PPanGGOLiN
Contents:
Developper doc
PPanGGOLiN
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Index
Index
A
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B
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C
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D
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E
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F
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G
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
A
add_dna() (ppanggolin.genome.Feature method)
add_protein() (ppanggolin.genome.Gene method)
add_spot_str() (in module ppanggolin.align.alignOnPang)
addEdge() (ppanggolin.pangenome.Pangenome method)
addFile() (ppanggolin.pangenome.Pangenome method)
addGene() (ppanggolin.geneFamily.GeneFamily method)
(ppanggolin.genome.Contig method)
addGeneFamily() (ppanggolin.pangenome.Pangenome method)
addGenes() (ppanggolin.pangenome.Edge method)
addOrganism() (ppanggolin.pangenome.Pangenome method)
addPartition() (ppanggolin.geneFamily.GeneFamily method)
addRegion() (ppanggolin.region.Spot method)
addRegions() (ppanggolin.pangenome.Pangenome method)
(ppanggolin.region.Spot method)
addRNA() (ppanggolin.genome.Contig method)
addSequence() (ppanggolin.geneFamily.GeneFamily method)
addSpots() (ppanggolin.pangenome.Pangenome method)
align() (in module ppanggolin.align.alignOnPang)
alignRep() (in module ppanggolin.cluster.cluster)
alignSeqToPang() (in module ppanggolin.align.alignOnPang)
alignSubparser() (in module ppanggolin.align.alignOnPang)
annotate_organism() (in module ppanggolin.annotate.synta)
annotatePangenome() (in module ppanggolin.annotate.annotate)
append() (ppanggolin.region.Region method)
B
borders() (ppanggolin.region.Spot method)
C
changes() (ppanggolin.RGP.genomicIsland.MatriceNode method)
checkInputFiles() (in module ppanggolin.main)
checkLog() (in module ppanggolin.main)
checkPangenomeForClustering() (in module ppanggolin.cluster.cluster)
checkPangenomeFormerClustering() (in module ppanggolin.cluster.cluster)
checkPangenomeFormerGraph() (in module ppanggolin.graph.makeGraph)
checkPangenomeFormerPartition() (in module ppanggolin.nem.partition)
checkPangenomeFormerRGP() (in module ppanggolin.RGP.genomicIsland)
checkPangenomeFormerSpots() (in module ppanggolin.RGP.spot)
checkPangenomeForNeighborsGraph() (in module ppanggolin.graph.makeGraph)
checkPangenomeInfo() (in module ppanggolin.formats.readBinaries)
checkParameterLogic() (in module ppanggolin.RGP.spot)
checkSim() (in module ppanggolin.RGP.spot)
checkTsvSanity() (in module ppanggolin.main)
clustering() (in module ppanggolin.cluster.cluster)
clusterSubparser() (in module ppanggolin.cluster.cluster)
cmdLine() (in module ppanggolin.main)
compBorder() (in module ppanggolin.RGP.spot)
compute_org_rgp() (in module ppanggolin.RGP.genomicIsland)
computeFamilyBitarrays() (ppanggolin.pangenome.Pangenome method)
computeNeighborsGraph() (in module ppanggolin.graph.makeGraph)
Contig (class in ppanggolin.genome)
contig (ppanggolin.region.Region property)
contigs (ppanggolin.genome.Organism property)
countUniqContent() (ppanggolin.region.Spot method)
countUniqOrderedSet() (ppanggolin.region.Spot method)
create_gene() (in module ppanggolin.annotate.annotate)
createdb() (in module ppanggolin.align.alignOnPang)
D
defineElementsOfInterest() (in module ppanggolin.RGP.spot)
detect_filetype() (in module ppanggolin.annotate.annotate)
