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Searched refs:singleCopyThreshold (Results 1 – 25 of 25) sorted by relevance

/dports/biology/checkm/CheckM-1.0.18/scripts/
H A DmarkerSetLOO.py44 def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, mostSpecificRank, minMarkers): argument
46 print 'Single-copy threshold: ' + str(singleCopyThreshold)
69 …amTable = img.filterPfamTable(genomeIds, pfamTable, ubiquityThreshold*0.9, singleCopyThreshold*0.9)
71 …rGenes(genomeIds, pfamTable, ubiquityThreshold*(len(genomeIds)-1), singleCopyThreshold*(len(genome…
88 …(genomeIdSubset, pfamTable, ubiquityThreshold*len(genomeIdSubset), singleCopyThreshold*len(genomeI…
99 …ubiquityThreshold*numGenomes)) + ', LOO Single-copy >= ' + str(int(singleCopyThreshold*numGenomes))
105 …plotFilename = './images/LOO.' + str(ubiquityThreshold) + '-' + str(singleCopyThreshold) + '.boxpl…
106 title = 'Ubiquity = %.2f' % ubiquityThreshold + ', Single-copy = %.2f' % singleCopyThreshold
H A DmarkerSetTest.py48 …def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, replicates, minGenomes, maxGeno… argument
61 print 'Single-copy threshold: ' + str(singleCopyThreshold)
80 …genomeIdSubset, countTable, ubiquityThreshold*len(genomeIdSubset), singleCopyThreshold*len(genomeI…
96 …uityThreshold*len(genomeIdSubset))) + ', Single-copy > ' + str(int(singleCopyThreshold*len(genomeI…
102 …omyStr.replace(';','_') + '.' + str(ubiquityThreshold) + '-' + str(singleCopyThreshold) + '.error…
103 …'; ') + '\n' + 'Ubiquity = %.2f' % ubiquityThreshold + ', Single-copy = %.2f' % singleCopyThreshold
107 …omyStr.replace(';','_') + '.' + str(ubiquityThreshold) + '-' + str(singleCopyThreshold) + '.boxpl…
H A DcreateTaxonomicSpecificMarkerSets.py45 def __workerThread(self, ubiquityThreshold, singleCopyThreshold, argument
65 …et = markerSetBuilder.buildMarkerSet(genomeIds, ubiquityThreshold, singleCopyThreshold, colocatedD…
74 ubiquityThreshold, singleCopyThreshold, argument
103 fout.write('SINGLE_COPY\t' + str(singleCopyThreshold) + '\n')
154 …def run(self, outputDir, ubiquityThreshold, singleCopyThreshold, minGenomes, colocatedDistThreshol… argument
177 …erProc = [mp.Process(target = self.__workerThread, args = (ubiquityThreshold, singleCopyThreshold,
183 … ubiquityThreshold, singleCopyThreshold,
H A DplotMarkerSetDistribution.py44 def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, numBins, numRndGenomes): argument
62 …countTable = img.filterTable(genomeIds, countTable, 0.9*ubiquityThreshold, 0.9*singleCopyThreshold)
63 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
76 …xonomyStr.replace(';','_') + '.' + str(ubiquityThreshold) + '-' + str(singleCopyThreshold) + '.tsv'
106 …xonomyStr.replace(';','_') + '.' + str(ubiquityThreshold) + '-' + str(singleCopyThreshold) + '.png'
H A DmarkerSetStabilityTest.py48 …def __processLineage(self, metadata, ubiquityThreshold, singleCopyThreshold, minGenomes, queueIn, … argument
63 …Genes(genomeIds, geneCountTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
72 …etGenomeIds, geneCountTable, ubiquityThreshold*numGenomesToSelect, singleCopyThreshold*numGenomesT…
108 …def run(self, outputFile, ubiquityThreshold, singleCopyThreshold, minGenomes, mostSpecificRank, nu… argument
128 …rget = self.__processLineage, args = (metadata, ubiquityThreshold, singleCopyThreshold, minGenomes…
H A DmarkerSetStability.py49 …def __processLineage(self, metadata, ubiquityThreshold, singleCopyThreshold, minGenomes, queueIn, … argument
