Index

A

addQueryToNetwork() (in module PopPUNK.network) addRandom() (in module PopPUNK.sketchlib) api() (in module PopPUNK.web) apply_threshold() (PopPUNK.models.RefineFit method) assign() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.LineageFit method) (PopPUNK.models.RefineFit method)

assign_query() (in module PopPUNK.assign) assign_query_hdf5() (in module PopPUNK.assign) assign_samples() (in module PopPUNK.models)

B

BGMMFit (class in PopPUNK.models)

C

calc_prevalence() (in module PopPUNK.web) check_and_set_gpu() (in module PopPUNK.utils) check_search_range() (in module PopPUNK.refine) checkNetworkVertexCount() (in module PopPUNK.network) checkSketchlibLibrary() (in module PopPUNK.sketchlib) checkSketchlibVersion() (in module PopPUNK.sketchlib) cliquePrune() (in module PopPUNK.network) ClusterFit (class in PopPUNK.models) construct_dense_weighted_network() (in module PopPUNK.network)

construct_network_from_assignments() (in module PopPUNK.network) construct_network_from_df() (in module PopPUNK.network) construct_network_from_edge_list() (in module PopPUNK.network) construct_network_from_sparse_matrix() (in module PopPUNK.network) constructDatabase() (in module PopPUNK.sketchlib) copy() (PopPUNK.models.ClusterFit method) createDatabaseDir() (in module PopPUNK.sketchlib) createMicroreact() (in module PopPUNK.plot) cugraph_to_graph_tool() (in module PopPUNK.network)

D

DBSCANFit (class in PopPUNK.models) decisionBoundary() (in module PopPUNK.utils) distHistogram() (in module PopPUNK.plot)

drawMST() (in module PopPUNK.plot) dtype (PopPUNK.models.NumpyShared attribute) (PopPUNK.refine.NumpyShared attribute)

E

edge_weights() (PopPUNK.models.LineageFit method) evaluate_dbscan_clusters() (in module PopPUNK.dbscan)

expand_cugraph_network() (in module PopPUNK.refine) extend() (PopPUNK.models.LineageFit method) extractReferences() (in module PopPUNK.network)

F

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

fit2dMultiGaussian() (in module PopPUNK.bgmm) fitDbScan() (in module PopPUNK.dbscan) fitKmerCurve() (in module PopPUNK.sketchlib)

G

generate_cugraph() (in module PopPUNK.network) generate_embedding() (in module PopPUNK.mandrake) generate_minimum_spanning_tree() (in module PopPUNK.network) get_database_statistics() (in module PopPUNK.sketchlib) get_grid() (in module PopPUNK.plot) get_match_search_depth() (in module PopPUNK.utils)

get_vertex_list() (in module PopPUNK.network) getCliqueRefs() (in module PopPUNK.network) getKmersFromReferenceDatabase() (in module PopPUNK.sketchlib) getSeqsInDb() (in module PopPUNK.sketchlib) getSketchSize() (in module PopPUNK.sketchlib) graphml_to_json() (in module PopPUNK.web) growNetwork() (in module PopPUNK.refine)

H

highlight_cluster() (in module PopPUNK.web)

I

isolateNameToLabel() (in module PopPUNK.utils)

iterDistRows() (in module PopPUNK.utils)

J

joinClusterDicts() (in module PopPUNK.utils)

joinDBs() (in module PopPUNK.sketchlib)

L

likelihoodBoundary() (in module PopPUNK.refine) LineageFit (class in PopPUNK.models) listDistInts() (in module PopPUNK.utils) load() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.LineageFit method) (PopPUNK.models.RefineFit method)

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

M

main() (in module PopPUNK.assign) (in module PopPUNK.visualise) module PopPUNK.assign PopPUNK.bgmm PopPUNK.dbscan PopPUNK.mandrake PopPUNK.models PopPUNK.network PopPUNK.plot PopPUNK.refine PopPUNK.sketchlib PopPUNK.sparse_mst PopPUNK.utils PopPUNK.visualise PopPUNK.web

multi_refine() (in module PopPUNK.refine)

N

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

newNetwork() (in module PopPUNK.refine) newNetwork2D() (in module PopPUNK.refine) no_scale() (PopPUNK.models.ClusterFit method) NumpyShared (class in PopPUNK.models) (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.LineageFit method) (PopPUNK.models.RefineFit method) plot_contours() (in module PopPUNK.plot) plot_database_evaluations() (in module PopPUNK.plot) plot_dbscan_results() (in module PopPUNK.plot) plot_evaluation_histogram() (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.assign module PopPUNK.bgmm module PopPUNK.dbscan module PopPUNK.mandrake module PopPUNK.models module

PopPUNK.network module PopPUNK.plot module PopPUNK.refine module PopPUNK.sketchlib module PopPUNK.sparse_mst module PopPUNK.utils module PopPUNK.visualise module PopPUNK.web module print_network_summary() (in module PopPUNK.network) printClusters() (in module PopPUNK.network) printExternalClusters() (in module PopPUNK.network) process_previous_network() (in module PopPUNK.network) process_weights() (in module PopPUNK.network) prune_graph() (in module PopPUNK.network)

Q

queryDatabase() (in module PopPUNK.sketchlib)

R

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

readRfile() (in module PopPUNK.utils) RefineFit (class in PopPUNK.models) refineFit() (in module PopPUNK.refine) remove_nodes_from_graph() (in module PopPUNK.network) remove_non_query_components() (in module PopPUNK.network) removeFromDB() (in module PopPUNK.sketchlib)

S

save() (PopPUNK.models.BGMMFit method) (PopPUNK.models.DBSCANFit method) (PopPUNK.models.LineageFit method) (PopPUNK.models.RefineFit method) save_network() (in module PopPUNK.network) set_env() (in module PopPUNK.utils) setupDBFuncs() (in module PopPUNK.utils)

shape (PopPUNK.models.NumpyShared attribute) (PopPUNK.refine.NumpyShared attribute) sketch_to_hdf5() (in module PopPUNK.web) sparse_mat_to_network() (in module PopPUNK.network) stderr_redirected() (in module PopPUNK.utils) storePickle() (in module PopPUNK.utils) summarise_clusters() (in module PopPUNK.web)

T

transformLine() (in module PopPUNK.utils)

translate_network_indices() (in module PopPUNK.network)

U

update_distance_matrices() (in module PopPUNK.utils)

V

vertex_betweenness() (in module PopPUNK.network)

W

writeClusterCsv() (in module PopPUNK.plot)

writeReferences() (in module PopPUNK.network)