draw_spot_gexf() (in module ppanggolin.align.alignOnPang)
draw_spots() (in module ppanggolin.RGP.spot)
drawCurrSpot() (in module ppanggolin.RGP.spot)
drawCurve() (in module ppanggolin.nem.rarefaction)
drawTilePlot() (in module ppanggolin.figures.tile_plot)
drawUCurve() (in module ppanggolin.figures.ucurve)
E
Edge (class in ppanggolin.pangenome)
edges (ppanggolin.geneFamily.GeneFamily property)
(ppanggolin.pangenome.Pangenome property)
ErasePangenome() (in module ppanggolin.formats.writeBinaries)
evaluate_nb_partitions() (in module ppanggolin.nem.partition)
extractRGP() (in module ppanggolin.RGP.genomicIsland)
F
families (ppanggolin.genome.Organism property)
(ppanggolin.region.Region property)
Feature (class in ppanggolin.genome)
figureSubparser() (in module ppanggolin.figures.drawing)
fill_annotations() (ppanggolin.genome.Feature method)
(ppanggolin.genome.Gene method)
fill_parents() (ppanggolin.genome.Feature method)
firstClustering() (in module ppanggolin.cluster.cluster)
G
Gene (class in ppanggolin.genome)
gene2famDesc() (in module ppanggolin.formats.writeBinaries)
geneDesc() (in module ppanggolin.formats.writeBinaries)
geneFamDesc() (in module ppanggolin.formats.writeBinaries)
geneFamilies (ppanggolin.pangenome.Pangenome property)
GeneFamily (class in ppanggolin.geneFamily)
genePairs (ppanggolin.pangenome.Edge property)
genes (ppanggolin.genome.Contig property)
(ppanggolin.genome.Organism property)
(ppanggolin.pangenome.Pangenome property)
geneSequenceDesc() (in module ppanggolin.formats.writeBinaries)
get_dna_sequence() (in module ppanggolin.annotate.synta)
get_multigenics() (ppanggolin.pangenome.Pangenome method)
get_num_lines() (in module ppanggolin.utils)
getBorderingGenes() (ppanggolin.region.Region method)
getFam2RGP() (in module ppanggolin.align.alignOnPang)
getFam2spot() (in module ppanggolin.align.alignOnPang)
getGene() (ppanggolin.pangenome.Pangenome method)
getGene2famLen() (in module ppanggolin.formats.writeBinaries)
getGeneFamily() (ppanggolin.pangenome.Pangenome method)
getGeneFamLen() (in module ppanggolin.formats.writeBinaries)
getGeneIDLen() (in module ppanggolin.formats.writeBinaries)
getGeneSequencesFromFastas() (in module ppanggolin.annotate.annotate)
getGeneSequencesFromFile() (in module ppanggolin.formats.readBinaries)
getGeneSequencesLen() (in module ppanggolin.formats.writeBinaries)
getGenesPerOrg() (ppanggolin.geneFamily.GeneFamily method)
getIndex() (ppanggolin.pangenome.Pangenome method)
getMaxLenAnnotations() (in module ppanggolin.formats.writeBinaries)
getNumberOfOrganisms() (in module ppanggolin.formats.readBinaries)
getOrAddContig() (ppanggolin.genome.Organism method)
getOrAddRegion() (ppanggolin.pangenome.Pangenome method)
getOrgDict() (ppanggolin.geneFamily.GeneFamily method)
(ppanggolin.pangenome.Edge method)
getProt() (in module ppanggolin.align.alignOnPang)
getProtInfo() (in module ppanggolin.align.alignOnPang)
getRGPLen() (in module ppanggolin.formats.writeBinaries)
getRNAs() (ppanggolin.region.Region method)
getSpotDesc() (in module ppanggolin.formats.writeBinaries)
getStatus() (in module ppanggolin.formats.readBinaries)
getUniqContent() (ppanggolin.region.Spot method)
getUniqOrderedSet() (ppanggolin.region.Spot method)
graphDesc() (in module ppanggolin.formats.writeBinaries)
graphSubparser() (in module ppanggolin.graph.makeGraph)
I
