Index

A

addQueryToNetwork() (in module PopPUNK.network) apply_threshold() (PopPUNK.models.RefineFit method) assembly_qc() (in module PopPUNK.utils) assign() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.RefineFit method)

assign_samples() (in module PopPUNK.bgmm) assign_samples_dbscan() (in module PopPUNK.dbscan)

B

BGMMFit (class in PopPUNK.models)

buildRapidNJ() (in module PopPUNK.plot)

C

calculateQueryQueryDistances() (in module PopPUNK.sketchlib) checkMashVersion() (in module PopPUNK.mash) checkSketchlibLibrary() (in module PopPUNK.sketchlib) checkSketchlibVersion() (in module PopPUNK.sketchlib) ClusterFit (class in PopPUNK.models)

constructDatabase() (in module PopPUNK.mash) (in module PopPUNK.sketchlib) constructNetwork() (in module PopPUNK.network) createDatabaseDir() (in module PopPUNK.mash) (in module PopPUNK.sketchlib)

D

DBSCANFit (class in PopPUNK.models) decisionBoundary() (in module PopPUNK.refine)

dtype (PopPUNK.mash.NumpyShared attribute) (PopPUNK.refine.NumpyShared attribute)

E

evaluate_dbscan_clusters() (in module PopPUNK.dbscan)

extractReferences() (in module PopPUNK.network)

F

fetchNetwork() (in module PopPUNK.network) findBetweenLabel() (in module PopPUNK.dbscan) findWithinLabel() (in module PopPUNK.bgmm) fit() (PopPUNK.models.BGMMFit method) (PopPUNK.models.ClusterFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.RefineFit method)

fit2dMultiGaussian() (in module PopPUNK.bgmm) fitDbScan() (in module PopPUNK.dbscan) fitKmerBlock() (in module PopPUNK.mash) fitKmerCurve() (in module PopPUNK.mash)

G

generate_phylogeny() (in module PopPUNK.plot) generate_tsne() (in module PopPUNK.tsne) get_grid() (in module PopPUNK.plot) getDatabaseName() (in module PopPUNK.mash) getKmersFromReferenceDatabase() (in module PopPUNK.mash) (in module PopPUNK.sketchlib)

getSeqsInDb() (in module PopPUNK.mash) (in module PopPUNK.sketchlib) getSketchSize() (in module PopPUNK.mash) (in module PopPUNK.sketchlib)

I

init_lock() (in module PopPUNK.mash)

iterDistRows() (in module PopPUNK.utils)

J

joinDBs() (in module PopPUNK.mash) (in module PopPUNK.sketchlib)

L

likelihoodBoundary() (in module PopPUNK.refine) load() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.RefineFit method)

loadClusterFit() (in module PopPUNK.models) log_likelihood() (in module PopPUNK.bgmm) log_multivariate_normal_density() (in module PopPUNK.bgmm)

N

name (PopPUNK.mash.NumpyShared attribute) (PopPUNK.refine.NumpyShared attribute) networkSummary() (in module PopPUNK.network)

newNetwork() (in module PopPUNK.refine) no_scale() (PopPUNK.models.ClusterFit method) NumpyShared (class in PopPUNK.mash) (class in PopPUNK.refine)

O

outputsForCytoscape() (in module PopPUNK.plot) outputsForGrapetree() (in module PopPUNK.plot)

outputsForMicroreact() (in module PopPUNK.plot) outputsForPhandango() (in module PopPUNK.plot)

P

plot() (PopPUNK.models.BGMMFit method) (PopPUNK.models.ClusterFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.RefineFit method) plot_contours() (in module PopPUNK.plot) plot_dbscan_results() (in module PopPUNK.plot) plot_fit() (in module PopPUNK.plot) plot_refined_results() (in module PopPUNK.plot) plot_results() (in module PopPUNK.plot) plot_scatter() (in module PopPUNK.plot) PopPUNK.bgmm (module)

PopPUNK.dbscan (module) PopPUNK.mash (module) PopPUNK.models (module) PopPUNK.network (module) PopPUNK.plot (module) PopPUNK.refine (module) PopPUNK.sketchlib (module) PopPUNK.tsne (module) PopPUNK.utils (module) printClusters() (in module PopPUNK.network) printExternalClusters() (in module PopPUNK.network)

Q

qcDistMat() (in module PopPUNK.utils)

queryDatabase() (in module PopPUNK.mash) (in module PopPUNK.sketchlib)

R

readDBParams() (in module PopPUNK.sketchlib) readIsolateTypeFromCsv() (in module PopPUNK.utils) readManualStart() (in module PopPUNK.refine) readMashDBParams() (in module PopPUNK.mash) readPickle() (in module PopPUNK.utils)

readRfile() (in module PopPUNK.utils) RefineFit (class in PopPUNK.models) refineFit() (in module PopPUNK.refine) removeFromDB() (in module PopPUNK.sketchlib) runSketch() (in module PopPUNK.mash)

S

save() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.RefineFit method)

setupDBFuncs() (in module PopPUNK.utils) shape (PopPUNK.mash.NumpyShared attribute) (PopPUNK.refine.NumpyShared attribute) storePickle() (in module PopPUNK.utils)

T

transformLine() (in module PopPUNK.refine)

translate_distMat() (in module PopPUNK.utils)

U

update_distance_matrices() (in module PopPUNK.utils)

W

withinBoundary() (in module PopPUNK.refine) writeClusterCsv() (in module PopPUNK.plot)

writeDummyReferences() (in module PopPUNK.network) writeReferences() (in module PopPUNK.network) writeTmpFile() (in module PopPUNK.utils)