63 …Genes(genomeIds, geneCountTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
74 …etGenomeIds, geneCountTable, ubiquityThreshold*numGenomesToSelect, singleCopyThreshold*numGenomesT…
109 …def run(self, outputFile, ubiquityThreshold, singleCopyThreshold, minGenomes, mostSpecificRank, nu… argument
143 …rget = self.__processLineage, args = (metadata, ubiquityThreshold, singleCopyThreshold, minGenomes…
H A DidentifyLineageStability.py45 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, minMarkers, mostSpecificRank, pe… argument
59 …countTable = img.filterTable(genomeIds, countTable, ubiquityThreshold*0.9, singleCopyThreshold*0.9)
62 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
76 …bsetGenomeIds, countTable, ubiquityThreshold*len(subsetGenomeIds), singleCopyThreshold*len(subsetG…
H A DidentifyDegenerateGenomes.py42 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, mostSpecificRank, minMarkers, co… argument
44 print 'Single-copy threshold: ' + str(singleCopyThreshold)
66 …countTable = img.filterTable(genomeIds, countTable, ubiquityThreshold*0.9, singleCopyThreshold*0.9)
68 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A DsimInferBestMarkerSet.py56 …ectMarkerSet(self, tree, internalNode, metadata, ubiquityThreshold, singleCopyThreshold, queueOut): argument
81 …etBuilder.buildBinMarkerSet(tree, internalNode, ubiquityThreshold, singleCopyThreshold, bMarkerSet…
131 …def __workerThread(self, tree, metadata, ubiquityThreshold, singleCopyThreshold, queueIn, queueOut… argument
139 …__selectMarkerSet(tree, internalNode, metadata, ubiquityThreshold, singleCopyThreshold, queueOut) …
165 def run(self, ubiquityThreshold, singleCopyThreshold, numThreads): argument
188 … = self.__workerThread, args = (tree, metadata, ubiquityThreshold, singleCopyThreshold, workerQueu…
H A DidentifyCompleteGenomes.py42 …def run(self, ubiquityThreshold, singleCopyThreshold, trustedCompleteness, trustedContamination, g… argument
61 … = img.filterTable(allLineageGenomeIds, countTable, 0.9*ubiquityThreshold, 0.9*singleCopyThreshold)
75 …GenomeIds, countTable, ubiquityThreshold*len(allLineageGenomeIds), singleCopyThreshold*len(allLine…
H A DcalculateConservativeMarkerGenes.py42 def run(self, ubiquityThreshold, singleCopyThreshold, rank): argument
66 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A DidentifyColocatedGenes.py42 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, minMarkers, mostSpecificRank, di… argument
60 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A DsimMarkerGenesVsMarkerSet.py45 …def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, percentCompletion, numReplicate… argument
53 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A Dsimulation.py60 …def __workerThread(self, tree, metadata, ubiquityThreshold, singleCopyThreshold, numReplicates, qu… argument
70 …r.buildBinMarkerSet(tree, testNode.parent_node, ubiquityThreshold, singleCopyThreshold, bMarkerSet…
220 def run(self, ubiquityThreshold, singleCopyThreshold, numReplicates, numThreads): argument
273 …rget=self.__workerThread, args=(tree, metadata, ubiquityThreshold, singleCopyThreshold, numReplica…
H A DsimLineageSpecificMarkerSets.py44 …def run(self, taxonomyStr, mostSpecificRank, minGenomes, ubiquityThreshold, singleCopyThreshold, p… argument
62 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A DsimulationScaffoldsRandom.py71 …erThread(self, tree, metadata, genomeIdsToTest, ubiquityThreshold, singleCopyThreshold, numReplica… argument