inferSingletons() (in module ppanggolin.cluster.cluster)
infoSubparser() (in module ppanggolin.info.info)
initMatrices() (in module ppanggolin.RGP.genomicIsland)
is_compressed() (in module ppanggolin.utils)
isContigBorder (ppanggolin.region.Region property)
isWholeContig (ppanggolin.region.Region property)
J
jaccard_similarities() (in module ppanggolin.utils)
L
launch() (in module ppanggolin.align.alignOnPang)
(in module ppanggolin.annotate.annotate)
(in module ppanggolin.cluster.cluster)
(in module ppanggolin.figures.drawing)
(in module ppanggolin.formats.writeFlat)
(in module ppanggolin.graph.makeGraph)
(in module ppanggolin.info.info)
(in module ppanggolin.nem.partition)
(in module ppanggolin.nem.rarefaction)
(in module ppanggolin.RGP.genomicIsland)
(in module ppanggolin.RGP.spot)
(in module ppanggolin.workflow.panRGP)
(in module ppanggolin.workflow.workflow)
launch_aragorn() (in module ppanggolin.annotate.synta)
launch_infernal() (in module ppanggolin.annotate.synta)
launch_prodigal() (in module ppanggolin.annotate.synta)
launch_raref_nem() (in module ppanggolin.nem.rarefaction)
launchAnnotateOrganism() (in module ppanggolin.annotate.annotate)
launchReadAnno() (in module ppanggolin.annotate.annotate)
launchReadOrganism() (in module ppanggolin.formats.readBinaries)
lineOrderGeneLists() (in module ppanggolin.RGP.spot)
linkMultigenicFamilies() (in module ppanggolin.align.alignOnPang)
linkNewGenomeFamilies() (in module ppanggolin.align.alignOnPang)
M
main() (in module ppanggolin.main)
makeColorsForFams() (in module ppanggolin.RGP.spot)
makeRarefactionCurve() (in module ppanggolin.nem.rarefaction)
makeSpotGraph() (in module ppanggolin.RGP.spot)
MatriceNode (class in ppanggolin.RGP.genomicIsland)
mkBitarray() (ppanggolin.geneFamily.GeneFamily method)
mkFilename() (in module ppanggolin.utils)
mkLocal2Gene() (in module ppanggolin.cluster.cluster)
mkOutdir() (in module ppanggolin.utils)
mkRegions() (in module ppanggolin.RGP.genomicIsland)
module
ppanggolin
ppanggolin.align.alignOnPang
ppanggolin.annotate.annotate
ppanggolin.annotate.synta
ppanggolin.cluster.cluster
ppanggolin.figures.drawing
ppanggolin.figures.tile_plot
ppanggolin.figures.ucurve
ppanggolin.formats.readBinaries
ppanggolin.formats.writeBinaries
ppanggolin.formats.writeFlat
ppanggolin.genome
ppanggolin.graph.makeGraph
ppanggolin.info.info
ppanggolin.main
ppanggolin.nem.partition
ppanggolin.nem.rarefaction
ppanggolin.region
ppanggolin.RGP.genomicIsland
ppanggolin.RGP.spot
ppanggolin.utils
ppanggolin.workflow.panRGP
ppanggolin.workflow.workflow
N
namedPartition (ppanggolin.geneFamily.GeneFamily property)
neighbors (ppanggolin.geneFamily.GeneFamily property)
nemSamples() (in module ppanggolin.nem.partition)
nemSingle() (in module ppanggolin.nem.partition)
number_of_geneFamilies() (ppanggolin.pangenome.Pangenome method)
number_of_genes() (ppanggolin.genome.Organism method)
number_of_organisms() (ppanggolin.pangenome.Pangenome method)
O
orderGeneLists() (in module ppanggolin.RGP.spot)
Organism (class in ppanggolin.genome)
organism (ppanggolin.region.Region property)
organisms (ppanggolin.geneFamily.GeneFamily property)
(ppanggolin.pangenome.Pangenome property)
overlap_filter() (in module ppanggolin.annotate.synta)
P
Pangenome (class in ppanggolin.pangenome)
panRGPSubparser() (in module ppanggolin.workflow.panRGP)
partition() (in module ppanggolin.nem.partition)
partition_nem() (in module ppanggolin.nem.partition)
