PyEvoMotion 0.1.0__py3-none-any.whl → 0.1.2__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.
- PyEvoMotion/cli.py +88 -11
- PyEvoMotion/core/base.py +373 -34
- PyEvoMotion/core/core.py +136 -43
- PyEvoMotion/core/parser.py +4 -1
- {pyevomotion-0.1.0.dist-info → pyevomotion-0.1.2.dist-info}/METADATA +72 -4
- pyevomotion-0.1.2.dist-info/RECORD +35 -0
- share/analyze_model_selection_accuracy.py +316 -0
- share/analyze_test_runs.py +436 -0
- share/anomalous_diffusion.pdf +0 -0
- share/confusion_matrix_heatmap.pdf +0 -0
- share/figUK.tsv +9949 -0
- share/figUK_plots.pdf +0 -0
- share/figUK_regression_results.json +65 -0
- share/figUK_run_args.json +14 -0
- share/figUK_stats.tsv +41 -0
- share/figUSA.tsv +9470 -0
- share/figUSA_plots.pdf +0 -0
- share/figUSA_regression_results.json +65 -0
- share/figUSA_run_args.json +14 -0
- share/figUSA_stats.tsv +34 -0
- share/figdataUK.tsv +10001 -0
- share/figdataUSA.tsv +10001 -0
- share/generate_sequences_from_synthdata.py +85 -0
- share/generate_sequences_from_test5_data.py +107 -0
- share/manuscript_figure.py +858 -43
- share/run_parallel_analysis.py +196 -0
- share/synth_figure.pdf +0 -0
- share/uk_time_windows.pdf +0 -0
- share/weekly_size.pdf +0 -0
- pyevomotion-0.1.0.dist-info/RECORD +0 -13
- {pyevomotion-0.1.0.dist-info → pyevomotion-0.1.2.dist-info}/WHEEL +0 -0
- {pyevomotion-0.1.0.dist-info → pyevomotion-0.1.2.dist-info}/entry_points.txt +0 -0
share/figUK_plots.pdf
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{
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"mean number of mutations model": {
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"parameters": {
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"b": 35.634115529420946
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"confidence_intervals": {
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"m": [
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],
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"b": [
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"expression": "mx + b",
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"confidence_level": 0.95,
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"r2": 0.9637010376538699
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},
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"scaled var number of mutations model": {
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"linear_model": {
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"parameters": {
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"m": 0.2701500514044973
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"confidence_intervals": {
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"m": [
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"expression": "mx",
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"r2": 0.23974456333891003,
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"confidence_level": 0.95
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},
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"power_law_model": {
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"parameters": {
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"d": 1.949675756351066,
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"alpha": 0.40103856972319674
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"confidence_intervals": {
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"d": [
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"alpha": [
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},
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"expression": "d*x^alpha",
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"r2": 0.7403444327630024,
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"confidence_level": 0.95
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},
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"model_selection": {
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"selected": "power_law",
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"linear_AIC": 173.79403093437475,
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"power_law_AIC": 133.0411534485154,
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"delta_AIC_linear": 40.75287748585936,
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"delta_AIC_power_law": 0.0,
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"akaike_weight_linear": 1.414572114240171e-09,
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"akaike_weight_power_law": 0.999999998585428
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}
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}
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{
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"seqs": "tests/data/test3/test3UK.fasta",
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"meta": "share/figdataUK.tsv",
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"out": "share/figUK",
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"delta_t": "7D",
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"show": false,
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"export_plots": true,
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"confidence_level": 0.95,
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"length_filter": 0,
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"kind": "total",
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"filter": null,
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"genome_positions": null,
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"date_range": "2020-10-01..2021-08-01"
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}
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share/figUK_stats.tsv
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date mean number of mutations var number of mutations size dt_idx
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2020-10-29 34.515151515151516 0.8689976689976701 66 0.0
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2020-11-05 35.029411764705884 0.9620915032679709 136 1.0
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2020-11-12 35.63250883392226 1.9921309174748796 283 2.0
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2020-11-19 36.07575757575758 2.5170742962621144 198 3.0
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2020-11-26 36.37826086956522 3.6685209796848266 230 4.0
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2020-12-03 36.20704845814978 4.297649214455573 227 5.0
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2020-12-10 36.555865921787706 3.715357651440464 358 6.0
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2020-12-17 37.040625 4.709943181818182 320 7.0
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2020-12-24 37.450171821305844 6.5794051427894376 291 8.0
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2020-12-31 37.649068322981364 6.614781060737982 322 9.0
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2021-01-07 37.97329376854599 5.907022749752713 337 10.0
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2021-01-14 38.126182965299684 7.1675717765443405 317 11.0
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2021-01-21 38.33774834437086 6.476909198917517 302 12.0
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2021-01-28 38.614285714285714 6.632053251408085 280 13.0
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2021-02-04 38.891373801916934 8.481752273285828 313 14.0
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2021-02-11 38.62369337979094 7.235520576984016 287 15.0
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2021-02-18 39.12367491166078 7.97401197904921 283 16.0
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2021-02-25 39.30167597765363 6.558596623006733 358 17.0
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2021-03-04 39.56273764258555 6.239369575944036 263 18.0
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2021-03-11 39.64939024390244 8.613699932870894 328 19.0
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2021-03-18 39.625 7.909090909090907 320 20.0
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2021-03-25 40.233676975945016 8.607275743571508 291 21.0
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2021-04-01 40.11 8.345719063545154 300 22.0
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2021-04-08 40.11552346570397 6.776461047454612 277 23.0
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2021-04-15 40.674121405750796 7.5344884082903265 313 24.0
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2021-04-22 40.55882352941177 8.050626808100292 306 25.0
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2021-04-29 41.38768115942029 9.140065876152836 276 26.0
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2021-05-06 41.098684210526315 7.442374500607957 304 27.0
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2021-05-13 41.06024096385542 8.75038865137971 249 28.0
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2021-05-20 41.205479452054796 9.091653721225812 292 29.0
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2021-05-27 40.85546875 9.69275428921569 256 30.0
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2021-06-03 41.12112676056338 8.886416805920257 355 31.0
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2021-06-10 41.49 6.96472361809045 200 32.0
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2021-06-17 41.723404255319146 7.741267493457731 188 33.0
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2021-06-24 42.27860696517413 6.611990049751241 201 34.0
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2021-07-01 42.541935483870965 8.717385839966484 155 35.0
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2021-07-08 42.71875 7.475198412698421 64 36.0
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2021-07-15 43.333333333333336 8.333333333333332 39 37.0
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2021-07-22 42.32142857142857 7.822077922077916 56 38.0
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2021-07-29 41.857142857142854 15.14285714285714 7 39.0
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