partis-bcr 1.0.8.post1.dev1__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.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.
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +95 -95
- test/new-results/get-selection-metrics-new-simu.yaml +1 -1
- test/new-results/test.log +2 -2
- test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
- test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
- test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
- test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
- test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
- test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
- test/paired/new-results/run-times.csv +6 -6
- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -6
- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
- test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
- test/paired/new-results/test.log +33 -33
- test/ref-results/partition-new-simu/iqtree/iclust-0/log +187 -151
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +34 -34
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +187 -151
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +2820 -2820
- test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -1
- test/ref-results/partition-new-simu/iqtree/iclust-1/log +166 -207
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +151 -151
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +166 -207
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +740 -740
- test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -1
- test/ref-results/partition-new-simu/iqtree/iclust-2/log +134 -135
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +17 -17
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +134 -135
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +763 -763
- test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -1
- test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +30 -30
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +7 -7
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +87 -87
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-0/log +198 -197
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +54 -54
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-1/log +112 -112
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +22 -22
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -6
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +84 -84
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -20
- test/ref-results/partition-new-simu/raxml/iclust-2/log +182 -182
- test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -1
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
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/home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa --msa-format FASTA
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Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.846063 (ML), weights&rates: (0.250000,0.875813) (0.250000,0.964710) (0.250000,1.029570) (0.250000,1.129908)
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RAxML-NG v. 1.2.1 released on 22.12.2023 by The Exelixis Lab.
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[00:00:00] Tree #10, final logLikelihood: -688.
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[00:00:00] Tree #10, final logLikelihood: -688.737991
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[00:00:00 -674.849261] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #11, final logLikelihood: -668.
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[00:00:00] Tree #11, final logLikelihood: -668.362419
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[00:00:00] Tree #12, initial LogLikelihood: -934.227552
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[00:00:00 -674.849503] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #12, final logLikelihood: -668.
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[00:00:00] Tree #12, final logLikelihood: -668.362318
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[00:00:00] Tree #13, initial LogLikelihood: -934.
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[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #17, final logLikelihood: -668.
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[00:00:00] Tree #18, initial LogLikelihood: -934.
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[00:00:00 -934.239923] Initial branch length optimization
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[00:00:00 -674.849193] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #18, final logLikelihood: -668.
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[00:00:00] Tree #18, final logLikelihood: -668.362454
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[00:00:00] Tree #19, initial LogLikelihood: -934.
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[00:00:00 -674.849233] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #19, final logLikelihood: -668.
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[00:00:00] Tree #19, final logLikelihood: -668.362478
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[00:00:00] Tree #20, initial LogLikelihood: -934.
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[00:00:00] Tree #20, initial LogLikelihood: -934.232961
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[00:00:00 -674.849080] Model parameter optimization (eps = 10.000000)
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[00:00:00] Tree #20, final logLikelihood: -668.
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[00:00:00] Tree #20, final logLikelihood: -668.362545
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Optimized model parameters:
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Partition 0: noname
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407
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Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.
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408
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Base frequencies (ML): 0.
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Substitution rates (ML): 0.
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Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.862356 (ML), weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897)
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408
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Base frequencies (ML): 0.220521 0.272281 0.285569 0.221629
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Substitution rates (ML): 0.586335 0.197169 0.228769 0.865038 1.202222 1.000000
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Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs
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Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates
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@@ -414,7 +414,7 @@ Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/par
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Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log
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Analysis started:
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Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:55
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Elapsed time: 0.
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Elapsed time: 0.393 seconds
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