| /dports/biology/checkm/CheckM-1.0.18/scripts/ |
| H A D | markerGeneCorrelation.py | 60 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
71 if markerGenesId in geneDistTable[genomeIds[i]]:
72 …geneOrderI.append(float(geneDistTable[genomeIds[i]][markerGenesId][0][0]) / metadata[genomeIds[i]]…
83 if markerGenesId in geneDistTable[genomeIds[j]]:
84 …geneOrderJ.append(float(geneDistTable[genomeIds[j]][markerGenesId][0][0]) / metadata[genomeIds[j]]…
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| H A D | simMarkerGenesVsMarkerSet.py | 56 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
57 colocatedGenes = img.colocatedGenes(geneDistTable)
79 …containedMarkerGenes = img.containedMarkerGenes(markerGenes, geneDistTable[genomeId], startPartial…
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| H A D | plotMarkerSetDistribution.py | 66 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
86 for _, data in geneDistTable[genomeId].iteritems():
95 …d + '\t' + '; '.join(metadata[genomeId]['taxonomy']) + '\t' + str(len(geneDistTable[genomeId])) + …
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| H A D | markerSetSize.py | 57 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
58 colocatedGenes = img.colocatedGenes(geneDistTable)
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| H A D | simLineageSpecificMarkerSets.py | 54 geneDistTable = []
65 mdt = img.geneDistTable(genomeIds, mg, spacingBetweenContigs=1e6)
71 geneDistTable.append(mdt)
91 …containedMarkerGenes = img.containedMarkerGenes(markerGenes[i], geneDistTable[i][genomeId], startP…
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| H A D | identifyColocatedGenes.py | 62 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
63 colocatedGenes = markerset.colocatedGenes(geneDistTable, distThreshold, genomeThreshold)
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| H A D | simulation.py | 74 …geneDistTable = self.img.geneDistTable([testGenomeId], binMarkerSets.getMarkerGenes(), spacingBetw…
77 print '# genes in table: ', len(geneDistTable[testGenomeId])
85 if mg in geneDistTable[testGenomeId]:
86 hits[mg] = geneDistTable[testGenomeId][mg]
125 …nes = self.markerSetBuilder.containedMarkerGenes(ms.getMarkerGenes(), geneDistTable[testGenomeId],…
135 …nes = self.markerSetBuilder.containedMarkerGenes(ms.getMarkerGenes(), geneDistTable[testGenomeId],…
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| H A D | identifyDegenerateGenomes.py | 72 geneDistTable = img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs=1e6)
73 colocatedGenes = markerset.colocatedGenes(geneDistTable)
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| H A D | markerSetTest.py | 81 … geneDistTable = img.geneDistTable(genomeIdSubset, markerGenes, spacingBetweenContigs=1e6)
82 colocatedGenes = img.colocatedGenes(geneDistTable)
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| H A D | simInferBestMarkerSet.py | 90 …geneDistTable = self.img.geneDistTable([testGenomeId], binMarkerGenes.getMarkerGenes(), spacingBet…
100 …nes = self.markerSetBuilder.containedMarkerGenes(ms.getMarkerGenes(), geneDistTable[testGenomeId],…
104 print geneDistTable[testGenomeId]
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| H A D | identifyCompleteGenomes.py | 78 … geneDistTable = img.geneDistTable(allLineageGenomeIds, markerGenes, spacingBetweenContigs=1e6)
79 colocatedGenes = markerset.colocatedGenes(geneDistTable, metadata)
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| H A D | simulationScaffoldsRandom.py | 84 …geneDistTable = self.img.geneDistTable([testGenomeId], binMarkerSets.getMarkerGenes(), spacingBetw…
92 if mg in geneDistTable[testGenomeId]:
93 hits[mg] = geneDistTable[testGenomeId][mg]
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| H A D | simulationScaffoldsByLength.py | 85 …geneDistTable = self.img.geneDistTable([testGenomeId], binMarkerSets.getMarkerGenes(), spacingBetw…
93 if mg in geneDistTable[testGenomeId]:
94 hits[mg] = geneDistTable[testGenomeId][mg]
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| /dports/biology/checkm/CheckM-1.0.18/scripts/deprecated/ |
| H A D | markerGeneCorrelation.py | 60 geneDistTable = img.geneDistTable(genomeIds, markerGenes)
71 if markerGenesId in geneDistTable[genomeIds[i]]:
72 …geneOrderI.append(float(geneDistTable[genomeIds[i]][markerGenesId][0][0]) / metadata[genomeIds[i]]…
83 if markerGenesId in geneDistTable[genomeIds[j]]:
84 …geneOrderJ.append(float(geneDistTable[genomeIds[j]][markerGenesId][0][0]) / metadata[genomeIds[j]]…
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| H A D | simMarkerGenesVsMarkerSet.py | 56 geneDistTable = img.geneDistTable(genomeIds, markerGenes)
57 colocatedGenes = img.colocatedGenes(geneDistTable)
79 …containedMarkerGenes = img.containedMarkerGenes(markerGenes, geneDistTable[genomeId], startPartial…
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| H A D | identifyColocatedGenes.py | 62 geneDistTable = img.geneDistTable(genomeIds, markerGenes)
63 colocatedGenes = markerset.colocatedGenes(geneDistTable, distThreshold, genomeThreshold)
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| /dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/ |
| H A D | markerSetBuilder.py | 159 def colocatedGenes(self, geneDistTable, distThreshold = 5000, genomeThreshold = 0.95): argument
163 for _, clusterIdToGeneLocs in geneDistTable.iteritems():
189 if float(count)/len(geneDistTable) > genomeThreshold:
569 geneDistTable = self.img.geneDistTable(genomeIds, markerGenes, spacingBetweenContigs)
570 colocatedGenes = self.colocatedGenes(geneDistTable)
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| /dports/biology/checkm/CheckM-1.0.18/checkm/util/ |
| H A D | img.py | 501 def geneDistTable(self, genomeIds, markerGenes, spacingBetweenContigs=0): member in IMG
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