partitionSubparser() (in module ppanggolin.nem.partition)
ppanggolin
module
ppanggolin.align.alignOnPang
module
ppanggolin.annotate.annotate
module
ppanggolin.annotate.synta
module
ppanggolin.cluster.cluster
module
ppanggolin.figures.drawing
module
ppanggolin.figures.tile_plot
module
ppanggolin.figures.ucurve
module
ppanggolin.formats.readBinaries
module
ppanggolin.formats.writeBinaries
module
ppanggolin.formats.writeFlat
module
ppanggolin.genome
module
ppanggolin.graph.makeGraph
module
ppanggolin.info.info
module
ppanggolin.main
module
ppanggolin.nem.partition
module
ppanggolin.nem.rarefaction
module
ppanggolin.region
module
ppanggolin.RGP.genomicIsland
module
ppanggolin.RGP.spot
module
ppanggolin.utils
module
ppanggolin.workflow.panRGP
module
ppanggolin.workflow.workflow
module
predictHotspots() (in module ppanggolin.RGP.spot)
predictRGP() (in module ppanggolin.RGP.genomicIsland)
printInfo() (in module ppanggolin.info.info)
projectPartition() (in module ppanggolin.align.alignOnPang)
projectRGP() (in module ppanggolin.align.alignOnPang)
R
raref_nem() (in module ppanggolin.nem.rarefaction)
rarefactionSubparser() (in module ppanggolin.nem.rarefaction)
read_chunks() (in module ppanggolin.formats.readBinaries)
read_compressed_or_not() (in module ppanggolin.utils)
read_faa() (in module ppanggolin.cluster.cluster)
read_fam2seq() (in module ppanggolin.cluster.cluster)
read_fasta() (in module ppanggolin.annotate.synta)
read_gene2fam() (in module ppanggolin.cluster.cluster)
read_org_gbff() (in module ppanggolin.annotate.annotate)
read_org_gff() (in module ppanggolin.annotate.annotate)
read_tsv() (in module ppanggolin.cluster.cluster)
readAlignments() (in module ppanggolin.align.alignOnPang)
readAnnoFile() (in module ppanggolin.annotate.annotate)
readAnnotation() (in module ppanggolin.formats.readBinaries)
readAnnotations() (in module ppanggolin.annotate.annotate)
readClustering() (in module ppanggolin.cluster.cluster)
readGeneFamilies() (in module ppanggolin.formats.readBinaries)
readGeneFamiliesInfo() (in module ppanggolin.formats.readBinaries)
readGraph() (in module ppanggolin.formats.readBinaries)
readInfo() (in module ppanggolin.formats.readBinaries)
readOrganism() (in module ppanggolin.formats.readBinaries)
readPangenome() (in module ppanggolin.formats.readBinaries)
readParameters() (in module ppanggolin.formats.readBinaries)
readRGP() (in module ppanggolin.formats.readBinaries)
readSpots() (in module ppanggolin.formats.readBinaries)
refineClustering() (in module ppanggolin.cluster.cluster)
Region (class in ppanggolin.region)
regions (ppanggolin.pangenome.Pangenome property)
remove_high_copy_number() (in module ppanggolin.graph.makeGraph)
restricted_float() (in module ppanggolin.utils)
reverse_complement() (in module ppanggolin.annotate.synta)
rewriteMatrix() (in module ppanggolin.RGP.genomicIsland)
RGPDesc() (in module ppanggolin.formats.writeBinaries)
rgpSubparser() (in module ppanggolin.RGP.genomicIsland)
RNA (class in ppanggolin.genome)
rowOrderGeneLists() (in module ppanggolin.RGP.spot)
run_partitioning() (in module ppanggolin.nem.partition)
S
select_spots() (in module ppanggolin.RGP.spot)
Spot (class in ppanggolin.region)
spot2rgp() (in module ppanggolin.formats.writeFlat)
spotDesc() (in module ppanggolin.formats.writeBinaries)
spotSubparser() (in module ppanggolin.RGP.spot)
start (ppanggolin.region.Region property)
