bella-companion 0.0.18__py3-none-any.whl → 0.0.19__py3-none-any.whl

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Files changed (7) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +1 -0
  2. bella_companion/eucovid/beast_configs/Nonparametric.xml +4 -4
  3. bella_companion/eucovid/run_beast.py +2 -2
  4. {bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/METADATA +1 -1
  5. {bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/RECORD +7 -7
  6. {bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/WHEEL +0 -0
  7. {bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/entry_points.txt +0 -0
bella_companion/eucovid/beast_configs/GLM.xml CHANGED
@@ -68,6 +68,7 @@
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  </plate>
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  <coefficients id="coefficientsGLM" spec="RealParameter" value="0.1"/>
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  <scaleFactor id="scaleFactorGLM" spec="RealParameter" value="1"/>
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+ <indicators spec="BooleanParameter" value="1"/>
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  </skylineValues>
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  <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
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  </migrationRate>
bella_companion/eucovid/beast_configs/Nonparametric.xml CHANGED
@@ -88,7 +88,7 @@
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  0.0 0.12 0.16 0.25
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  0.0 0.13 0.17 0.21
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  </arg>
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- <arg id="migrationRateScaler" spec="RealParameter" value="0.5"/>
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+ <arg id="f" spec="RealParameter" value="0.5"/>
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  </skylineValues>
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  </migrationRate>
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@@ -116,7 +116,7 @@
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  <stateNode idref="Re"/>
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  <stateNode idref="samplingProportion"/>
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  <stateNode idref="migrationRate"/>
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- <stateNode idref="migrationRateScaler"/>
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+ <stateNode idref="f"/>
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  <stateNode idref="kappa"/>
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  <stateNode idref="gammaShape"/>
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  </state>
@@ -155,7 +155,7 @@
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  <distribution spec="SmartZeroExcludingPrior" x="@migrationRate">
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  <LogNormal name="distr" M="0.0" S="1.0"/>
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  </distribution>
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- <distribution spec="ZeroExcludingPrior" x="@migrationRateScaler">
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+ <distribution spec="ZeroExcludingPrior" x="@f">
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  <Uniform name="distr" lower="0.0" upper="1.0"/>
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  </distribution>
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  <prior name="distribution" x="@gammaShape">
@@ -180,7 +180,7 @@
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  <operator spec="BactrianScaleOperator" parameter="@Re" weight="5.0" />
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  <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0" />
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  <operator spec="SmartScaleOperator" parameter="@migrationRate" weight="5.0" />
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- <operator spec="BactrianScaleOperator" parameter="@migrationRateScaler" weight="5.0"/>
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+ <operator spec="BactrianScaleOperator" parameter="@f" weight="5.0"/>
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  <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
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  <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
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bella_companion/eucovid/run_beast.py CHANGED
@@ -22,14 +22,14 @@ def run_beast():
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  all_predictors_data = " ".join(
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  [
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  f"-D msa_file={msa_file}",
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- f"-D changeTimes={predictors_dir / 'changetimes_all_7e.tsv'}",
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+ f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
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  f"-D predictorFiles={all_predictor_files}",
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  ]
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  )
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  flight_predictor_data = " ".join(
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  [
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  f"-D msa_file={msa_file}",
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- f"-D changeTimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
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+ f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
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  f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
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  ]
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  )
{bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: bella-companion
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- Version: 0.0.18
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+ Version: 0.0.19
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.18.dist-info → bella_companion-0.0.19.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
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  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
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  bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
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- bella_companion/eucovid/beast_configs/GLM.xml,sha256=Qn3AP1NvMDXnCQp_qZvVOjoDQujuurQop4IqgJs6lKQ,11670
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+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=ng13sapf8qe1OGm3xSjl-N_4Fa0gWEOPU172z2XpyQM,11731
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  bella_companion/eucovid/beast_configs/MLP.xml,sha256=4niHx3FmSsmKyDv9eNS1g9cZ6ShHbWjzXIbfg8pQa-k,11347
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- bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=S9B7mzbPWAQ2ngjpaaswUBF8Cigfha1StkFJtSVz2fo,11620
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+ bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=oDOxiXPlL5zwuvyOPkdZmdSprivYNbDScjT1IvWnZFI,11548
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  bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
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  bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
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  bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
@@ -20,7 +20,7 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
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  bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
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  bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
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  bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
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- bella_companion/eucovid/run_beast.py,sha256=BTttqmFNaUslDfpXTwF8qcIbiyLg3cvsPmdQkuqGvG4,3654
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+ bella_companion/eucovid/run_beast.py,sha256=L_Ng1kG8o94kK3HNeVj1Yq6FsPjolGWWxfnxRrcQeu0,3662
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  bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
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  bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
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  bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
@@ -69,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
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  bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
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  bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
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  bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
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- bella_companion-0.0.18.dist-info/METADATA,sha256=Mha1XlV0JnOlM3ru7d0vSBc0uPwvX66v_ggOFcgJDKw,576
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- bella_companion-0.0.18.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- bella_companion-0.0.18.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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- bella_companion-0.0.18.dist-info/RECORD,,
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+ bella_companion-0.0.19.dist-info/METADATA,sha256=xTGQXsmCvuL4RhWlp5-EmPs1vQWApd-A11r-ICeUmxo,576
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+ bella_companion-0.0.19.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ bella_companion-0.0.19.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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+ bella_companion-0.0.19.dist-info/RECORD,,