CaMWhWo4B32FWDF5ohfVAJf8_QwQ9sSkp0,104436
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 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/all-mean-mute-freqs.csv,sha256=yR5AuVGrcUAOe72bT-nEJap_zn3AwCpaXSrFGELbDyA,740
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/d_gene-probs.csv,sha256=p07NACPyIrtcnGVLP8tHoSHCBiO_H7OazG_siOykHws,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/j_gene-probs.csv,sha256=40-_sM8ZQBd6J9r__bewvD1wb3DELCmaRHpLak-xa0s,75
@@ -1979,7 +1979,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV2-30_star_01.yaml,sha256=otPu6N94wuSVkMB8R4ZUYp0k0NLTXBreU1OCCc1VYBk,107159
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-11_star_01.yaml,sha256=dizIw0o2xB1DiUzb_HneMaz3yIIyxS0d2HiPCdwo2fA,102590
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-15_star_01.yaml,sha256=1z0A-rW4uPkaZ0u-3Vu9fxdBoNqsf8MXfaT6yjkaKxw,103093
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@@ -6805,8 +6805,8 @@ test/ref-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute
 test/ref-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv,sha256=PHIIaj2iqO9j_2G9QQFo7DKsra61A4_2skRWCeeonxY,152
 test/ref-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
 test/ref-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
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-test/ref-results/partition-new-simu/raxml-annotations.yaml,sha256=6FByt533Ynx0WNz3bKdJctiGpa0sxN2F1vaiWMA1ab4,35816
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 test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=qokRcGSD1p1XlPUBpYFMm8HYpMKfb4ed4d5PwKMVC6E,4377
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@@ -6817,75 +6817,75 @@ test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=1Fxnsh
 test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=UdE9X7VYtEqKx8zo0lP2gQh9mTnpsrT_R8p0jkS_wgs,3133
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test/new-results/get-selection-metrics-new-simu.yaml