81 …r.buildBinMarkerSet(tree, testNode.parent_node, ubiquityThreshold, singleCopyThreshold, bMarkerSet…
235 def run(self, ubiquityThreshold, singleCopyThreshold, numReplicates, minScaffolds, numThreads): argument
303 …hread, args = (tree, metadata, genomeIdsToTest, ubiquityThreshold, singleCopyThreshold, numReplica…
H A DsimulationScaffoldsByLength.py72 …erThread(self, tree, metadata, genomeIdsToTest, ubiquityThreshold, singleCopyThreshold, numReplica… argument
82 …r.buildBinMarkerSet(tree, testNode.parent_node, ubiquityThreshold, singleCopyThreshold, bMarkerSet…
241 def run(self, ubiquityThreshold, singleCopyThreshold, numReplicates, minScaffolds, numThreads): argument
307 …hread, args = (tree, metadata, genomeIdsToTest, ubiquityThreshold, singleCopyThreshold, numReplica…
H A DqcGenomes.py57 …putMetadataFile, outputMetadataFile, outputDir, ubiquityThreshold, singleCopyThreshold, trustedCom… argument
111 …= markerSetBuilder.buildMarkerSet(finishedGenomes[lineage], ubiquityThreshold, singleCopyThreshold)
H A DmarkerSetSelection.py55 …def __stabilityTest(self, genomeIds, ubiquityThreshold = 0.97, singleCopyThreshold = 0.97, stabili… argument
69 …looGenomeIds, geneCountTable, ubiquityThreshold*len(looGenomeIds), singleCopyThreshold*len(looGeno…
H A DtaxonomicTreeWorkflow.py259 def __taxonomicMarkers(self, taxaStr, metadata, ubiquityThreshold, singleCopyThreshold): argument
276 …erGenes = self.markerSetBuilder.buildMarkerGenes(genomeIds, ubiquityThreshold, singleCopyThreshold)
/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/
H A DmarkerSetBuilder.py131 def markerGenes(self, genomeIds, countTable, ubiquityThreshold, singleCopyThreshold): argument
132 if ubiquityThreshold < 1 or singleCopyThreshold < 1:
154 if ubiquity >= ubiquityThreshold and singleCopy >= singleCopyThreshold:
538 def buildMarkerGenes(self, genomeIds, ubiquityThreshold, singleCopyThreshold): argument
558 …Genes(genomeIds, geneCountTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
564 …def buildMarkerSet(self, genomeIds, ubiquityThreshold, singleCopyThreshold, spacingBetweenContigs … argument
567 markerGenes = self.buildMarkerGenes(genomeIds, ubiquityThreshold, singleCopyThreshold)
587 …def buildBinMarkerSet(self, tree, curNode, ubiquityThreshold, singleCopyThreshold, bMarkerSet = Tr… argument
620 … markerSet = self.buildMarkerSet(genomeIds, ubiquityThreshold, singleCopyThreshold)
636 …def buildDomainMarkerSet(self, tree, curNode, ubiquityThreshold, singleCopyThreshold, bMarkerSet =… argument
[all …]
H A DdecorateTree.py58 def __calculateMarkerSet(self, genomeLabels, ubiquityThreshold=0.97, singleCopyThreshold=0.97): argument
66 …markerSet = self.markerSetBuilder.buildMarkerSet(genomeIds, ubiquityThreshold, singleCopyThreshold)
/dports/biology/checkm/CheckM-1.0.18/scripts/deprecated/
H A DidentifyColocatedGenes.py42 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, minMarkers, mostSpecificRank, di… argument
60 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
H A DsimMarkerGenesVsMarkerSet.py45 …def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, percentCompletion, numReplicate… argument
53 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
/dports/biology/checkm/CheckM-1.0.18/checkm/util/
H A Dimg.py289 … def filterGeneCountTable(self, genomeIds, table, ubiquityThreshold=0.9, singleCopyThreshold=0.9): argument
303 … len(genomeIds) < ubiquityThreshold) or (float(singleCopy) / len(genomeIds) < singleCopyThreshold):