bella-companion 0.0.38__tar.gz → 0.0.43__tar.gz

{bella_companion-0.0.38 → bella_companion-0.0.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.38
+Version: 0.0.43
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

bella_companion-0.0.43/bella_companion/eucovid/beast_configs/GLM.xml

@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+<beast
+    namespace="
+        :beast.base.evolution
+        :beast.base.evolution.alignment
+        :beast.base.evolution.branchratemodel
+        :beast.base.evolution.likelihood
+        :beast.base.evolution.operator
+        :beast.base.evolution.operator.kernel
+        :beast.base.evolution.sitemodel
+        :beast.base.evolution.substitutionmodel
+        :beast.base.evolution.tree
+        :beast.base.evolution.tree.coalescent
+        :beast.base.inference
+        :beast.base.inference.parameter
+        :beast.base.inference.operator.kernel
+        :bdmmprime.distribution
+        :bdmmprime.mapping
+        :bdmmprime.trajectories
+        :bdmmprime.parameterization
+        :bdmmprime.util
+        :bdmmprime.util.operators
+        :bdmmprime.util.priors
+        :feast.fileio"
+    version="2.7"
+>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
+    <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
+    <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
+    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
+    <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
+
+    <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
+    <TaxonSet id="taxonSet" alignment="@alignment"/>
+    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
+    <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
+    <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
+    <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
+
+    <run spec="MCMC" chainLength="10000000">
+        <state id="state" spec="State">
+            <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
+                <populationModel spec="ConstantPopulation" popSize="0.1"/>
+            </stateNode>
+            <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
+            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
+            <stateNode id="migrationRateW" spec="RealParameter" value="0"/>
+            <stateNode id="migrationRateScaler" spec="RealParameter" value="0.1"/>
+            <stateNode id="processLength" spec="RealParameter" value="10.0"/>
+            <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
+            <stateNode id="kappa" spec="RealParameter" value="2.0"/>
+        </state>
+    
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
+                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
+                    <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
+                        <substModel spec="HKY" kappa="@kappa">
+                            <frequencies spec="Frequencies" data="@alignment"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
+                </distribution>
+            </distribution>
+
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
+                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
+                        <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
+                        <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
+                            <skylineValues spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
+                                <plate var="predictorFile" range="$(predictorFiles)">
+                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
+                                </plate>
+                                <indicators spec="BooleanParameter" value="1"/>
+                            </skylineValues>
+                            <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
+                        </migrationRate> 
+                        <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
+                    </parameterization>
+                    <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
+                </distribution>
+
+                <prior name="distribution" x="@processLength">
+                    <LogNormal name="distr" M="-1.0" S="0.2"/>
+                </prior>
+                <distribution spec="SmartZeroExcludingPrior" x="@Re">
+                    <LogNormal name="distr" M="0.8" S="0.5"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.15"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.093"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.10"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.005"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
+                    <Uniform name="distr" lower="0" upper="0.057"/>
+                </distribution>
+                <prior name="distribution" x="@migrationRateW">
+                    <Normal name="distr" mean="0.0" sigma="1.0"/>
+                </prior>
+                <prior name="distribution" x="@migrationRateScaler">
+                    <LogNormal name="distr" M="0.0" S="0.8"/>
+                </prior>
+                <prior name="distribution" x="@gammaShape">
+                    <Exponential name="distr" mean="0.5"/>
+                </prior>
+                <prior id="KappaPrior" name="distribution" x="@kappa">
+                    <LogNormal name="distr" M="1.0" S="1.25"/>
+                </prior>
+            </distribution>
+        </distribution>
+
+        <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
+        <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
+        <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
+        <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
+        <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
+        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
+        <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
+        <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1"> 
+            <transformations spec="Transform$NoTransform" f="@migrationRateW"/>
+        </operator>
+        <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
+
+        <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="BDMMPrime"/>
+            <log idref="gammaShape"/>
+            <log idref="kappa"/>
+            <log idref="processLength"/>
+            <log idref="ReSP"/>
+            <log idref="samplingProportionSP"/>
+            <log idref="migrationRateSP"/>
+            <log idref="migrationRateW"/>
+            <log idref="migrationRateScaler"/>
+        </logger>
+        <logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
+            <log idref="typeMappedTree"/>
+        </logger>
+        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
+            <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
+        </logger>
+        <logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
+            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
+        </logger>
+    </run>
+</beast>