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0.21915764250378367}, "lbr": {"97366cf0d8": 0.0, "20a0129b57": 0.0, "Node1": 1.2698143790030876, "31e052ee14": 0.0, "13de8675ec": 0.0, "33aaa62e12": 0.0, "91796617a0": 0.00016283931644033088, "4233d708fe": 1.2730717600677643, "XnaiveX": 0.0}, "lbf": {"97366cf0d8": 0.0, "20a0129b57": 0.0, "Node1": 10.577195614616683, "31e052ee14": 0.0, "13de8675ec": 0.0, "33aaa62e12": 0.0, "91796617a0": 0.003077014099006546, "4233d708fe": 10.588666708369407, "XnaiveX": 10.587826640491166}, "aa-tree": "[&R] (((97366cf0d8:0.0,20a0129b57:0.0)Node1:0.0,31e052ee14:0.0,13de8675ec:0.0,(33aaa62e12:0.0)91796617a0:0.0)4233d708fe:0.0)XnaiveX;\n", "aa-lbi": {"97366cf0d8": -7.816792314480525e-06, "20a0129b57": -7.816792314480525e-06, "Node1": -7.816792314480525e-06, "31e052ee14": -7.816792314480525e-06, "13de8675ec": -7.816792314480525e-06, "33aaa62e12": -7.816792314480525e-06, "91796617a0": -7.816792314480525e-06, "4233d708fe": -7.816792314480525e-06, "XnaiveX": -7.816792314480525e-06}, "aa-lbr": {"97366cf0d8": 0.0, "20a0129b57": 0.0, "Node1": 0.0, "31e052ee14": 0.0, "13de8675ec": 0.0, "33aaa62e12": 0.0, "91796617a0": 0.0, "4233d708fe": 0.0, "XnaiveX": 0.0}, "aa-lbf": {"97366cf0d8": 0.0, "20a0129b57": 0.0, "Node1": 0.0, "31e052ee14": 0.0, "13de8675ec": 0.0, "33aaa62e12": 0.0, "91796617a0": 0.0, "4233d708fe": 0.0, "XnaiveX": 0.0}}}, {"unique_ids": ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7", "Node1", "Node3", "Node4", "Node5", "Node6"], "lb": {"tree": "[&R] ((c8a90cc3d7:0.016006,((((73431a9b10:0.005284)bf50fa2017:0.002644,(17f57acf2e:0.002632,162cb1691f:0.005305)Node3:0.005307)Node4:1e-06,948b83fb4d:0.005307)Node5:0.00264,73d6c6e558:0.007946)Node6:1e-06)Node1:0.002638)XnaiveX;\n", "cons-dist-aa": {"162cb1691f": -4, "17f57acf2e": -2, "73431a9b10": -1, "73d6c6e558": -4, "948b83fb4d": -1, "bf50fa2017": -1, "c8a90cc3d7": -6, "Node1": -1, "Node3": -2, "Node4": 0, "Node5": 0, "Node6": -1}, "lbi": {"c8a90cc3d7": 0.001056313333333558, "73431a9b10": 0.022614948731750913, "bf50fa2017": 0.3166073532320486, "17f57acf2e": 0.07657463186082135, "162cb1691f": 0.022384502502963897, "Node3": 0.31640963283801715, "Node4": 0.6201628266196499, "948b83fb4d": 0.06301460119113088, "Node5": 0.6201997498489367, "73d6c6e558": 0.02281019921398838, "Node6": 0.6273121481194683, "Node1": 0.6272700063647452, "XnaiveX": 0.33971513842717843}, "lbr": {"c8a90cc3d7": 0.0, "73431a9b10": 0.0, "bf50fa2017": 0.4385921655966751, "17f57acf2e": 0.0, "162cb1691f": 0.0, "Node3": 1.1183570989926281, "Node4": 0.7812198562228089, "948b83fb4d": 0.0, "Node5": 1.67970338587788, "73d6c6e558": 0.0, "Node6": 1.3233152565839676, "Node1": 3.640156724290387, "XnaiveX": 0.0}, "lbf": {"c8a90cc3d7": 0.0, "73431a9b10": 0.0, "bf50fa2017": 2.780124548468202, "17f57acf2e": 0.0, "162cb1691f": 0.0, "Node3": 4.812234014943255, "Node4": 6.482481167867299, "948b83fb4d": 0.0, "Node5": 9.2651322984344, "73d6c6e558": 0.0, "Node6": 8.494563444674098, "Node1": 11.699045596577553, "XnaiveX": 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test/new-results/test.log

@@ -8,14 +8,14 @@ smith-waterman  (new-allele fitting)
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
-    water time: 0.0  (ig-sw 0.0  processing 0.0)
+    water time: 0.1  (ig-sw 0.0  processing 0.1)
 smith-waterman  (writing parameters)
   vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/simu/sw (1.3 sec)
+    writing parameters to test/new-results/test/parameters/simu/sw (1.2 sec)
     water time: 1.3  (ig-sw 1.3  processing 0.0)
   writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
 (0.1 sec)

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.666 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
+ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1661.140 Time 0.08
-Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-1/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.652 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
+ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.07
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.06 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.07
-Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.08 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.08
+Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 132 times)
 Initial topology in 0.00 seconds
 Refining topology: 10 rounds ME-NNIs, 2 rounds ME-SPRs, 5 rounds ML-NNIs
-Total branch-length 0.072 after 0.00 sec
+Total branch-length 0.072 after 0.01 sec
 ML-NNI round 1: LogLk = -1300.914 NNIs 1 max delta 0.86 Time 0.01
 GTR Frequencies: 0.2567 0.2538 0.2729 0.2166
 GTR rates(ac ag at cg ct gt) 0.8119 1.2276 0.7151 1.1364 0.4746 1.0000

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -794.513 Time 0.04
-Total time: 0.05 seconds Unique: 7/7 Bad splits: 0/4
+ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -794.513 Time 0.03
+Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4

test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log

@@ -15,7 +15,7 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -613.867 NNIs 0 max delta 0.00 Time 0.02
+ML-NNI round 2: LogLk = -613.867 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -613.867 NNIs 0 max delta 0.00 Time 0.03 (final)
 Optimize all lengths: LogLk = -613.867 Time 0.03