The RGP package

This package computes Regions of Genome Plasticity, and cluster them into spots of insertion.

Submodules

ppanggolin.RGP.genomicIsland module

class ppanggolin.RGP.genomicIsland.MatriceNode(state, score, prev, gene)[source]

Bases: object

changes(state, score)[source]

ppanggolin.RGP.genomicIsland.checkPangenomeFormerRGP(pangenome, force)[source]: checks pangenome status and .h5 files for former rgp, delete them if allowed or raise an error

ppanggolin.RGP.genomicIsland.compute_org_rgp(organism, persistent_penalty, variable_gain, min_length, min_score, multigenics, naming='contig')[source]

ppanggolin.RGP.genomicIsland.extractRGP(contig, node, ID, naming)[source]: Extract the region from the given starting node

ppanggolin.RGP.genomicIsland.initMatrices(contig, persistent_penalty, variable_gain, multi)[source]: initialize the vector of score/state nodes

ppanggolin.RGP.genomicIsland.launch(args)[source]

ppanggolin.RGP.genomicIsland.mkRegions(contig, matrix, min_length, min_score, persistent, continuity, multi, naming='contig')[source]

ppanggolin.RGP.genomicIsland.predictRGP(pangenome, force=False, persistent_penalty=3, variable_gain=1, min_length=3000, min_score=4, dup_margin=0.05, cpu=1)[source]

ppanggolin.RGP.genomicIsland.rewriteMatrix(contig, matrix, index, persistent, continuity, multi)[source]: ReWrite the matrice from the given index of the node that started a region.

ppanggolin.RGP.genomicIsland.rgpSubparser(subparser)[source]

ppanggolin.RGP.genomicIsland.testNamingScheme(pangenome)[source]

ppanggolin.RGP.spot module

ppanggolin.RGP.spot.checkPangenomeFormerSpots(pangenome, force)[source]: checks pangenome status and .h5 files for former spots, delete them if allowed or raise an error

ppanggolin.RGP.spot.checkParameterLogic(overlapping_match, set_size, exact_match)[source]

ppanggolin.RGP.spot.checkSim(pairBorder1, pairBorder2, overlapping_match, exact_match, set_size)[source]: Checks if the two pairs of ‘exact_match’ first gene families are identical, or eventually if they overlap in an ordered way at least ‘overlapping_match’

ppanggolin.RGP.spot.compBorder(border1, border2, overlapping_match, exact_match, set_size)[source]

ppanggolin.RGP.spot.defineElementsOfInterest(genelist, elements)[source]

ppanggolin.RGP.spot.drawCurrSpot(genelists, ordered_counts, elements, famCol, filename)[source]

ppanggolin.RGP.spot.draw_spots(spots, output, cpu, overlapping_match, exact_match, set_size, multigenics, elements, verbose=False)[source]

ppanggolin.RGP.spot.launch(args)[source]

ppanggolin.RGP.spot.lineOrderGeneLists(geneLists, overlapping_match, exact_match, set_size)[source]

ppanggolin.RGP.spot.makeColorsForFams(fams)[source]

ppanggolin.RGP.spot.makeSpotGraph(rgps, multigenics, output, spot_graph=False, overlapping_match=2, set_size=3, exact_match=1)[source]

ppanggolin.RGP.spot.orderGeneLists(geneLists, ordered_counts, overlapping_match, exact_match, set_size)[source]

ppanggolin.RGP.spot.predictHotspots(pangenome, output, force=False, cpu=1, spot_graph=False, overlapping_match=2, set_size=3, exact_match=1, draw_hotspot=False, interest='')[source]

ppanggolin.RGP.spot.rowOrderGeneLists(geneLists, ordered_counts)[source]

ppanggolin.RGP.spot.select_spots(pangenome, spots, elements, min_presence_ratio=0.05, min_org_ratio=0.01)[source]

ppanggolin.RGP.spot.spotSubparser(subparser)[source]

ppanggolin.RGP.spot.subgraph(spot, output, filename, with_border=True, set_size=3, multigenics=None)[source]: write a pangenome subgraph of the gene families of a spot in gexf format

ppanggolin.RGP.spot.writeBorders_spots(spots, pangenome, output)[source]

ppanggolin.RGP.spot.write_RGP_content_graph(spots, output)[source]