def selectPhageHostPairs(self,**kw):
"""Pick pairs of phages and hosts from p-h DB stratified at a genus level"""
opt = self.opt
giToTaxa = loadGiTaxBin()
taxaTree = self.getTaxaTree()
#taxaTree.getRootNode().setIsUnderUnclass()
mapFastaRecordsToTaxaTree(inSeqs=opt.dbSeqInp,taxaTree=taxaTree,giToTaxa=giToTaxa)
self.loadPhageHostDb()
seqPicker = PhageHostSeqPicker(taxaTree=taxaTree)
seqPicker.pickSeqHosts()
seqPicker.groupSeqHosts()
seqPicker.printGroupSeqHosts()
seqPicker.pickPairs(maxMicSpe=1,maxMicSeq=1,maxVir=1,maxVirSeq=1)
seqPicker.checkPairs(giToTaxa=giToTaxa)
dbPhPairsFile = self.store.getObjPath(opt.dbPhPairs)
seqPicker.save(dbPhPairsFile)
seqPicker.load(dbPhPairsFile)
seqPicker.checkPairs(giToTaxa=giToTaxa)
seqPicker.saveSeqIds(self.store.getObjPath(opt.dbPhPairsSeqIds))
# import all selected FASTA sequences into internal format
siOpt = Struct()
siOpt.runMode = "inproc"
siOpt.inSeq = opt.dbSeqInp
siOpt.outFeat = opt.dbPhPairsSeq
siOpt.inSeqIds = self.store.getObjPath(opt.dbPhPairsSeqIds)
siOpt.inFormat = "ncbi"
seqImpApp = SeqImportApp(opt=siOpt)
seqImpApp.run()
seqPicker = PhageHostSeqPicker(taxaTree=taxaTree)
dbPhPairsFile = self.store.getObjPath(opt.dbPhPairs)
seqPicker.load(dbPhPairsFile)
for div in ("mic","vir","all"):
self.store.saveIdLabs(seqPicker.makeIdLabsPicks(div=div),name="idlab."+div)
self.exportVirSamples()
def run_SeqImportApp():
opt = makeOptSeqImportApp()
app = SeqImportApp(opt=opt)
jobs = app.run()