bella_companion-0.0.43/bella_companion/eucovid/beast_configs/MLP.xml

@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+<beast
+    namespace="
+        :beast.base.evolution
+        :beast.base.evolution.alignment
+        :beast.base.evolution.branchratemodel
+        :beast.base.evolution.likelihood
+        :beast.base.evolution.operator
+        :beast.base.evolution.operator.kernel
+        :beast.base.evolution.sitemodel
+        :beast.base.evolution.substitutionmodel
+        :beast.base.evolution.tree
+        :beast.base.evolution.tree.coalescent
+        :beast.base.inference
+        :beast.base.inference.parameter
+        :beast.base.inference.operator.kernel
+        :bdmmprime.distribution
+        :bdmmprime.mapping
+        :bdmmprime.trajectories
+        :bdmmprime.parameterization
+        :bdmmprime.util
+        :bdmmprime.util.operators
+        :bdmmprime.util.priors
+        :feast.fileio"
+    version="2.7"
+>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
+    <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
+    <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
+    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
+    <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
+
+    <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
+    <TaxonSet id="taxonSet" alignment="@alignment"/>
+    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
+    <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
+    <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
+    <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
+
+    <run spec="MCMC" chainLength="10000000">
+        <state id="state" spec="State">
+            <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
+                <populationModel spec="ConstantPopulation" popSize="0.1"/>
+            </stateNode>
+            <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
+            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
+            <plate var="n" range="$(layersRange)">
+                <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
+            </plate>
+            <stateNode id="processLength" spec="RealParameter" value="10.0"/>
+            <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
+            <stateNode id="kappa" spec="RealParameter" value="2.0"/>
+        </state>
+    
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
+                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
+                    <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
+                        <substModel spec="HKY" kappa="@kappa">
+                            <frequencies spec="Frequencies" data="@alignment"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
+                </distribution>
+            </distribution>
+
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
+                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
+                        <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" />
+                        <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
+                        <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
+                            <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
+                                <plate var="predictorFile" range="$(predictorFiles)">
+                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
+                                </plate>
+                                <plate var="n" range="$(layersRange)">
+                                    <weights idref="migrationRateW$(n)"/>
+                                </plate>
+                            </skylineValues>
+                            <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
+                        </migrationRate> 
+                        <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
+                    </parameterization>
+                    <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
+                </distribution>
+
+                <prior name="distribution" x="@processLength">
+                    <LogNormal name="distr" M="-1.0" S="0.2"/>
+                </prior>
+                <distribution spec="SmartZeroExcludingPrior" x="@Re">
+                    <LogNormal name="distr" M="0.8" S="0.5"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.15"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.093"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.10"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
+                    <Uniform name="distr" lower="0" upper="0.005"/>
+                </distribution>
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
+                    <Uniform name="distr" lower="0" upper="0.057"/>
+                </distribution>
+                <plate var="n" range="$(layersRange)">
+                    <prior name="distribution" x="@migrationRateW$(n)">
+                        <Normal name="distr" mean="0.0" sigma="1.0"/>
+                    </prior>
+                </plate>
+                <prior name="distribution" x="@gammaShape">
+                    <Exponential name="distr" mean="0.5"/>
+                </prior>
+                <prior id="KappaPrior" name="distribution" x="@kappa">
+                    <LogNormal name="distr" M="1.0" S="1.25"/>
+                </prior>
+            </distribution>
+        </distribution>
+
+        <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
+        <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
+        <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
+        <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
+        <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
+        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
+        <plate var="n" range="$(layersRange)">
+            <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
+        </plate>
+        <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
+
+        <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="BDMMPrime"/>
+            <log idref="gammaShape"/>
+            <log idref="kappa"/>
+            <log idref="processLength"/>
+            <log idref="ReSP"/>
+            <log idref="samplingProportionSP"/>
+            <log idref="migrationRateSP"/>
+            <log idref="migrationRate"/>
+        </logger>
+        <logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
+            <log idref="typeMappedTree"/>
+        </logger>
+        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
+            <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
+        </logger>
+        <logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
+            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
+        </logger>
+    </run>
+</beast>