class GenomePartition(object): "object to store info about genome and partition it into windows" def __init__(self, db, genomeFileSpec, winSize, overlap, maxGap, minUnplacedSize=0, liftFile=None, unplacedChroms=None): self.db = db self.seqs = GenomeSeqs(db, genomeFileSpec) # flag unplaced chroms before loading lift, as it changes # partitioning if unplacedChroms != None: unplacedChroms.flagSeqs(self.seqs) if liftFile != None: self.seqs.defineSeqRegionsFromLifts(liftFile) self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap, minUnplacedSize) def dump(self, fh): "print info about object" fh.write("=========== GENOME REGIONS ===========\n") self.seqs.dump(fh) fh.write("=========== WINDOWS ===========\n") self.windows.dump(fh) fh.flush()
def __init__(self, db, genomeFileSpec, winSize, overlap, maxGap, minUnplacedSize=0, liftFile=None, unplacedChroms=None): self.db = db self.seqs = GenomeSeqs(db, genomeFileSpec) # flag unplaced chroms before loading lift, as it changes # partitioning if unplacedChroms != None: unplacedChroms.flagSeqs(self.seqs) if liftFile != None: self.seqs.defineSeqRegionsFromLifts(liftFile) self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap, minUnplacedSize)