/dports/biology/checkm/CheckM-1.0.18/scripts/ |
H A D | markerSetLOO.py | 44 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
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H A D | markerSetTest.py | 48 …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…
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H A D | createTaxonomicSpecificMarkerSets.py | 45 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,
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H A D | plotMarkerSetDistribution.py | 44 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'
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H A D | markerSetStabilityTest.py | 48 …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…
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H A D | markerSetStability.py | 49 …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…
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H A D | identifyLineageStability.py | 45 …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…
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H A D | identifyDegenerateGenomes.py | 42 …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…
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H A D | simInferBestMarkerSet.py | 56 …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…
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H A D | identifyCompleteGenomes.py | 42 …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…
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H A D | calculateConservativeMarkerGenes.py | 42 def run(self, ubiquityThreshold, singleCopyThreshold, rank): argument 66 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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H A D | identifyColocatedGenes.py | 42 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, minMarkers, mostSpecificRank, di… argument 60 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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H A D | simMarkerGenesVsMarkerSet.py | 45 …def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, percentCompletion, numReplicate… argument 53 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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H A D | simulation.py | 60 …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…
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H A D | simLineageSpecificMarkerSets.py | 44 …def run(self, taxonomyStr, mostSpecificRank, minGenomes, ubiquityThreshold, singleCopyThreshold, p… argument 62 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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H A D | simulationScaffoldsRandom.py | 71 …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…
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H A D | simulationScaffoldsByLength.py | 72 …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…
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H A D | qcGenomes.py | 57 …putMetadataFile, outputMetadataFile, outputDir, ubiquityThreshold, singleCopyThreshold, trustedCom… argument 111 …= markerSetBuilder.buildMarkerSet(finishedGenomes[lineage], ubiquityThreshold, singleCopyThreshold)
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H A D | markerSetSelection.py | 55 …def __stabilityTest(self, genomeIds, ubiquityThreshold = 0.97, singleCopyThreshold = 0.97, stabili… argument 69 …looGenomeIds, geneCountTable, ubiquityThreshold*len(looGenomeIds), singleCopyThreshold*len(looGeno…
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H A D | taxonomicTreeWorkflow.py | 259 def __taxonomicMarkers(self, taxaStr, metadata, ubiquityThreshold, singleCopyThreshold): argument 276 …erGenes = self.markerSetBuilder.buildMarkerGenes(genomeIds, ubiquityThreshold, singleCopyThreshold)
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/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/ |
H A D | markerSetBuilder.py | 131 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 …]
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H A D | decorateTree.py | 58 def __calculateMarkerSet(self, genomeLabels, ubiquityThreshold=0.97, singleCopyThreshold=0.97): argument 66 …markerSet = self.markerSetBuilder.buildMarkerSet(genomeIds, ubiquityThreshold, singleCopyThreshold)
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/dports/biology/checkm/CheckM-1.0.18/scripts/deprecated/ |
H A D | identifyColocatedGenes.py | 42 …def run(self, ubiquityThreshold, singleCopyThreshold, minGenomes, minMarkers, mostSpecificRank, di… argument 60 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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H A D | simMarkerGenesVsMarkerSet.py | 45 …def run(self, taxonomyStr, ubiquityThreshold, singleCopyThreshold, percentCompletion, numReplicate… argument 53 …rkerGenes(genomeIds, countTable, ubiquityThreshold*len(genomeIds), singleCopyThreshold*len(genomeI…
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/dports/biology/checkm/CheckM-1.0.18/checkm/util/ |
H A D | img.py | 289 … def filterGeneCountTable(self, genomeIds, table, ubiquityThreshold=0.9, singleCopyThreshold=0.9): argument 303 … len(genomeIds) < ubiquityThreshold) or (float(singleCopy) / len(genomeIds) < singleCopyThreshold):
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