startGene (ppanggolin.region.Region property)
stop (ppanggolin.region.Region property)
stopGene (ppanggolin.region.Region property)
subgraph() (in module ppanggolin.RGP.spot)
summarize_spots() (in module ppanggolin.formats.writeFlat)
syntaSubparser() (in module ppanggolin.annotate.annotate)
syntaxic_annotation() (in module ppanggolin.annotate.synta)
T
testNamingScheme() (in module ppanggolin.RGP.genomicIsland)
U
updateGeneFamPartition() (in module ppanggolin.formats.writeBinaries)
updateGeneFragments() (in module ppanggolin.formats.writeBinaries)
W
workflowSubparser() (in module ppanggolin.workflow.workflow)
write_compressed_or_not() (in module ppanggolin.utils)
write_nem_input_files() (in module ppanggolin.nem.partition)
write_partitions_cgview() (in module ppanggolin.align.alignOnPang)
write_RGP_content_graph() (in module ppanggolin.RGP.spot)
write_RGPs_cgview() (in module ppanggolin.align.alignOnPang)
write_tmp_fasta() (in module ppanggolin.annotate.synta)
writeAnnotations() (in module ppanggolin.formats.writeBinaries)
writeBorders() (in module ppanggolin.formats.writeFlat)
writeBorders_spots() (in module ppanggolin.RGP.spot)
writeFastaGenFam() (in module ppanggolin.formats.writeFlat)
writeFastaProtFam() (in module ppanggolin.formats.writeFlat)
writeFlatFiles() (in module ppanggolin.formats.writeFlat)
writeFlatSubparser() (in module ppanggolin.formats.writeFlat)
writeGbffRegions() (in module ppanggolin.align.alignOnPang)
writeGeneFamilies() (in module ppanggolin.formats.writeBinaries)
writeGeneFamiliesTSV() (in module ppanggolin.formats.writeFlat)
writeGeneFamInfo() (in module ppanggolin.formats.writeBinaries)
writeGeneFamSequences() (in module ppanggolin.align.alignOnPang)
writeGenePresenceAbsence() (in module ppanggolin.formats.writeFlat)
writeGeneSequences() (in module ppanggolin.formats.writeBinaries)
(in module ppanggolin.formats.writeFlat)
writeGeneSequencesFromAnnotations() (in module ppanggolin.formats.writeFlat)
writeGEXF() (in module ppanggolin.formats.writeFlat)
writeGEXFedges() (in module ppanggolin.formats.writeFlat)
writeGEXFend() (in module ppanggolin.formats.writeFlat)
writeGEXFheader() (in module ppanggolin.formats.writeFlat)
writeGEXFnodes() (in module ppanggolin.formats.writeFlat)
writeGffRegions() (in module ppanggolin.align.alignOnPang)
writeGraph() (in module ppanggolin.formats.writeBinaries)
writeInfo() (in module ppanggolin.formats.writeBinaries)
writeJSON() (in module ppanggolin.formats.writeFlat)
writeJSONedge() (in module ppanggolin.formats.writeFlat)
writeJSONedges() (in module ppanggolin.formats.writeFlat)
writeJSONGeneFam() (in module ppanggolin.formats.writeFlat)
writeJSONheader() (in module ppanggolin.formats.writeFlat)
writeJSONnodes() (in module ppanggolin.formats.writeFlat)
writeMatrix() (in module ppanggolin.formats.writeFlat)
writeOrgFile() (in module ppanggolin.formats.writeFlat)
writePangenome() (in module ppanggolin.formats.writeBinaries)
writeParts() (in module ppanggolin.formats.writeFlat)
writeProjections() (in module ppanggolin.formats.writeFlat)
writeRegions() (in module ppanggolin.formats.writeFlat)
writeRGP() (in module ppanggolin.formats.writeBinaries)
writeSpots() (in module ppanggolin.formats.writeBinaries)
(in module ppanggolin.formats.writeFlat)
writeStats() (in module ppanggolin.formats.writeFlat)
writeStatus() (in module ppanggolin.formats.writeBinaries)